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| Duke Herbarium Lichens: All Publications (in the database)List most recent publications in the database. :chronological alphabetical combined listing:%% Lutzoni, Francois M. @article{fds376708, Author = {U'Ren, JM and Oita, S and Lutzoni, F and Miadlikowska, J and Ball, B and Carbone, I and May, G and Zimmerman, NB and Valle, D and Trouet, V and Arnold, AE}, Title = {Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth's largest terrestrial biome.}, Journal = {Current biology : CB}, Volume = {34}, Number = {5}, Pages = {1148-1156.e7}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1016/j.cub.2024.01.063}, Abstract = {Understanding how symbiotic associations differ across environmental gradients is key to predicting the fate of symbioses as environments change, and it is vital for detecting global reservoirs of symbiont biodiversity in a changing world.<sup>1</sup><sup>,</sup><sup>2</sup><sup>,</sup><sup>3</sup> However, sampling of symbiotic partners at the full-biome scale is difficult and rare. As Earth's largest terrestrial biome, boreal forests influence carbon dynamics and climate regulation at a planetary scale. Plants and lichens in this biome host the highest known phylogenetic diversity of fungal endophytes, which occur within healthy photosynthetic tissues and can influence hosts' resilience to stress.<sup>4</sup><sup>,</sup><sup>5</sup> We examined how communities of endophytes are structured across the climate gradient of the boreal biome, focusing on the dominant plant and lichen species occurring across the entire south-to-north span of the boreal zone in eastern North America. Although often invoked for understanding the distribution of biodiversity, neither a latitudinal gradient nor mid-domain effect<sup>5</sup><sup>,</sup><sup>6</sup><sup>,</sup><sup>7</sup> can explain variation in endophyte diversity at this trans-biome scale. Instead, analyses considering shifts in forest characteristics, Picea biomass and age, and nutrients in host tissues from 46° to 58° N reveal strong and distinctive signatures of climate in defining endophyte assemblages in each host lineage. Host breadth of endophytes varies with climate factors, and biodiversity hotspots can be identified at plant-community transitions across the boreal zone at a global scale. Placed against a backdrop of global circumboreal sampling,<sup>4</sup> our study reveals the sensitivity of endophytic fungi, their reservoirs of biodiversity, and their important symbiotic associations, to climate.}, Doi = {10.1016/j.cub.2024.01.063}, Key = {fds376708} } @article{fds375868, Author = {Magain, N and Miadlikowska, J and Goffinet, B and Goward, T and Pardo-De la Hoz, CJ and Jüriado, I and Simon, A and Mercado-Díaz, JA and Barlow, T and Moncada, B and Lücking, R and Spielmann, A and Canez, L and Wang, LS and Nelson, P and Wheeler, T and Lutzoni, F and Sérusiaux, E}, Title = {High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science}, Journal = {Persoonia: Molecular Phylogeny and Evolution of Fungi}, Volume = {51}, Pages = {1-88}, Year = {2023}, Month = {December}, url = {http://dx.doi.org/10.3767/persoonia.2023.51.01}, Abstract = {Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification.}, Doi = {10.3767/persoonia.2023.51.01}, Key = {fds375868} } @article{fds373327, Author = {Miadlikowska, J and Magain, N and Medeiros, ID and Pardo-De La Hoz, CJ and Carbone, I and Lagreca, S and Barlow, T and Myllys, L and Schmull, M and Lutzoni, F}, Title = {Towards a nomenclatural clarification of the Peltigera ponojensis/monticola clade including metagenomic sequencing of type material and the introduction of P. globulata Miadl. & Magain sp. nov.}, Journal = {Lichenologist}, Volume = {55}, Number = {5}, Pages = {315-324}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1017/S0024282923000373}, Abstract = {Peltigera globulata Miadl. & Magain, a new species in the P. ponojensis/monticola species complex of section Peltigera, is formally described. This clade was previously given the interim designation Peltigera sp. 17. It is found in sun-exposed and xeric habitats at high altitudes in Peru and Ecuador. Peltigera globulata can be easily recognized by its irregularly globulated margins covered mostly by thick, white pruina, somewhat resembling the sorediate thallus margins of P. soredians, another South American species from section Peltigera. The hypervariable region of ITS1 (ITS1-HR), which is in general highly variable among species of section Peltigera, does not have diagnostic value for species identification within the P. ponojensis/monticola complex. Nevertheless, no significant level of gene flow was detected among eight lineages representing a clade of putative species (including P. globulata) within this complex. ITS sequences from the holotype specimens of P. monticola Vitik. (collected in 1979) and P. soredians Vitik. (collected in 1981) and lectotype specimens of P. antarctica C. W. Dodge (collected in 1941) and P. aubertii C. W. Dodge (collected in 1952) were successfully obtained through Sanger and Illumina metagenomic sequencing. BLAST results of these sequences revealed that the type specimen of P. monticola falls within the P. monticola/ponojensis 7 clade, which represents P. monticola s. str., and confirmed that the type specimen of P. aubertii falls within a clade identified previously as P. aubertii based on morphology. The ITS sequence from the type specimen of P. soredians, which superficially resembles P. globulata, confirms its placement in the P. rufescens clade. Finally, we discovered that the name P. antarctica was erroneously applied to a lineage in the P. ponojensis/monticola clade. The ITS sequence from the type specimen of P. antarctica represents a lineage within the P. rufescens clade, which is sister to the P. ponojensis/monticola clade.}, Doi = {10.1017/S0024282923000373}, Key = {fds373327} } @article{fds371575, Author = {Pardo-De la Hoz and CJ and Magain, N and Piatkowski, B and Cornet, L and Dal Forno and M and Carbone, I and Miadlikowska, J and Lutzoni, F}, Title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria.}, Journal = {Systematic biology}, Volume = {72}, Number = {3}, Pages = {694-712}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1093/sysbio/syad008}, Abstract = {Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].}, Doi = {10.1093/sysbio/syad008}, Key = {fds371575} } @article{fds368295, Author = {Medeiros, ID and Lutzoni, F}, Title = {Contribution to a modern treatment of Graphidaceae biodiversity in South Africa: genera of tribe Graphideae with hyaline ascospores}, Journal = {Lichenologist}, Volume = {54}, Number = {5}, Pages = {253-270}, Year = {2022}, Month = {September}, url = {http://dx.doi.org/10.1017/S0024282922000263}, Abstract = {Additions and corrections are provided for the South African species of Graphidaceae tribe Graphideae with hyaline ascospores. Allographa oldayana I. Medeiros sp. nov. is described as new to science based on morphological, chemical and molecular data. The new species is characterized by lirellae with striate labia and a complete thalline margin, a completely carbonized excipulum, large, muriform ascospores, and the presence of hirtifructic acid. Allographa consanguinea (Müll. Arg.) Lücking, A. leptospora (Vain.) Lücking & Kalb, Diorygma aff. minisporum Kalb et al., Graphis crebra Vain., Gr. dupaxana Vain., Gr. furcata Fée, Gr. handelii Zahlbr., Gr. longula Kremp., Gr. pinicola Zahlbr., Gr. proserpens Vain, Gr. subhiascens (Müll. Arg.) Lücking and Platythecium sp. are reported as new records for South Africa. Allographa striatula (Ach.) Lücking & Kalb, Graphis analoga Nyl. and Gr. scripta (L.) Ach. are shown to be misapplied names that should be removed from the South African checklist. The new combination Mangoldia bylii (Vain.) I. Medeiros comb. nov. (bas. Graphis bylii Vain) is made; this represents an earlier name for M. atronitens (A. W. Archer) Lücking et al. Taxonomic notes are provided for Graphis bylii var. lividula Vain. and Gr. denudans Vain., species that are known only from their South African holotypes. Phylogenetic analyses that include new DNA sequence data from the nrLSU, mtSSU and RPB2 loci confirm the generic placements of several species for which molecular data were lacking: Allographa consanguinea, Glyphis atrofusca (Müll. Arg.) Lücking, Graphis crebra and Gr. subhiascens.}, Doi = {10.1017/S0024282922000263}, Key = {fds368295} } @article{fds362963, Author = {Chen, K-H and Liao, H-L and Arnold, AE and Korotkin, HB and Wu, SH and Matheny, PB and Lutzoni, F}, Title = {Comparative transcriptomics of fungal endophytes in co-culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates.}, Journal = {The New phytologist}, Volume = {234}, Number = {5}, Pages = {1832-1847}, Year = {2022}, Month = {June}, url = {http://dx.doi.org/10.1111/nph.18078}, Abstract = {Mosses harbor fungi whose interactions within their hosts remain largely unexplored. Trophic ranges of fungal endophytes from the moss Dicranum scoparium were hypothesized to encompass saprotrophism. This moss is an ideal host to study fungal trophic lability because of its natural senescence gradient, and because it can be grown axenically. Dicranum scoparium was co-cultured with each of eight endophytic fungi isolated from naturally occurring D. scoparium. Moss growth rates, and gene expression levels (RNA sequencing) of fungi and D. scoparium, were compared between axenic and co-culture treatments. Functional lability of two fungal endophytes was tested by comparing their RNA expression levels when colonizing living vs dead gametophytes. Growth rates of D. scoparium were unchanged, or increased, when in co-culture. One fungal isolate (Hyaloscyphaceae sp.) that promoted moss growth was associated with differential expression of auxin-related genes. When grown with living vs dead gametophytes, Coniochaeta sp. switched from having upregulated carbohydrate transporter activity to upregulated oxidation-based degradation, suggesting an endophytism to saprotrophism transition. However, no such transition was detected for Hyaloscyphaceae sp. Individually, fungal endophytes did not negatively impact growth rates of D. scoparium. Our results support the long-standing hypothesis that some fungal endophytes can switch to saprotrophism.}, Doi = {10.1111/nph.18078}, Key = {fds362963} } @article{fds362151, Author = {Geml, J and Arnold, AE and Semenova-Nelsen, TA and Nouhra, ER and Drechsler-Santos, ER and Góes-Neto, A and Morgado, LN and Ódor, P and Hegyi, B and Oriol, G and Ibáñez, A and Tedersoo, L and Lutzoni, F}, Title = {Community dynamics of soil-borne fungal communities along elevation gradients in neotropical and palaeotropical forests.}, Journal = {Molecular ecology}, Volume = {31}, Number = {7}, Pages = {2044-2060}, Year = {2022}, Month = {April}, url = {http://dx.doi.org/10.1111/mec.16368}, Abstract = {Because of their steep gradients in abiotic and biotic factors, mountains offer an ideal setting to illuminate the mechanisms that underlie patterns of species distributions and community assembly. We compared the composition of taxonomically and functionally diverse fungal communities in soils along five elevational gradients in mountains of the Neo- and Palaeotropics (northern Argentina, southern Brazil, Panama, Malaysian Borneo and Papua New Guinea). Both the richness and composition of soil fungal communities reflect environmental factors, particularly temperature and soil pH, with some shared patterns among neotropical and palaeotropical regions. Community dynamics are characterized by replacement of species along elevation gradients, implying a relatively narrow elevation range for most fungi, which appears to be driven by contrasting environmental preferences among both functional and taxonomic groups. For functional groups dependent on symbioses with plants (especially ectomycorrhizal fungi), the distribution of host plants drives richness and community composition, resulting in important differences in elevational patterns between neotropical and palaeotropical montane communities. The pronounced compositional and functional turnover along elevation gradients implies that tropical montane forest fungi will be sensitive to climate change, resulting in shifts in composition and functionality over time.}, Doi = {10.1111/mec.16368}, Key = {fds362151} } @article{fds360544, Author = {Franco, MEE and Wisecaver, JH and Arnold, AE and Ju, Y-M and Slot, JC and Ahrendt, S and Moore, LP and Eastman, KE and Scott, K and Konkel, Z and Mondo, SJ and Kuo, A and Hayes, RD and Haridas, S and Andreopoulos, B and Riley, R and LaButti, K and Pangilinan, J and Lipzen, A and Amirebrahimi, M and Yan, J and Adam, C and Keymanesh, K and Ng, V and Louie, K and Northen, T and Drula, E and Henrissat, B and Hsieh, H-M and Youens-Clark, K and Lutzoni, F and Miadlikowska, J and Eastwood, DC and Hamelin, RC and Grigoriev, IV and U'Ren, JM}, Title = {Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes.}, Journal = {The New phytologist}, Volume = {233}, Number = {3}, Pages = {1317-1330}, Year = {2022}, Month = {February}, url = {http://dx.doi.org/10.1111/nph.17873}, Abstract = {Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.}, Doi = {10.1111/nph.17873}, Key = {fds360544} } @article{fds362906, Author = {Pardo-De la Hoz and CJ and Medeiros, ID and Gibert, JP and Chagnon, P-L and Magain, N and Miadlikowska, J and Lutzoni, F}, Title = {Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks.}, Journal = {Ecology and evolution}, Volume = {12}, Number = {3}, Pages = {e8649}, Year = {2022}, Month = {February}, url = {http://dx.doi.org/10.1002/ece3.8649}, Abstract = {Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α-diversity. To calculate the PSS index, we then compare observed partner phylogenetic α-diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host-parasite, avian seed-dispersal, lichenized fungi-cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much-needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss.}, Doi = {10.1002/ece3.8649}, Key = {fds362906} } @article{fds357896, Author = {Cornet, L and Magain, N and Baurain, D and Lutzoni, F}, Title = {Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens.}, Journal = {Molecular phylogenetics and evolution}, Volume = {162}, Pages = {107100}, Year = {2021}, Month = {September}, url = {http://dx.doi.org/10.1016/j.ympev.2021.107100}, Abstract = {Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic. In this study, we developed a synteny-based approach and searched for Collinear Orthologous Regions (COR), under the assumption that genes that are present in the same order and orientation across a wide monophyletic clade are less likely to have undergone HGT. We searched sixteen reference Nostocales genomes and identified 99 genes, part of 28 COR comprising three to eight genes each. We then developed a bioinformatic pipeline, designed to minimize inter-genome contamination and processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset to 90 genes representing 25 COR, which were used to infer phylogenetic relationships within Nostocales and among lichenized Cyanobacteria. This dataset was narrowed down further to 71 genes representing 22 COR by selecting only genes part of one (largest) operon per COR. We found a relatively high level of congruence among trees derived from the 90-gene dataset, but congruence was only slightly higher among genes within a COR compared to genes across COR. However, topological congruence was significantly higher among the 71 genes part of one operon per COR. Nostocales phylogenies resulting from concatenation and species tree approaches based on the 90- and 71-gene datasets were highly congruent, but the most highly supported result was obtained when using synteny, collinearity, and operon information (i.e., 71-gene dataset) as gene selection criteria, which outperformed larger datasets with more genes.}, Doi = {10.1016/j.ympev.2021.107100}, Key = {fds357896} } @article{fds357291, Author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan, DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, EÁ and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni, FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux, J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao, LL and Groenewald, JZ}, Title = {New and Interesting Fungi. 4.}, Journal = {Fungal systematics and evolution}, Volume = {7}, Pages = {255-343}, Year = {2021}, Month = {June}, url = {http://dx.doi.org/10.3114/fuse.2021.07.13}, Abstract = {An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: <i>Superstratomycetales</i> and <i>Superstratomycetaceae</i> (based on <i>Superstratomyces</i> <i>)</i>. New genera: <i>Haudseptoria</i> (based on <i>Haudseptoria typhae</i>); <i>Hogelandia</i> (based on <i>Hogelandia lambearum</i>); <i>Neoscirrhia</i> (based on <i>Neoscirrhia osmundae</i>); <i>Nothoanungitopsis</i> (based on <i>Nothoanungitopsis urophyllae</i>); <i>Nothomicrosphaeropsis</i> (based on <i>Nothomicrosphaeropsis welwitschiae</i>); <i>Populomyces</i> (based on <i>Populomyces zwinianus</i>); <i>Pseudoacrospermum</i> (based on <i>Pseudoacrospermum goniomae</i>). New species: <i>Apiospora sasae</i> on dead culms of <i>Sasa veitchii</i> (Netherlands); <i>Apiospora stipae</i> on dead culms of <i>Stipa gigantea</i> (Spain); <i>Bagadiella eucalyptorum</i> on leaves of <i>Eucalyptus</i> sp. (Australia); <i>Calonectria singaporensis</i> from submerged leaf litter (Singapore); <i>Castanediella neomalaysiana</i> on leaves of <i>Eucalyptus</i> sp. (Malaysia); <i>Colletotrichum pleopeltidis</i> on leaves of <i>Pleopeltis</i> sp. (South Africa); <i>Coniochaeta deborreae</i> from soil (Netherlands); <i>Diaporthe durionigena</i> on branches of <i>Durio zibethinus</i> (Vietnam); <i>Floricola juncicola</i> on dead culm of <i>Juncus</i> sp. (France); <i>Haudseptoria typhae</i> on leaf sheath of <i>Typha</i> sp. (Germany); <i>Hogelandia lambearum</i> from soil (Netherlands); <i>Lomentospora valparaisensis</i> from soil (Chile); <i>Neofusicoccum mystacidii</i> on dead stems of <i>Mystacidium capense</i> (South Africa); <i>Neomycosphaerella guibourtiae</i> on leaves of <i>Guibourtia</i> sp. (Angola); <i>Niesslia neoexosporioides</i> on dead leaves of <i>Carex paniculata</i> (Germany); <i>Nothoanungitopsis urophyllae</i> on seed capsules of <i>Eucalyptus urophylla</i> (South Africa); <i>Nothomicrosphaeropsis welwitschiae</i> on dead leaves of <i>Welwitschia mirabilis</i> (Namibia); <i>Paracremonium bendijkiorum</i> from soil (Netherlands); <i>Paraphoma ledniceana</i> on dead wood of <i>Buxus sempervirens</i> (Czech Republic); <i>Paraphoma salicis</i> on leaves of <i>Salix cf. alba</i> (Ukraine); <i>Parasarocladium wereldwijsianum</i> from soil (Netherlands); <i>Peziza ligni</i> on masonry and plastering (France); <i>Phyllosticta phoenicis</i> on leaves of <i>Phoenix reclinata</i> (South Africa); <i>Plectosphaerella slobbergiarum</i> from soil (Netherlands); <i>Populomyces zwinianus</i> from soil (Netherlands); <i>Pseudoacrospermum goniomae</i> on leaves of <i>Gonioma kamassi</i> (South Africa); <i>Pseudopyricularia festucae</i> on leaves of <i>Festuca californica</i> (USA); <i>Sarocladium sasijaorum</i> from soil (Netherlands); <i>Sporothrix hypoxyli</i> in sporocarp of <i>Hypoxylon petriniae</i> on <i>Fraxinus</i> wood (Netherlands); <i>Superstratomyces albomucosus</i> on <i>Pycnanthus angolensis</i> (Netherlands); <i>Superstratomyces atroviridis</i> on <i>Pinus sylvestris</i> (Netherlands); <i>Superstratomyces flavomucosus</i> on leaf of <i>Hakea multilinearis</i> (Australia); <i>Superstratomyces tardicrescens</i> from human eye specimen (USA); <i>Taeniolella platani</i> on twig of <i>Platanus hispanica</i> (Germany), and <i>Tympanis pini</i> on twigs of <i>Pinus sylvestris</i> (Spain). <b>Citation:</b> Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. <i>Fungal Systematics and Evolution</i> <b>7:</b> 255-343. doi: 10.3114/fuse.2021.07.13.}, Doi = {10.3114/fuse.2021.07.13}, Key = {fds357291} } @article{fds355538, Author = {Oita, S and Ibáñez, A and Lutzoni, F and Miadlikowska, J and Geml, J and Lewis, LA and Hom, EFY and Carbone, I and U'Ren, JM and Arnold, AE}, Title = {Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale.}, Journal = {Communications biology}, Volume = {4}, Number = {1}, Pages = {313}, Year = {2021}, Month = {March}, url = {http://dx.doi.org/10.1038/s42003-021-01826-7}, Abstract = {Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves-fungal endophytes-that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.}, Doi = {10.1038/s42003-021-01826-7}, Key = {fds355538} } @article{fds361298, Author = {Medeiros, ID and Mazur, E and Miadlikowska, J and Flakus, A and Rodriguez-Flakus, P and Pardo-De la Hoz and CJ and Cieślak, E and Śliwa, L and Lutzoni, F}, Title = {Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis.}, Journal = {Frontiers in microbiology}, Volume = {12}, Pages = {774839}, Year = {2021}, Month = {January}, url = {http://dx.doi.org/10.3389/fmicb.2021.774839}, Abstract = {Shifts in climate along elevation gradients structure mycobiont-photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (<i>Trebouxia</i> alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, <i>RPB1</i>, <i>RPB2</i>, and <i>MCM7</i>) and two photobiont loci (ITS, <i>rbc</i>L); we designed new primers to amplify Lecanoraceae <i>RPB1</i> and <i>RPB2</i> with a nested PCR approach. Mycobionts belonged to <i>Lecanora</i> s.lat., <i>Bryonora</i>, <i>Myriolecis</i>, <i>Protoparmeliopsis</i>, the "<i>Lecanora</i>" <i>polytropa</i> group, and the "<i>L</i>." saligna group. All of these clades except for <i>Lecanora</i> s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. <i>Trebouxia</i> clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from <i>Trebouxia</i> clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while <i>Trebouxia</i> clades A and S dominate open habitats at high elevation. We did not find <i>Trebouxia</i> clade D. Several putative new species were found in <i>Trebouxia</i> clades A, C, and I. These included one putative species in clade A associated with <i>Myriolecis</i> species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with <i>Lecanora</i> on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with <i>Trebouxia</i> from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and <i>Trebouxia</i> photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of <i>Trebouxia</i> diversity and distribution.}, Doi = {10.3389/fmicb.2021.774839}, Key = {fds361298} } @article{fds348889, Author = {Haridas, S and Albert, R and Binder, M and Bloem, J and LaButti, K and Salamov, A and Andreopoulos, B and Baker, SE and Barry, K and Bills, G and Bluhm, BH and Cannon, C and Castanera, R and Culley, DE and Daum, C and Ezra, D and González, JB and Henrissat, B and Kuo, A and Liang, C and Lipzen, A and Lutzoni, F and Magnuson, J and Mondo, SJ and Nolan, M and Ohm, RA and Pangilinan, J and Park, H-J and Ramírez, L and Alfaro, M and Sun, H and Tritt, A and Yoshinaga, Y and Zwiers, L-H and Turgeon, BG and Goodwin, SB and Spatafora, JW and Crous, PW and Grigoriev, IV}, Title = {101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.}, Journal = {Studies in mycology}, Volume = {96}, Pages = {141-153}, Year = {2020}, Month = {June}, url = {http://dx.doi.org/10.1016/j.simyco.2020.01.003}, Abstract = {<i>Dothideomycetes</i> is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class <i>Dothideomycetes</i> and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of <i>Dothideomycetes</i> has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 <i>Dothideomycetes</i> introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the <i>Dothideomycetes</i> phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.}, Doi = {10.1016/j.simyco.2020.01.003}, Key = {fds348889} } @article{fds357525, Author = {Miadlikowska, J and Magain, N and Buck, WR and Castillo, RV and Barlow, GT and Pardo-De la Hoz and CJ and LaGreca, S and Lutzoni, F}, Title = {Peltigera hydrophila (Lecanoromycetes, Ascomycota), a new semi-aquatic cyanolichen species from Chile}, Journal = {Plant and Fungal Systematics}, Volume = {65}, Number = {1}, Pages = {210-218}, Year = {2020}, Month = {June}, url = {http://dx.doi.org/10.35535/pfsyst-2020-0016}, Abstract = {Peltigera hydrophila, a new species from Chile tentatively distinguished based on phylogenetic evidence but not yet named, is formally described here. Morphological differences (e.g., non-tomentose thallus) and habitat preferences (semi-aquatic) corroborate molecular and phylogenetic distinctiveness of this early diverging lineage in section Peltigera. Due to overlapping ecological ranges, P. hydrophila shares some morphological traits with aquatic species from the phylogenetically unrelated section Hydrothyriae.}, Doi = {10.35535/pfsyst-2020-0016}, Key = {fds357525} } @article{fds357526, Author = {Magain, N and Goffinet, B and Simon, A and Seelan, JSS and Medeiros, ID and Lutzoni, F and Miadlikowska, J}, Title = {Peltigera serusiauxii (Lecanoromycetes, Ascomycota), a new species from Papua New Guinea and Malaysia}, Journal = {Plant and Fungal Systematics}, Volume = {65}, Number = {1}, Pages = {139-146}, Year = {2020}, Month = {June}, url = {http://dx.doi.org/10.35535/pfsyst-2020-0009}, Abstract = {Peltigera serusiauxii is proposed here as a new species from Papua New Guinea and Sabah, northern Borneo (Malaysia). The species belongs to the polydactyloid clade of section Polydactylon. Because of its large thalli with a glabrous upper surface, this species was previously identified as P. dolichorhiza, but it differs by its polydactylon-type lower surface and the high amount of dolichorrhizin. It appears to be a strict specialist in its association with Nostoc phylogroup IX throughout its known distribution. This is one of many undescribed species remaining to be formally described within the genus Peltigera, especially in Asia and Australasia.}, Doi = {10.35535/pfsyst-2020-0009}, Key = {fds357526} } @article{fds347322, Author = {Darnajoux, R and Magain, N and Renaudin, M and Lutzoni, F and Bellenger, J-P and Zhang, X}, Title = {Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {116}, Number = {49}, Pages = {24682-24688}, Year = {2019}, Month = {December}, url = {http://dx.doi.org/10.1073/pnas.1913314116}, Abstract = {Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems. On land, low molybdenum (Mo) availability has been shown to limit BNF by the most common form of nitrogenase (Nase), which requires Mo in its active site. Vanadium (V) and iron-only Nases have been suggested as viable alternatives to countering Mo limitation of BNF; however, field data supporting this long-standing hypothesis have been lacking. Here, we elucidate the contribution of vanadium nitrogenase (V-Nase) to BNF by cyanolichens across a 600-km latitudinal transect in eastern boreal forests of North America. Widespread V-Nase activity was detected (∼15-50% of total BNF rates), with most of the activity found in the northern part of the transect. We observed a 3-fold increase of V-Nase contribution during the 20-wk growing season. By including the contribution of V-Nase to BNF, estimates of new N input by cyanolichens increase by up to 30%. We find that variability in V-based BNF is strongly related to Mo availability, and we identify a Mo threshold of ∼250 ng·g<sub>lichen</sub><sup>-1</sup> for the onset of V-based BNF. Our results provide compelling ecosystem-scale evidence for the use of the V-Nase as a surrogate enzyme that contributes to BNF when Mo is limiting. Given widespread findings of terrestrial Mo limitation, including the carbon-rich circumboreal belt where global change is most rapid, additional consideration of V-based BNF is required in experimental and modeling studies of terrestrial biogeochemistry.}, Doi = {10.1073/pnas.1913314116}, Key = {fds347322} } @article{fds366356, Author = {Flakus, A and Etayo, J and Miadlikowska, J and Lutzoni, F and Kukwa, M and Matura, N and Rodriguez-Flakus, P}, Title = {Biodiversity assessment of ascomycetes inhabiting Lobariella lichens in Andean cloud forests led to one new family, three new genera and 13 new species of lichenicolous fungi}, Journal = {Plant and Fungal Systematics}, Volume = {64}, Number = {2}, Pages = {283-344}, Year = {2019}, Month = {December}, url = {http://dx.doi.org/10.2478/pfs-2019-0022}, Abstract = {Neotropical mountain forests are characterized by having hyperdiverse and unusual fungi inhabiting lichens. The great majority of these lichenicolous fungi (i.e., detectable by light microscopy) remain undescribed and their phylogenetic relationships are mostly unknown. This study focuses on lichenicolous fungi inhabiting the genus Lobariella (Peltigerales), one of the most important lichen hosts in the Andean cloud forests. Based on molecular and morphological data, three new genera are introduced: Lawreyella gen. nov. (Cordieritidaceae, for Unguiculariopsis lobariella), Neobaryopsis gen. nov. (Cordycipitaceae), and Pseudodidymocyrtis gen. nov. (Didymosphaeriaceae). Nine additional new species are described (Abrothallus subhalei sp. nov., Atronectria lobariellae sp. nov., Corticifraga microspora sp. nov., Epithamnolia rugosopycnidiata sp. nov., Lichenotubeufia cryptica sp. nov., Neobaryopsis andensis sp. nov., Pseudodidymocyrtis lobariellae sp. nov., Rhagadostomella hypolobariella sp. nov., and Xylaria lichenicola sp. nov.). Phylogenetic placements of 13 lichenicolous species are reported here for Abrothallus, Arthonia, Globonectria, Lawreyella, Monodictys, Neobaryopsis, Pseudodidymocyrtis, Sclerococcum, Trichonectria and Xylaria. The name Sclerococcum ricasoliae comb. nov. is reestablished for the neotropical populations formerly named S. lobariellum (Sclerococcales). A key to sexual and asexual states of 40 species of lobariellicolous ascomycetous fungi is provided. Teleomorph-anamorph connections were established for several species using molecular methods and/or visual observations in nature. Additionally, we found that the anamorphic species Cornutispora ophiurospora inhabiting Lobariella was often accompanied by ascomata of Spirographa. Results of phylogenetic analyses, including newly generated sequences of several Cornutispora and Spirographa species inhabiting various host lichens, support the conclusion that Cornutispora is a synonym of Spirographa. Our Maximum Likelihood inference based on multiple loci show that all studied Spirographa (including Cornutispora) belong to a new lineage within Ostropales. Based on these highly supported phylogenetic placements and the distinct character states of their conidiomata, in comparison with other Lecanoromycetes, a new family is proposed - Spirographaceae fam. nov. This new lineage includes broadly distributed mycoparasites, inhabiting various lichen and fungal hosts, and representing an early diversification event preceding the lichen-forming clade of Fissurinaceae, Gomphillaceae and Graphidaceae. Two lichenicolous species, Asteroglobulus giselae and Pleoscutula arsenii, were found to be nested within the Spirographa clade, and their teleomorph-anamorph connections were confirmed based on genotypic and phenotypic data. This phylogenetic result is corroborated by their highly similar ascomata anatomy. Together these results strongly indicate that both species are congeneric with Spirographa. As a result, four new species (S. aggregata sp. nov., S. galligena sp. nov., S. maroneae sp. nov., and S. parmotrematis sp. nov.) and 15 new combinations are proposed (Spirographa ascaridiella comb. nov., S. arsenii comb. nov., S. ciliata comb. nov., S. giselae comb. nov., S. herteliana comb. nov., S. hypotrachynae comb. nov., S. intermedia comb. nov., S. lichenicola comb. nov., S. limaciformis comb. nov., S. ophiurospora comb. nov., S. pittii comb. nov., S. pyramidalis comb. nov., S. triangularis comb. nov., S. tricupulata comb. nov., and S. vermiformis comb. nov.). Species of the genus Spirographa, as outlined here, are strongly host-specific, mainly at the generic level of their host. Some host genera can harbour more than one Spirographa species.}, Doi = {10.2478/pfs-2019-0022}, Key = {fds366356} } @article{fds346566, Author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Zimmerman, NB and Carbone, I and May, G and Arnold, AE}, Title = {Host availability drives distributions of fungal endophytes in the imperilled boreal realm.}, Journal = {Nature ecology & evolution}, Volume = {3}, Number = {10}, Pages = {1430-1437}, Year = {2019}, Month = {October}, url = {http://dx.doi.org/10.1038/s41559-019-0975-2}, Abstract = {Boreal forests represent the world's largest terrestrial biome and provide ecosystem services of global importance. Highly imperilled by climate change, these forests host Earth's greatest phylogenetic diversity of endophytes, a hyperdiverse group of symbionts that are defined by their occurrence within living, symptomless plant and lichen tissues. Endophytes shape the ecological and evolutionary trajectories of plants and are therefore key to the function and resilience of terrestrial ecosystems. A critical step in linking the ecological functions of endophytes with those of their hosts is to understand the distributions of these symbionts at the global scale; however, turnover in host taxa with geography and climate can confound insights into endophyte biogeography. As a result, global drivers of endophyte diversity and distributions are not known. Here, we leverage sampling from phylogenetically diverse boreal plants and lichens across North America and Eurasia to show that host filtering in distinctive environments, rather than turnover with geographical or environmental distance, is the main determinant of the community composition and diversity of endophytes. We reveal the distinctiveness of boreal endophytes relative to soil fungi worldwide and endophytes from diverse temperate biomes, highlighting a high degree of global endemism. Overall, the distributions of endophytes are directly linked to the availability of compatible hosts, highlighting the role of biotic interactions in shaping fungal communities across large spatial scales, and the threat that climate change poses to biological diversity and function in the imperilled boreal realm.}, Doi = {10.1038/s41559-019-0975-2}, Key = {fds346566} } @article{fds345375, Author = {Armaleo, D and Müller, O and Lutzoni, F and Andrésson, ÓS and Blanc, G and Bode, HB and Collart, FR and Dal Grande and F and Dietrich, F and Grigoriev, IV and Joneson, S and Kuo, A and Larsen, PE and Logsdon, JM and Lopez, D and Martin, F and May, SP and McDonald, TR and Merchant, SS and Miao, V and Morin, E and Oono, R and Pellegrini, M and Rubinstein, N and Sanchez-Puerta, MV and Savelkoul, E and Schmitt, I and Slot, JC and Soanes, D and Szövényi, P and Talbot, NJ and Veneault-Fourrey, C and Xavier, BB}, Title = {The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.}, Journal = {BMC Genomics}, Volume = {20}, Number = {1}, Pages = {605}, Year = {2019}, Month = {July}, url = {http://dx.doi.org/10.1186/s12864-019-5629-x}, Abstract = {BACKGROUND: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS: A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS: The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.}, Doi = {10.1186/s12864-019-5629-x}, Key = {fds345375} } @article{fds342447, Author = {Chen, K-H and Liao, H-L and Bellenger, J-P and Lutzoni, F}, Title = {Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium.}, Journal = {Environmental microbiology}, Volume = {21}, Number = {7}, Pages = {2273-2289}, Year = {2019}, Month = {July}, url = {http://dx.doi.org/10.1111/1462-2920.14605}, Abstract = {Bryophytes harbour microbiomes, including diverse communities of fungi. The molecular mechanisms by which perennial mosses interact with these fungal partners along their senescence gradients are unknown, yet this is an ideal system to study variation in gene expression associated with trophic state transitions. We investigated differentially expressed genes of fungal communities and their host Dicranum scoparium across its naturally occurring senescence gradient using a metatranscriptomic approach. Higher activity of fungal nutrient-related (carbon, nitrogen, phosphorus and sulfur) transporters and Carbohydrate-Active enZyme (CAZy) genes was detected toward the bottom, partially decomposed, layer of the moss. The most prominent variation in the expression levels of fungal nutrient transporters was from inorganic nitrogen-related transporters, whereas the breakdown of organonitrogens was detected as the most enriched gene ontology term for the host D. scoparium, for those transcripts having higher expression in the partially decomposed layer. The abundance of bacterial rRNA transcripts suggested that more living members of Cyanobacteria are associated with the photosynthetic layer of D. scoparium, while members of Rhizobiales are detected throughout the gametophytes. Plant genes for specific fungal-plant communication, including defense responses, were differentially expressed, suggesting that different genetic pathways are involved in plant-microbe crosstalk in photosynthetic tissues compared to partially decomposed tissues.}, Doi = {10.1111/1462-2920.14605}, Key = {fds342447} } @article{fds344727, Author = {Chagnon, PL and Magain, N and Miadlikowska, J and Lutzoni, F}, Title = {Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera}, Journal = {Journal of Ecology}, Volume = {107}, Number = {4}, Pages = {1645-1661}, Year = {2019}, Month = {July}, url = {http://dx.doi.org/10.1111/1365-2745.13207}, Abstract = {Ecological interactions range from purely specialized to extremely generalized in nature. Recent research has showed very high levels of specialization in the cyanolichens involving Peltigera (mycobionts) and their Nostoc photosynthetic partners (cyanobionts). Yet, little is known about the mechanisms contributing to the establishment and maintenance of such high specialization levels. Here, we characterized interactions between Peltigera and Nostoc partners at a global scale, using more than one thousand thalli. We used tools from network theory, community phylogenetics and biogeographical history reconstruction to evaluate how these symbiotic interactions may have evolved. After splitting the interaction matrix into modules of preferentially interacting partners, we evaluated how module membership might have evolved along the mycobionts’ phylogeny. We also teased apart the contributions of geographical overlap vs phylogeny in driving interaction establishment between Peltigera and Nostoc taxa. Module affiliation rarely evolves through the splitting of large ancestral modules. Instead, new modules appear to emerge independently, which is often associated with a fungal speciation event. We also found strong phylogenetic signal in these interactions, which suggests that partner switching is constrained by conserved traits. Therefore, it seems that a high rate of fungal diversification following a switch to a new cyanobiont can lead to the formation of large modules, with cyanobionts associating with multiple closely retated Peltigera species. Finally, when restricting our analyses to Peltigera sister species, the latter differed more through partner acquisition/loss than replacement (i.e., switching). This pattern vanishes as we look at sister species that have diverged longer ago. This suggests that fungal speciation may be accompanied by a stepwise process of (a) novel partner acquisition and (b) loss of the ancestral partner. This could explain the maintenance of high specialization levels in this symbiotic system where the transmission of the cyanobiont to the next generation is assumed to be predominantly horizontal. Synthesis. Overall, our study suggests that oscillation between generalization and ancestral partner loss may maintain high specialization within the lichen genus Peltigera, and that partner selection is not only driven by partners’ geographical overlap, but also by their phylogenetically conserved traits.}, Doi = {10.1111/1365-2745.13207}, Key = {fds344727} } @article{fds345376, Author = {Carbone, I and White, JB and Miadlikowska, J and Arnold, AE and Miller, MA and Magain, N and U'Ren, JM and Lutzoni, F}, Title = {T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.}, Journal = {Microbiology resource announcements}, Volume = {8}, Number = {29}, Pages = {e00328-e00319}, Year = {2019}, Month = {July}, url = {http://dx.doi.org/10.1128/mra.00328-19}, Abstract = {The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.}, Doi = {10.1128/mra.00328-19}, Key = {fds345376} } @article{fds340995, Author = {Miadlikowska, J and Magain, N and Pardo-De La Hoz and CJ and Niu, D and Goward, T and Sérusiaux, E and Lutzoni, F}, Title = {Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision}, Journal = {Plant and Fungal Systematics}, Volume = {63}, Number = {2}, Pages = {45-64}, Year = {2018}, Month = {December}, url = {http://dx.doi.org/10.2478/pfs-2018-0007}, Abstract = {Closely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.}, Doi = {10.2478/pfs-2018-0007}, Key = {fds340995} } @article{fds340627, Author = {Lutzoni, F and Nowak, MD and Alfaro, ME and Reeb, V and Miadlikowska, J and Krug, M and Arnold, AE and Lewis, LA and Swofford, DL and Hibbett, D and Hilu, K and James, TY and Quandt, D and Magallón, S}, Title = {Contemporaneous radiations of fungi and plants linked to symbiosis.}, Journal = {Nature communications}, Volume = {9}, Number = {1}, Pages = {5451}, Year = {2018}, Month = {December}, url = {http://dx.doi.org/10.1038/s41467-018-07849-9}, Abstract = {Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous.}, Doi = {10.1038/s41467-018-07849-9}, Key = {fds340627} } @article{fds339810, Author = {Hoz, CJPDL and Magain, N and Lutzoni, F and Goward, T and Restrepo, S and Miadlikowska, J}, Title = {Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera}, Journal = {Frontiers in Microbiology}, Volume = {9}, Number = {NOV}, Publisher = {FRONTIERS MEDIA SA}, Year = {2018}, Month = {November}, url = {http://dx.doi.org/10.3389/fmicb.2018.02770}, Abstract = {Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.}, Doi = {10.3389/fmicb.2018.02770}, Key = {fds339810} } @article{fds339561, Author = {Korotkin, HB and Swenie, RA and Miettinen, O and Budke, JM and Chen, K-H and Lutzoni, F and Smith, ME and Matheny, PB}, Title = {Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales.}, Journal = {American journal of botany}, Volume = {105}, Number = {11}, Pages = {1869-1887}, Year = {2018}, Month = {November}, url = {http://dx.doi.org/10.1002/ajb2.1183}, Abstract = {<h4>Premise of the study</h4>The Hymenochaetales are dominated by lignicolous saprotrophic fungi involved in wood decay. However, the group also includes bryophilous and terricolous taxa, but their modes of nutrition are not clear. Here, we investigate patterns of carbon and nitrogen utilization in numerous non-lignicolous Hymenochaetales and provide a phylogenetic context in which these non-canonical ecological guilds arose.<h4>Methods</h4>We combined stable isotope analyses of δ<sup>13</sup> C and δ<sup>15</sup> N and phylogenetic analyses to explore assignment and evolution of nutritional modes. Clustering procedures and statistical tests were performed to assign trophic modes to Hymenochaetales and test for differences between varying ecologies. Genomes of Hymenochaetales were mined for presence of enzymes involved in plant cell wall and lignin degradation and sucrolytic activity.<h4>Key results</h4>Three different trophic clusters were detected - biotrophic, saprotrophic, and a second biotrophic cluster including many bryophilous Hymenochaetales and mosses. Non-lignicolous Hymenochaetales are generally biotrophic. All lignicolous Hymenochaetales clustered as saprotrophic and most terricolous Hymenochaetales clustered as ectomycorrhizal. Overall, at least 15 species of Hymenochaetales are inferred as biotrophic. Bryophilous species of Rickenella can degrade plant cell walls and lignin, and cleave sucrose to glucose consistent with a parasitic or endophytic life style.<h4>Conclusions</h4>Most non-lignicolous Hymenochaetales are biotrophic. Stable isotope values of many bryophilous Hymenochaetales cluster as ectomycorrhizal or in a biotrophic cluster indicative of parasitism or an endophytic life style. Overall, trophic mode diversity in the Hymenochaetales is greater than anticipated, and non-lignicolous ecological traits and biotrophic modes of nutrition are evolutionarily derived features.}, Doi = {10.1002/ajb2.1183}, Key = {fds339561} } @article{fds339618, Author = {Magain, N and Truong, C and Goward, T and Niu, D and Goffinet, B and Sérusiaux, E and Vitikainen, O and Lutzoni, F and Miadlikowska, J}, Title = {Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in peltigera section peltigera (Lichenized ascomycota: Lecanoromycetes)}, Journal = {Taxon}, Volume = {67}, Number = {5}, Pages = {836-870}, Publisher = {WILEY}, Year = {2018}, Month = {October}, url = {http://dx.doi.org/10.12705/675.3}, Abstract = {This comprehensive phylogenetic revision of sections Peltigera and Retifoveatae of the cyanolichen genus Peltigera is based on DNA sequences from more than 500 specimens from five continents. We amplified five loci (nrITS, β-tubulin and three intergenic spacers part of colinear orthologous regions [COR]) for the mycobiont, and the rbcLX locus for the cyanobacterial partner Nostoc. Phylogenetic inferences (RAxML, BEAST) and species delimitation methods (bGMYC, bPTP, bPP) suggest the presence of 88 species in section Peltigera, including 50 species new to science, hence uncovering a surprisingly high proportion of previously unnoticed biodiversity. The hypervariable region in ITS1 (ITS1-HR) is a powerful marker to identify species within sections Peltigera and Retifoveatae. Most newly delimited species are restricted to a single biogeographic region, however, up to ten species have a nearly cosmopolitan distribution. The specificity of mycobionts in their association with Nostoc cyanobionts ranges from strict specialists (associate with only one Nostoc phylogroup) to broad generalists (up to eight Nostoc phylogroups uncovered), with widespread species recruiting a broader selection of Nostoc phylogroups than species with limited distributions. In contrast, species from the P. didactyla clade characterized by small thalli and asexual vegetative propagules (soredia) associate with fewer Nostoc phylogroups (i.e., are more specialized) despite their broad distributions, and show significantly higher rates of nucleotide substitutions.}, Doi = {10.12705/675.3}, Key = {fds339618} } @article{fds336262, Author = {Chagnon, PL and Magain, N and Miadlikowska, J and Lutzoni, F}, Title = {Strong specificity and network modularity at a very fine phylogenetic scale in the lichen genus Peltigera.}, Journal = {Oecologia}, Volume = {187}, Number = {3}, Pages = {767-782}, Publisher = {Springer Nature}, Year = {2018}, Month = {July}, url = {http://dx.doi.org/10.1007/s00442-018-4159-6}, Abstract = {Identifying the drivers and evolutionary consequences of species interactions is a major goal of community ecology. Network-based analyses can provide mathematical tools to detect non-random patterns of interactions, and potentially help predicting the consequences of such patterns on evolutionary dynamics of symbiotic systems. Here, we characterize the structure of a lichen network at a very fine phylogenetic scale, by identifying the photosynthetic partners (i.e., cyanobacteria of the genus Nostoc) of lichenized fungi belonging to a monophyletic section of a single genus (i.e., section Polydactylon of the genus Peltigera), worldwide. Even at such a fine phylogenetic scale, we found that interactions were highly modular and anti-nested, indicating strong preferences in interactions. When considering local Peltigera communities, i.e., datasets at small spatial scales with only a slightly broader phylogenetic range, interactions remained modular but were asymmetric, with generalist Nostoc partners interacting with specialized Peltigera species. This asymmetry was not detected with our global spatial scale dataset. We discuss these results in the light of lichen community assembly, and explore how such interaction patterns may influence coevolution in lichens and the evolutionary stability of the mutualism in general.}, Doi = {10.1007/s00442-018-4159-6}, Key = {fds336262} } @article{fds336998, Author = {Lu, J and Magain, N and Miadlikowska, J and Coyle, JR and Truong, C and Lutzoni, F}, Title = {Bioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen-forming genus Peltigera.}, Journal = {American journal of botany}, Volume = {105}, Number = {7}, Pages = {1198-1211}, Year = {2018}, Month = {July}, url = {http://dx.doi.org/10.1002/ajb2.1119}, Abstract = {<h4>Premise of the study</h4>Factors shaping spatiotemporal patterns of associations in mutualistic systems are poorly understood. We used the lichen-forming fungi Peltigera and their cyanobacterial partners Nostoc to investigate the spatial structure of this symbiosis at an intrabiome scale and to identify potential factors shaping these associations.<h4>Methods</h4>Ninety-three thalli were sampled in Québec, Canada, along a south-north and an east-west transect of ~1300 km each. We identified the two main partners (Peltigera species and Nostoc phylogroups) using molecular markers and modeled the effects of environmental variables and partner occurrence on Peltigera-Nostoc distributions.<h4>Key results</h4>Peltigera species showed a high degree of specialization toward cyanobionts, whereas two Nostoc phylogroups dominated both transects by associating with several Peltigera species. Peltigera species had narrower ranges than these two main cyanobionts. Distributions of three Peltigera species were highly associated with precipitation and temperature variables, which was not detected for Nostoc phylogroups at this spatial scale.<h4>Conclusions</h4>For these cyanolichens, factors driving patterns of symbiotic associations are scale dependent. Contrary to global-scale findings, generalist Peltigera species were not more widespread within the boreal biome than specialists. Nostoc availability was not the only driver of Peltigera species' geographic ranges; environmental factors also contributed to their intrabiome distributions. Climatic conditions (especially precipitation) limited the range of some Peltigera species more than the range of their cyanobacterial partners at an intrabiome (boreal) scale.}, Doi = {10.1002/ajb2.1119}, Key = {fds336998} } @article{fds335251, Author = {Chen, K-H and Liao, H-L and Arnold, AE and Bonito, G and Lutzoni, F}, Title = {RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi.}, Journal = {The New phytologist}, Volume = {218}, Number = {4}, Pages = {1597-1611}, Publisher = {WILEY}, Year = {2018}, Month = {June}, url = {http://dx.doi.org/10.1111/nph.15092}, Abstract = {Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.}, Doi = {10.1111/nph.15092}, Key = {fds335251} } @article{fds335252, Author = {Kauff, F and Bachran, A and Schultz, M and Hofstetter, V and Lutzoni, F and Büdel, B}, Title = {Molecular data favours a monogeneric Peltulaceae (Lichinomycetes)}, Journal = {Lichenologist}, Volume = {50}, Number = {3}, Pages = {313-327}, Publisher = {Cambridge University Press (CUP)}, Year = {2018}, Month = {May}, url = {http://dx.doi.org/10.1017/S0024282918000105}, Abstract = {The family Peltulaceae is currently composed of the three genera Peltula, Phyllopeltula and Neoheppia. The last two genera, both with two species, are distinguished from Peltula only by a small number of morphological characters. The morphology of the genus Peltula varies from peltate-umbilicate thalli to squamulose-semifruticose or squamulose-compound types, as well as subfoliose-compound and crustose types. All types have an upper epinecral layer and possess medullary cavities of various sizes; a lower cortex is normally present but is usually not developed in the subfoliose and crustose types. The genera Neoheppia and Phyllopeltula differ from the common Peltula morphology by crustose-areolate and subfoliose-compound thalli, respectively. Both Neoheppia and Phyllopeltula are additionally characterized by the absence of medullary cavities and lower cortices. To investigate the phylogenetic validity of Phyllopeltula and Neoheppia, we sequenced six loci from representatives of these two genera together with 37 species from Peltula. Despite the relatively high amount of conflict among loci, the results clearly indicate that both Phyllopeltula and Neoheppia are not monophyletic, and are nested within the genus Peltula. Consequently, we subsumed species of these two genera within the genus Peltula.}, Doi = {10.1017/S0024282918000105}, Key = {fds335252} } @article{fds329168, Author = {Magain, N and Miadlikowska, J and Mueller, O and Gajdeczka, M and Truong, C and Salamov, AA and Dubchak, I and Grigoriev, IV and Goffinet, B and Sérusiaux, E and Lutzoni, F}, Title = {Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon.}, Journal = {Molecular phylogenetics and evolution}, Volume = {117}, Pages = {10-29}, Year = {2017}, Month = {December}, url = {http://dx.doi.org/10.1016/j.ympev.2017.08.013}, Abstract = {Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. Asa proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) - a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.}, Doi = {10.1016/j.ympev.2017.08.013}, Key = {fds329168} } @article{fds326982, Author = {Heiđmarsson, S and Gueidan, C and Miadlikowska, J and Lutzoni, F}, Title = {Multi-locus phylogeny supports the placement of endocarpon pulvinatum within staurothele s. Str. (lichenised ascomycetes, eurotiomycetes, verrucariaceae)}, Journal = {Phytotaxa}, Volume = {306}, Number = {1}, Pages = {37-48}, Publisher = {MAGNOLIA PRESS}, Year = {2017}, Month = {May}, url = {http://dx.doi.org/10.11646/phytotaxa.306.1.3}, Abstract = {Within the lichen family Verrucariaceae, the genera Endocarpon, Willeya and Staurothele are characterised by muriform ascospores and the presence of algal cells in the hymenium. Endocarpon thalli are squamulose to subfruticose, whereas Willeya and Staurothele include only crustose species. Endocarpon pulvinatum, an arctic-alpine species newly reported for Iceland, is one of the few Endocarpon with a subfruticose thallus formed by long and narrow erected squamules. Molecular phylogenetic analyses of four loci (ITS, nrLSU, mtSSU, and mcm7) newly obtained from E. pulvinatum specimens from Iceland, Finland and North America does not confirm its current classification within the mostly squamulose genus Endocarpon, but instead supports its placement within the crustose genus Staurothele. The new combination Staurothele pulvinata is therefore proposed here. It includes also E. tortuosum, which was confirmed as a synonym of E. pulvinatum based on a single sequence.}, Doi = {10.11646/phytotaxa.306.1.3}, Key = {fds326982} } @article{fds326983, Author = {Carbone, I and White, JB and Miadlikowska, J and Arnold, AE and Miller, MA and Kauff, F and U'Ren, JM and May, G and Lutzoni, F}, Title = {T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.}, Journal = {Bioinformatics (Oxford, England)}, Volume = {33}, Number = {8}, Pages = {1160-1168}, Year = {2017}, Month = {April}, url = {http://dx.doi.org/10.1093/bioinformatics/btw808}, Abstract = {<h4>Motivation</h4>High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades.<h4>Results</h4>In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree.<h4>Availability and implementation</h4>T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources.<h4>Contact</h4>icarbon@ncsu.edu.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.}, Doi = {10.1093/bioinformatics/btw808}, Key = {fds326983} } @article{fds320862, Author = {Darnajoux, R and Zhang, X and McRose, DL and Miadlikowska, J and Lutzoni, F and Kraepiel, AML and Bellenger, J-P}, Title = {Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates.}, Journal = {The New phytologist}, Volume = {213}, Number = {2}, Pages = {680-689}, Year = {2017}, Month = {January}, url = {http://dx.doi.org/10.1111/nph.14166}, Abstract = {Cryptogamic species and their associated cyanobacteria have attracted the attention of biogeochemists because of their critical roles in the nitrogen cycle through symbiotic and asymbiotic biological fixation of nitrogen (BNF). BNF is mediated by the nitrogenase enzyme, which, in its most common form, requires molybdenum at its active site. Molybdenum has been reported as a limiting nutrient for BNF in many ecosystems, including tropical and temperate forests. Recent studies have suggested that alternative nitrogenases, which use vanadium or iron in place of molybdenum at their active site, might play a more prominent role in natural ecosystems than previously recognized. Here, we studied the occurrence of vanadium, the role of molybdenum availability on vanadium acquisition and the contribution of alternative nitrogenases to BNF in the ubiquitous cyanolichen Peltigera aphthosa s.l. We confirmed the use of the alternative vanadium-based nitrogenase in the Nostoc cyanobiont of these lichens and its substantial contribution to BNF in this organism. We also showed that the acquisition of vanadium is strongly regulated by the abundance of molybdenum. These findings show that alternative nitrogenase can no longer be neglected in natural ecosystems, particularly in molybdenum-limited habitats.}, Doi = {10.1111/nph.14166}, Key = {fds320862} } @misc{fds332335, Author = {Magain, N and Miadlikowska, J and Goffinet, B and Sérusiaux, E and Lutzoni, F}, Title = {Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota).}, Journal = {Systematic biology}, Volume = {66}, Number = {1}, Pages = {74-99}, Year = {2017}, Month = {January}, url = {http://dx.doi.org/10.1093/sysbio/syw065}, Abstract = {Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here, we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred from five nuclear loci and the rbcLX region, respectively. These sequences were obtained from 206 lichen thalli, representing ca. 40 closely related Peltigera species sampled worldwide, doubling the number of known species in this group. We found a broad spectrum of specificity for both partners ranging from strict specialists to generalists. Overall, mycobionts are more specialized than cyanobionts by associating mostly with one or a few Nostoc phylogroups, whereas most cyanobionts associate frequently with several Peltigera species. Specialist mycobionts are older than generalists, supporting the hypothesis that specialization of mycobionts to one or few cyanobionts, is favored through time in geographic areas where species have been established for long periods of time. The relatively recent colonization of a new geographic area (Central and South America) by members of section Polydactylon is associated with a switch to a generalist pattern of association and an increased diversification rate by the fungal partner, suggesting that switches to generalism are rare events that are advantageous in new environments. We detected higher genetic diversity in generalist mycobionts. We also found that Peltigera species specialized on a single Nostoc phylogroup have narrower geographical distributions compared with generalist species.}, Doi = {10.1093/sysbio/syw065}, Key = {fds332335} } @article{fds323162, Author = {van Nieuwenhuijzen, EJ and Miadlikowska, JM and Houbraken, JAMP and Adan, OCG and Lutzoni, FM and Samson, RA}, Title = {Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni.}, Journal = {Studies in mycology}, Volume = {85}, Pages = {107-124}, Year = {2016}, Month = {September}, url = {http://dx.doi.org/10.1016/j.simyco.2016.11.008}, Abstract = {A culture-based survey of staining fungi on oil-treated timber after outdoor exposure in Australia and the Netherlands uncovered new taxa in <i>Pezizomycotina</i>. Their taxonomic novelty was confirmed by phylogenetic analyses of multi-locus sequences (ITS, nrSSU, nrLSU, mitSSU, <i>RPB1</i>, <i>RPB2</i>, and <i>EF-1α</i>) using multiple reference data sets. These previously unknown taxa are recognised as part of a new order (<i>Superstratomycetales</i>) potentially closely related to <i>Trypetheliales</i> (<i>Dothideomycetes</i>), and as a new species of <i>Cyanodermella</i>, <i>C. oleoligni</i> in <i>Stictidaceae</i> (<i>Ostropales</i>) part of the mostly lichenised class <i>Lecanoromycetes</i>. Within <i>Superstratomycetales</i> a single genus named <i>Superstratomyces</i> with three putative species: <i>S. flavomucosus</i>, <i>S. atroviridis</i>, and <i>S. albomucosus</i> are formally described. Monophyly of each circumscribed <i>Superstratomyces</i> species was highly supported and the intraspecific genetic variation was substantially lower than interspecific differences detected among species based on the ITS, nrLSU, and <i>EF-1α</i> loci. Ribosomal loci for all members of <i>Superstratomyces</i> were noticeably different from all fungal sequences available in GenBank. All strains from this genus grow slowly in culture, have darkly pigmented mycelia and produce pycnidia. The strains of <i>C. oleoligni</i> form green colonies with slimy masses and develop green pycnidia on oatmeal agar. These new taxa could not be classified reliably at the class and lower taxonomic ranks by sequencing from the substrate directly or based solely on culture-dependent morphological investigations. Coupling phenotypic observations with multi-locus sequencing of fungi isolated in culture enabled these taxonomic discoveries. Outdoor situated timber provides a great potential for culturable undescribed fungal taxa, including higher rank lineages as revealed by this study, and therefore, should be further explored.}, Doi = {10.1016/j.simyco.2016.11.008}, Key = {fds323162} } @article{fds320863, Author = {Hestmark, G and Lutzoni, F and Miadlikowska, J}, Title = {Photobiont associations in co-occurring umbilicate lichens with contrasting modes of reproduction in coastal Norway}, Journal = {Lichenologist}, Volume = {48}, Number = {5}, Pages = {545-557}, Publisher = {Cambridge University Press (CUP)}, Year = {2016}, Month = {September}, url = {http://dx.doi.org/10.1017/S0024282916000232}, Abstract = {The identity and phylogenetic placement of photobionts associated with two lichen-forming fungi, Umbilicaria spodochroa and Lasallia pustulata were examined. These lichens commonly grow together in high abundance on coastal cliffs in Norway, Sweden and Finland. The mycobiont of U. spodochroa reproduces sexually through ascospores, and must find a suitable algal partner in the environment to re-establish the lichen symbiosis. Lasallia pustulata reproduces mainly vegetatively using symbiotic propagules (isidia) containing both symbiotic partners (photobiont and mycobiont). Based on DNA sequences of the internal transcribed spacer region (ITS) we detected seven haplotypes of the green-algal genus Trebouxia in 19 pairs of adjacent thalli of U. spodochroa and L. pustulata from five coastal localities in Norway. As expected, U. spodochroa associated with a higher diversity of photobionts (seven haplotypes) than the mostly asexually reproducing L. pustulata (four haplotypes). The latter was associated with the same haplotype in 15 of the 19 thalli sampled. Nine of the lichen pairs examined share the same algal haplotype, supporting the hypothesis that the mycobiont of U. spodochroa might associate with the photobiont 'pirated' from the abundant isidia produced by L. pustulata that are often scattered on the cliff surfaces. Up to six haplotypes of Trebouxia were found within a single sampling site, indicating a low level of specificity of both mycobionts for their algal partner. Most photobiont strains associated with species of Umbilicaria and Lasallia, including samples from this study, represent phylogenetically closely related taxa of Trebouxia grouped within a small number of main clades (Trebouxia sp., T. simplex/T. jamesii, and T. incrustata+T. gigantea). Three of the photobiont haplotypes were found only in U. spodochroa thalli.}, Doi = {10.1017/S0024282916000232}, Key = {fds320863} } @article{fds320864, Author = {Chagnon, P-L and U'Ren, JM and Miadlikowska, J and Lutzoni, F and Arnold, AE}, Title = {Erratum to: Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.}, Journal = {Oecologia}, Volume = {181}, Number = {2}, Pages = {633}, Publisher = {Springer Nature}, Year = {2016}, Month = {June}, url = {http://dx.doi.org/10.1007/s00442-016-3589-2}, Doi = {10.1007/s00442-016-3589-2}, Key = {fds320864} } @article{fds320865, Author = {U'Ren, JM and Miadlikowska, J and Zimmerman, NB and Lutzoni, F and Stajich, JE and Arnold, AE}, Title = {Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).}, Journal = {Molecular phylogenetics and evolution}, Volume = {98}, Pages = {210-232}, Year = {2016}, Month = {May}, url = {http://dx.doi.org/10.1016/j.ympev.2016.02.010}, Abstract = {The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.}, Doi = {10.1016/j.ympev.2016.02.010}, Key = {fds320865} } @article{fds290766, Author = {Chagnon, P-L and U'Ren, JM and Miadlikowska, J and Lutzoni, F and Arnold, AE}, Title = {Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.}, Journal = {Oecologia}, Volume = {180}, Number = {1}, Pages = {181-191}, Year = {2016}, Month = {January}, ISSN = {0029-8549}, url = {http://dx.doi.org/10.1007/s00442-015-3457-5}, Abstract = {Understanding the factors that shape community assembly remains one of the most enduring and important questions in modern ecology. Network theory can reveal rules of community assembly within and across study systems and suggest novel hypotheses regarding the formation and stability of communities. However, such studies generally face the challenge of disentangling the relative influence of factors such as interaction type and environmental conditions on shaping communities and associated networks. Endophytic and endolichenic symbioses, characterized by microbial species that occur within healthy plants and lichen thalli, represent some of the most ubiquitous interactions in nature. Fungi that engage in these symbioses are hyperdiverse, often horizontally transmitted, and functionally beneficial in many cases, and they represent the diversification of multiple phylogenetic groups. We evaluated six measures of ecological network structure for >4100 isolates of endophytic and endolichenic fungi collected systematically from five sites across North America. Our comparison of these co-occurring interactions in biomes ranging from tundra to subtropical forest showed that the type of interactions (i.e., endophytic vs. endolichenic) had a much more pronounced influence on network structure than did environmental conditions. In particular, endophytic networks were less nested, less connected, and more modular than endolichenic networks in all sites. The consistency of the network structure within each interaction type, independent of site, is encouraging for current efforts devoted to gathering metadata on ecological network structure at a global scale. We discuss several mechanisms potentially responsible for such patterns and draw attention to knowledge gaps in our understanding of networks for diverse interaction types.}, Doi = {10.1007/s00442-015-3457-5}, Key = {fds290766} } @article{fds228765, Author = {Darnajoux, R and Lutzoni, F and Miadlikowska, J and Bellenger, J-P}, Title = {Determination of elemental baseline using peltigeralean lichens from Northeastern Canada (Québec): Initial data collection for long term monitoring of the impact of global climate change on boreal and subarctic area in Canada.}, Journal = {The Science of the total environment}, Volume = {533}, Pages = {1-7}, Year = {2015}, Month = {November}, ISSN = {0048-9697}, url = {http://dx.doi.org/10.1016/j.scitotenv.2015.06.030}, Abstract = {Northeastern Canada is mostly free of anthropogenic activities. The extent to which this territory has been impacted by anthropogenic atmospheric depositions remains to be studied. The main goal of our study was to establish background levels for metals in boreal muscicolous/terricolous macrolichens over non-urbanized areas of northeastern Canada (Québec). Concentrations of 18 elements (Na, Mg, Al, P, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Cd, and Pb) were determined for three species of the genus Peltigera (Peltigera aphthosa (L.) Willd. s.l., Peltigera neopolydactyla (Gyeln.) Gyeln. s.l., Peltigera scabrosa Th. Fr. s.l.), and Nephroma arcticum (L.) Torss., along a 1080 km south-north transect and along a of 730 km west-east transect. We report that elemental contents in the sampled lichen thalli are very low and similar to background levels found in other studies performed in pristine places (high elevation or remote ecosystems) throughout the world. Overall, our results demonstrate that most of the boreal and subarctic zone of Québec (northeastern Canada) is still pristine. The elemental baseline established in these lichen populations will contribute to monitor metal pollution in boreal and sub-polar ecosystems due to global climate change and future industrial expansion.}, Doi = {10.1016/j.scitotenv.2015.06.030}, Key = {fds228765} } @article{fds228767, Author = {Oono, R and Lefèvre, E and Simha, A and Lutzoni, F}, Title = {A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda).}, Journal = {Fungal biology}, Volume = {119}, Number = {10}, Pages = {917-928}, Year = {2015}, Month = {October}, ISSN = {1878-6146}, url = {http://dx.doi.org/10.1016/j.funbio.2015.07.003}, Abstract = {Fungal endophytes represent one of the most ubiquitous plant symbionts on Earth and are phylogenetically diverse. The structure and diversity of endophyte communities have been shown to depend on host taxa and climate, but there have been relatively few studies exploring endophyte communities throughout host maturity. We compared foliar fungal endophyte communities between seedlings and adult trees of loblolly pines (Pinus taeda) at the same seasons and locations by culturing and culture-independent methods. We sequenced the internal transcribed spacer region and adjacent partial large subunit nuclear ribosomal RNA gene (ITS-LSU amplicon) to delimit operational taxonomic units and phylogenetically characterize the communities. Despite the lower infection frequency in seedlings compared to adult trees, seedling needles were receptive to a more diverse community of fungal endophytes. Culture-free method confirmed the presence of commonly cultured OTUs from adult needles but revealed several new OTUs from seedling needles that were not found with culturing methods. The two most commonly cultured OTUs in adults were rarely cultured from seedlings, suggesting that host age is correlated with a selective enrichment for specific endophytes. This shift in endophyte species dominance may be indicative of a functional change between these fungi and their loblolly pine hosts.}, Doi = {10.1016/j.funbio.2015.07.003}, Key = {fds228767} } @article{fds228764, Author = {Gaya, E and Fernández-Brime, S and Vargas, R and Lachlan, RF and Gueidan, C and Ramírez-Mejía, M and Lutzoni, F}, Title = {The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {112}, Number = {37}, Pages = {11600-11605}, Year = {2015}, Month = {September}, ISSN = {0027-8424}, url = {http://dx.doi.org/10.1073/pnas.1507072112}, Abstract = {Adaptive radiations play key roles in the generation of biodiversity and biological novelty, and therefore understanding the factors that drive them remains one of the most important challenges of evolutionary biology. Although both intrinsic innovations and extrinsic ecological opportunities contribute to diversification bursts, few studies have looked at the synergistic effect of such factors. Here we investigate the Teloschistales (Ascomycota), a group of >1,000 lichenized species with variation in species richness and phenotypic traits that hinted at a potential adaptive radiation. We found evidence for a dramatic increase in diversification rate for one of four families within this order--Teloschistaceae--which occurred ∼ 100 Mya (Late Cretaceous) and was associated with a switch from bark to rock and from shady to sun-exposed habitats. This adaptation to sunny habitats is likely to have been enabled by a contemporaneous key novel phenotypic innovation: the production in both vegetative structure (thallus) and fruiting body (apothecia) of anthraquinones, secondary metabolites known to protect against UV light. We found that the two ecological factors (sun exposure and rock substrate) and the phenotypic innovation (anthraquinones in the thallus) were all significant when testing for state-dependent shifts in diversification rates, and together they seem likely to be responsible for the success of the Teloschistaceae, one of the largest lichen-forming fungal lineages. Our results support the idea that adaptive radiations are driven not by a single factor or key innovation, but require a serendipitous combination of both intrinsic biotic and extrinsic abiotic and ecological factors.}, Doi = {10.1073/pnas.1507072112}, Key = {fds228764} } @article{fds228766, Author = {Chen, K-H and Miadlikowska, J and Molnár, K and Arnold, AE and U'Ren, JM and Gaya, E and Gueidan, C and Lutzoni, F}, Title = {Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.}, Journal = {Molecular phylogenetics and evolution}, Volume = {85}, Pages = {117-130}, Year = {2015}, Month = {April}, ISSN = {1055-7903}, url = {http://dx.doi.org/10.1016/j.ympev.2015.01.008}, Abstract = {Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.}, Doi = {10.1016/j.ympev.2015.01.008}, Key = {fds228766} } @article{fds290767, Author = {Gueidan, C and Hill, DJ and Miadlikowska, J and Lutzoni, F}, Title = {Pezizomycotina: Lecanoromycetes}, Pages = {89-120}, Booktitle = {Volume VII of The Mycota Part B}, Publisher = {Springer Berlin Heidelberg}, Address = {Berlin, Germany}, Editor = {D. J. McLaughlin and J. W. Spatafora}, Year = {2015}, Month = {January}, url = {http://dx.doi.org/10.1007/978-3-662-46011-5_4}, Abstract = {Lecanoromycetes is the class of Ascomycota with the largest number of lichen-forming fungi. Members of this class are important components of most terrestrial ecosystems and occur in various habitats and on different substrates, from tropical to polar regions. Morphological, anatomical, and chemical characters have traditionally been used to classify orders, families, and genera within Lecanoromycetes. In the last two decades, molecular phylogenies have shown that traditional classification systems were not always consistent with the evolutionary history of this fungal class, resulting in changes in the delimitation of orders and families. Here, we revisit the taxonomic value of the main characters traditionally used for classification in light of current molecular phylogenies. The current delimitation of the 14 orders of Lecanoromycetes is also discussed, and recent changes in classification are highlighted.}, Doi = {10.1007/978-3-662-46011-5_4}, Key = {fds290767} } @article{fds228763, Author = {Miadlikowska, J and Kauff, F and Högnabba, F and Oliver, JC and Molnár, K and Fraker, E and Gaya, E and Hafellner, J and Hofstetter, V and Gueidan, C and Otálora, MAG and Hodkinson, B and Kukwa, M and Lücking, R and Björk, C and Sipman, HJM and Burgaz, AR and Thell, A and Passo, A and Myllys, L and Goward, T and Fernández-Brime, S and Hestmark, G and Lendemer, J and Lumbsch, HT and Schmull, M and Schoch, CL and Sérusiaux, E and Maddison, DR and Arnold, AE and Lutzoni, F and Stenroos, S}, Title = {A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.}, Journal = {Molecular phylogenetics and evolution}, Volume = {79}, Pages = {132-168}, Year = {2014}, Month = {October}, ISSN = {1055-7903}, url = {http://dx.doi.org/10.1016/j.ympev.2014.04.003}, Abstract = {The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.}, Doi = {10.1016/j.ympev.2014.04.003}, Key = {fds228763} } @article{fds228768, Author = {Oono, R and Lutzoni, F and Arnold, AE and Kaye, L and U'Ren, JM and May, G and Carbone, I}, Title = {Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.}, Journal = {American journal of botany}, Volume = {101}, Number = {8}, Pages = {1362-1374}, Year = {2014}, Month = {August}, ISSN = {0002-9122}, url = {http://dx.doi.org/10.3732/ajb.1400141}, Abstract = {<h4>Unlabelled</h4>•<h4>Premise of the study</h4>Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.•<h4>Methods</h4>We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.•<h4>Key results</h4>Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.•<h4>Conclusions</h4>We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales.}, Doi = {10.3732/ajb.1400141}, Key = {fds228768} } @article{fds228769, Author = {Miadlikowska, J and Richardson, D and Magain, N and Ball, B and Anderson, F and Cameron, R and Lendemer, J and Truong, C and Lutzoni, F}, Title = {Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).}, Journal = {American journal of botany}, Volume = {101}, Number = {7}, Pages = {1141-1156}, Year = {2014}, Month = {July}, ISSN = {0002-9122}, url = {http://dx.doi.org/10.3732/ajb.1400267}, Abstract = {• Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.• Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria.• Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes.• Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America.}, Doi = {10.3732/ajb.1400267}, Key = {fds228769} } @article{fds228770, Author = {Darnajoux, R and Constantin, J and Miadlikowska, J and Lutzoni, F and Bellenger, J-P}, Title = {Is vanadium a biometal for boreal cyanolichens?}, Journal = {The New phytologist}, Volume = {202}, Number = {3}, Pages = {765-771}, Year = {2014}, Month = {May}, ISSN = {0028-646X}, url = {http://dx.doi.org/10.1111/nph.12777}, Abstract = {Molybdenum (Mo) nitrogenase has long been considered the predominant isoenzyme responsible for dinitrogen fixation worldwide. Recent findings have challenged the paradigm of Mo hegemony, and highlighted the role of alternative nitrogenases, such as the vanadium-nitrogenase. Here, we first characterized homeostasis of vanadium (V) along with other metals in situ in the dinitrogen fixing cyanolichen Peltigera aphthosa. These lichens were sampled in natural sites exposed to various levels of atmospheric metal deposition. These results were compared with laboratory experiments where Anabaena variabilis, which is also hosting the V-nitrogenase, and a relatively close relative of the lichen cyanobiont Nostoc, was subjected to various levels of V. We report here that V is preferentially allocated to cephalodia, specialized structures where dinitrogen fixation occurs in tri-membered lichens. This specific allocation is biologically controlled and tightly regulated. Vanadium homeostasis in lichen cephalodia exposed to various V concentrations is comparable to the one observed in Anabaena variabilis and other dinitrogen fixing organisms using V-nitrogenase. Overall, our findings support current hypotheses that V could be a more important factor in mediating nitrogen input in high latitude ecosystems than previously recognized. They invite the reassessment of current theoretical models linking metal dynamics and dinitrogen fixation in boreal and subarctic ecosystems.}, Doi = {10.1111/nph.12777}, Key = {fds228770} } @article{fds220818, Author = {Oono, R. and Lutzoni, F. and Arnold, A. E. and Kaye, L. and U’ren, J. M. and May, G. and Carbone, I.}, Title = {Genetic variation in horizontally transmitted symbionts of pine needles reveals population structure in cryptic species}, Journal = {American Naturalist}, Year = {2014}, Key = {fds220818} } @article{fds220820, Author = {Miadlikowska, J. and Kauff, F. and Högnabba, F. and Oliver, J. C. and Molnár, K. and Fraker, E. and Gaya, E. and Hafellner, J. and Hofstetter, V. and Gueidan, C. and Kukwa, M. and Lücking, M. and Björk, C. and Sipman, H. J. M. and Burgaz, A. R. and Thell, A. and Passo, A. and Myllys, L. and Goward, T. and Fernández-Brime, S. and Hestmark, G. and Lendemer, J. and Lumbsch, H. T. and Schmull, M. and Schoch, C. and Sérusiaux, E. and Maddison, D. R. and Arnold, A. E. and Stenroos, S. and Lutzoni, F.}, Title = {Multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 312 genera and 66 families}, Journal = {Molecular Phylogenetics and Evolution}, Year = {2014}, Key = {fds220820} } @article{fds228787, Author = {McDonald, TR and Mueller, O and Dietrich, FS and Lutzoni, F}, Title = {High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.}, Journal = {BMC Genomics}, Volume = {14}, Pages = {225}, Year = {2013}, Month = {April}, url = {http://dx.doi.org/10.1186/1471-2164-14-225}, Abstract = {BACKGROUND: Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiomyceta. The horizontally transferred gene has subsequently been lost in most of the group but has been selectively retained in lichenizing fungi. However, some groups of lichens appear to have secondarily lost the archaeal ammonium transporter. Definitive assessment of gene loss can only be made via whole genome sequencing. RESULTS: Ammonium transporter/ammonia permease gene sequences were recovered from the assembled genomes of eight lichenizing fungi in key clades including the Caliciales, the Peltigerales, the Ostropomycetidae, the Acarosporomycetidae, the Verrucariales, the Arthoniomycetidae and the Lichinales. The genes recovered were included in a refined phylogenetic analysis. The hypothesis that lichens symbiotic with a nitrogen-fixing cyanobacterium as a primary photobiont or lichens living in high nitrogen environments lose the plant-like ammonium transporters was upheld, but did not account for additional losses of ammonium transporters/ammonia permeases in the lichens from the Acarosporomycetidae, Chaetotheriomycetes and Arthoniomycetes. In addition, the four ammonium transporter/ammonia permease genes from Cladonia grayi were shown to be functional by expressing the lichen genes in a strain of Saccharomyces cerevisiae in which all three native ammonium transporters were deleted, and assaying for growth on limiting ammonia as a sole nitrogen source. CONCLUSIONS: Given sufficient coverage, next-generation sequencing technology can definitively address the loss of a gene in a genome when using environmental DNA isolated from lichen thalli collected from their natural habitats. Lichen-forming fungi have been losing ammonium transporters/ammonia permease genes at a slower rate than the most closely related non-lichenized lineages. These horizontally transferred genes in the Cladonia grayi genome encode functional ammonium transporters/ammonia permeases.}, Doi = {10.1186/1471-2164-14-225}, Key = {fds228787} } @article{fds228788, Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F}, Title = {Assessing population structure and host specialization in lichenized cyanobacteria.}, Journal = {The New phytologist}, Volume = {198}, Number = {2}, Pages = {557-566}, Year = {2013}, Month = {April}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23406441}, Abstract = {Coevolutionary theory predicts that the distribution of obligately symbiotic organisms will be determined by the dispersal ability and ecological range of both partners. We examined this prediction for lichen-forming fungi that form obligate symbioses with cyanobacteria. We compared genotypes of both partners of 250 lichens collected at multiple spatial scales in British Columbia, Canada. Multilocus sequence data collected from a subset of 128 of the specimens were used to determine the degree of recombination within the cyanobacterial populations. We found that six distinct clusters of cyanobacterial genotypes are distributed throughout the known global phylogeny of the genus Nostoc, and that each appears to be evolving clonally. Fungal specialization is high, with each species associating with either one or two of the cyanobacterial clusters, while cyanobacterial specialization varies, with clusters associating with between one and 12 different fungal species. Specialization also varies geographically, with some combinations restricted to a single site despite the availability of both partners elsewhere. Photobiont association patterns are determined by a combination of genetically based specificity, spatial population structure, and ecological factors and cannot be easily predicted by photobiont dispersal syndromes.}, Doi = {10.1111/nph.12165}, Key = {fds228788} } @article{fds228785, Author = {Hodkinson, BP and Allen, JL and Forrest, L and Goffinet, B and Sérusiaux, E and Andrésson, ÓS and Miao, V and Bellenger, JP and Lutzoni, F}, Title = {Lichen-symbiotic Cyanobacteria have an alternative vanadium-dependent nitrogen fixation system}, Journal = {New Phytologist}, Volume = {49}, Number = {1}, Pages = {11-19}, Publisher = {Informa UK Limited}, Year = {2013}, url = {http://dx.doi.org/10.1080/09670262.2013.873143}, Abstract = {In past decades, environmental nitrogen fixation has been attributed almost exclusively to the action of enzymes in the well-studied molybdenum-dependent nitrogen fixation system. However, recent evidence has shown that nitrogen fixation by alternative pathways may be more frequent than previously suspected. In this study, the nitrogen fixation systems employed by lichen-symbiotic cyanobacteria were examined to determine whether their diazotrophy can be attributed, in part, to an alternative pathway. The mining of metagenomic data (generated through pyrosequencing) and PCR assays were used to determine which nitrogen-fixation systems are present in cyanobacteria from the genus Nostoc associated with four samples from different geographical regions, representing different lichen-forming fungal species in the genus Peltigera. A metatranscriptomic sequence library from an additional specimen was examined to determine which genes associated with N2 fixation are transcriptionally expressed. Results indicated that both the standard molybdenum-dependent system and an alternative vanadium-dependent system are present and actively transcribed in the lichen symbiosis. This study shows for the first time that an alternative system is utilized by cyanobacteria associated with fungi. The ability of lichen-associated cyanobacteria to switch between pathways could allow them to colonize a wider array of environments, including habitats characterized by low temperature and trace metal (e.g. molybdenum) availability. We discuss the implications of these findings for environmental studies that incorporate acetylene-reduction assay data. © 2014 British Phycological Society.}, Doi = {10.1080/09670262.2013.873143}, Key = {fds228785} } @article{fds228786, Author = {McDonald, TR and Gaya, E and Lutzoni, F}, Title = {Twenty-five aposymbiotic cultures of lichenizing fungi available for experimental studies on symbiotic systems}, Journal = {Symbiosis}, Volume = {59}, Number = {3}, Pages = {165-171}, Publisher = {Springer Nature}, Year = {2013}, ISSN = {0334-5114}, url = {http://dx.doi.org/10.1007/s13199-013-0228-0}, Abstract = {In this study we describe the techniques used to culture 25 mycobionts spanning three classes and five orders of the leotiomyceta (Ascomycota). We find that five media, including potato-carrot, malt extract-yeast extract (MY), Bold's basal medium with nitrogen (NMBBM), oatmeal, and yeast extract with supplements (YES), are sufficient to induce ascospore germination of many lichenizing fungi and are also suitable for maintaining growth of the culture over the long term. Regular physical disruption of the cultures in liquidmedia is recommended to stimulate continued growth. Genomes of five of these lichen-forming fungal strains have been sequenced. The identity of each culture was confirmed by sequencing the nuclear ribosomal internal transcribed spacer (ITS) or the mitochondrial small subunit (mitSSU) from each strain. Additionally, the level of sequencing in terms of total number of genes sequenced for each taxon is provided. All fungal cultures have been deposited in public culture collections and, therefore, are available to the scientific community for conducting in vitro experiments. © Springer Science+Business Media Dordrecht 2013.}, Doi = {10.1007/s13199-013-0228-0}, Key = {fds228786} } @article{fds228789, Author = {Fernández Brime and S and Llimona, X and Lutzoni, F and Gaya, E}, Title = {Phylogenetic study of Diploschistes (Graphidaceae, Ostropales, lichen-forming Ascomycota), based on morphological, chemical and molecular data}, Journal = {Taxon}, Volume = {62}, Number = {2}, Pages = {267-280}, Year = {2013}, ISSN = {0040-0262}, url = {http://dx.doi.org/10.12705/622.10}, Abstract = {The genus Diploschistes includes crustose lichen-forming fungi with a carbonized proper excipulum with lateral paraphyses, and a chemistry dominated by orcinol depsides. However, the taxon D. ocellatus lacks these excipular characters and has β-orcinol depsidones, raising doubts about its inclusion within this genus. Using a two-locus dataset (mtSSU, nuLSU), our phylogenetic analyses confirm the classification of D. ocellatus within Diploschistes. Three different groups have been recognized within this genus, based on ascomatal morphology: Actinostomus (perithecioid), Scruposus (urceolate), and Ocellatus (lecanoroid). These groups have been widely used in monographic studies and keys, but their taxonomic value has not been confirmed yet. Here we inferred phylogenetic relationships within Diploschistes, with a special emphasis on the D. scruposus complex, using a combined dataset consisting of morphological, chemical, nrITS, and mtSSU data in order to determine if these species groups and phenotypically based species delimitations were monophyletic. Based on our results, a new subgeneric treatment for Diploschistes is proposed, and the taxonomic value of fruiting body types is confirmed. The clade corresponding to D. ocellatus consists of two well-supported subclades, one of them grouping specimens without ascomata, having only pycnidia. It is also remarkable that the clade containing specimens of D. diacapsis subsp. neutrophilus appears distantly related to the clade containing all other accessions of D. diacapsis. Our analysis revealed that for some taxa, such as D. scruposus and D. interpediens, molecular variability did not correlate with either morphological or chemical diversity.}, Doi = {10.12705/622.10}, Key = {fds228789} } @article{fds228790, Author = {Gazis, R and Miadlikowska, J and Lutzoni, F and Arnold, AE and Chaverri, P}, Title = {Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes.}, Journal = {Molecular phylogenetics and evolution}, Volume = {65}, Number = {1}, Pages = {294-304}, Year = {2012}, Month = {October}, ISSN = {1055-7903}, url = {http://dx.doi.org/10.1016/j.ympev.2012.06.019}, Abstract = {Through a culture-based survey of living sapwood and leaves of rubber trees (Hevea spp.) in remote forests of Peru, we discovered a new major lineage of Ascomycota, equivalent to a class rank. Multilocus phylogenetic analyses reveal that this new lineage originated during the radiation of the 'Leotiomyceta', which resulted not only in the evolution of the Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, and Sordariomycetes, but also of the majority of hyperdiverse foliar endophytes. Because its origin is nested within this major burst of fungal diversification, we could not recover strong support for its phylogenetic relationship within the 'Leotiomyceta'. Congruent with their long phylogenetic history and distinctive preference for growing in sapwood, this new lineage displays unique morphological, physiological, and ecological traits relative to known endophytes and currently described members of the 'Leotiomyceta'. In marked contrast to many foliar endophytes, the strains we isolated fail to degrade cellulose and lignin in vitro. Discovery of the new class, herein named Xylonomycetes and originally mis-identified by ITSrDNA sequencing alone, highlights the importance of inventorying tropical endophytes from unexplored regions, using multilocus data sets to infer the phylogenetic placement of unknown strains, and the need to sample diverse plant tissues using traditional methods to enhance efforts to discover the evolutionary, taxonomic, and functional diversity of symbiotrophic fungi.}, Doi = {10.1016/j.ympev.2012.06.019}, Key = {fds228790} } @article{fds228791, Author = {Liwa, L and Miadlikowska, J and Redelings, BD and Molnar, K and Lutzoni, F}, Title = {Are widespread morphospecies from the Lecanora dispersa group (lichen-forming Ascomycota) monophyletic?}, Journal = {Bryologist}, Volume = {115}, Number = {2}, Pages = {265-277}, Publisher = {American Bryological and Lichenological Society}, Year = {2012}, Month = {June}, ISSN = {0007-2745}, url = {http://dx.doi.org/10.1639/0007-2745-115.2.265}, Abstract = {To evaluate the current delimitation of broadly distributed morphospecies from the Lecanora dispersa group, the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S and ITS2) was analyzed phylogenetically and compared to phenotypic data variation within and among species. Phylogenetic relationships among 34 individuals representing eight species from the L. dispersa group, collected mainly from Poland and other European countries, were inferred using two types of Bayesian analyses (with and without a priori alignments), maximum likelihood and maximum parsimony approaches. The highest phylogenetic resolution and the largest number of significantly supported internodes resulted from the Bayesian analysis without a priori alignment. Inferred phylogenies confirmed a broader delimitation of the L. dispersa group, to include four additional lobate taxa: L. contractula, L. pruinosa, L. reuteri, and L. thuleana ( Arctopeltis thuleana). Lecanora crenulata, L. dispersa, L. reuterii, and the core of L. albescens and L. semipallida were all found to be monophyletic with high support (by at least one phylogenetic analysis) except the first species. Based on the ITS region, phenotypically similar individuals, thought to belong to one monophyletic group, were found to belong to multiple distantly related groups (e.g., members of L. albescens and L. hagenii), suggesting that morphological, anatomical and chemical characters may not be consistent in predicting species boundaries within the L. dispersa group. Potential undescribed species were found within phenotypically defined L. albescens and L. semipallida. Phylo-taxonomic studies of the L. dispersa group with more loci and a more extensive taxon sampling are urgently needed. © 2012 The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745-115.2.265}, Key = {fds228791} } @article{fds228784, Author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Laetsch, AD and Arnold, AE}, Title = {Host and geographic structure of endophytic and endolichenic fungi at a continental scale.}, Journal = {American journal of botany}, Volume = {99}, Number = {5}, Pages = {898-914}, Year = {2012}, Month = {May}, ISSN = {0002-9122}, url = {http://dx.doi.org/10.3732/ajb.1100459}, Abstract = {<h4>Premise of the study</h4>Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities.<h4>Methods</h4>Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of five North American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska).<h4>Key results</h4>Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, reflecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences reflected climate factors more strongly than geographic distance alone.<h4>Conclusions</h4>Our study provides a first evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition reflect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specificity, metabolic capability, and comparative genomics.}, Doi = {10.3732/ajb.1100459}, Key = {fds228784} } @article{fds228792, Author = {Gaya, E and Högnabba, F and Holguin, A and Molnar, K and Fernández-Brime, S and Stenroos, S and Arup, U and Søchting, U and Van den Boom, P and Lücking, R and Sipman, HJM and Lutzoni, F}, Title = {Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).}, Journal = {Molecular phylogenetics and evolution}, Volume = {63}, Number = {2}, Pages = {374-387}, Year = {2012}, Month = {May}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22306043}, Abstract = {The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity--the Megalosporaceae--which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data.}, Doi = {10.1016/j.ympev.2012.01.012}, Key = {fds228792} } @article{fds228793, Author = {Geml, J and Kauff, F and Brochmann, C and Lutzoni, F and Laursen, GA and Redhead, SA and Taylor, DL}, Title = {Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota).}, Journal = {Fungal biology}, Volume = {116}, Number = {3}, Pages = {388-400}, Year = {2012}, Month = {March}, ISSN = {1878-6146}, url = {http://dx.doi.org/10.1016/j.funbio.2011.12.009}, Abstract = {Species of the genus Lichenomphalia are mostly restricted to arctic-alpine environments with the exception of Lichenomphalia umbellifera which is also common in northern forests. Although Lichenomphalia species inhabit vast regions in several continents, no information is available on their genetic variation across geographic regions and the underlying population-phylogenetic patterns. We collected samples from arctic and subarctic regions, as well as from newly discovered subantarctic localities for the genus. Phylogenetic, nonparametric permutation methods, and coalescent analyses were used to assess phylogeny and population divergence and to estimate the extent and direction of gene flow among distinct geographic populations. All known species formed monophyletic groups, supporting their morphology-based delimitation. In addition, we found two subantarctic phylogenetic species (Lichenomphalia sp. and Lichenomphalia aff. umbellifera), of which the latter formed a well-supported sister group to L. umbellifera. We found no significant genetic differentiation among conspecific North American and Eurasian populations in Lichenomphalia. We detected high intercontinental gene flow within the northern polar region, suggesting rapid (re)colonisation of suitable habitats in response to climatic fluctuations and preventing pronounced genetic differentiation. On the other hand, our phylogenetic analyses suggest that dispersal between northern circumpolar and subantarctic areas likely happened very rarely and led to the establishment and subsequent divergence of lineages. Due to limited sampling in the Southern Hemisphere, it is currently uncertain whether the northern lineages occur in Gondwanan regions. On the other hand, our results strongly suggest that the southern lineages do not occur in the circumpolar north. Although rare transequatorial dispersal and subsequent isolation may explain the emergence of at least two subantarctic phylogenetic species lineages in Lichenomphalia, more samples from the Southern Hemisphere are needed to better understand the phylogeographic history of the genus.}, Doi = {10.1016/j.funbio.2011.12.009}, Key = {fds228793} } @article{fds228794, Author = {McDonald, TR and Dietrich, FS and Lutzoni, F}, Title = {Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.}, Journal = {Mol Biol Evol}, Volume = {29}, Number = {1}, Pages = {51-60}, Year = {2012}, Month = {January}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21680869}, Abstract = {The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with AMTs and ammonia permeases forming two distinct and possibly monophyletic groups.}, Doi = {10.1093/molbev/msr123}, Key = {fds228794} } @article{fds228795, Author = {Hodkinson, BP and Gottel, NR and Schadt, CW and Lutzoni, F}, Title = {Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.}, Journal = {Environmental microbiology}, Volume = {14}, Number = {1}, Pages = {147-161}, Year = {2012}, Month = {January}, ISSN = {1462-2912}, url = {http://dx.doi.org/10.1111/j.1462-2920.2011.02560.x}, Abstract = {Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.}, Doi = {10.1111/j.1462-2920.2011.02560.x}, Key = {fds228795} } @article{fds228796, Author = {Prieto, M and Martínez, I and Aragón, G and Gueidan, C and Lutzoni, F}, Title = {Molecular phylogeny of Heteroplacidium, Placidium, and related catapyrenioid genera (Verrucariaceae, lichen-forming Ascomycota).}, Journal = {American journal of botany}, Volume = {99}, Number = {1}, Pages = {23-35}, Year = {2012}, Month = {January}, ISSN = {0002-9122}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000299167700014&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {<h4>Premise of the study</h4>Verrucariaceae is a fascinating lineage of lichenized fungi for which generic and species delimitation is problematic due to the scarcity of discriminating morphological characters. Members of this family inhabit rocks, but they further colonize soils, barks, mosses, and other lichens. Our aim is to contribute to the DNA-based inference of the Verrucariaceae tree of life and to investigate characters that could be useful for proposing a more natural classification. We focused on catapyrenioid genera, which are often part of biological soil crusts, a cryptogam-dominated ecosystem contributing to soil formation and stabilization in arid environments. Understanding their evolution and taxonomy is essential to assess their roles in these fragile and important ecosystems.<h4>Methods</h4>A multigene phylogeny of Verrucariaceae including catapyrenioid genera is presented. We further examined the phylogenetic relationships among members of Heteroplacidium and Placidium. The evolution of selected characters was inferred using the latter phylogeny.<h4>Key results</h4>Anthracocarpon and Involucropyrenium were closely related to Endocarpon. Placidium comprised two monophyletic clades sister to Heteroplacidium. Inferred ancestral states of diagnostic characters revealed that the type of medulla and the pycnidia location were homoplasious within the Placidium clade. In contrast, the presence of rhizines was a synapomorphy for Clavascidium.<h4>Conclusions</h4>Our results provide new information on the usefulness of characters for delineating groups in Verrucariaceae. Taxonomic changes are proposed to reflect more natural groupings: Heteroplacidium podolepis is transferred to Placidium, and Clavascidium is recognized as a different genus. Eight new combinations are proposed for Clavascidium.}, Doi = {10.3732/ajb.1100239}, Key = {fds228796} } @article{fds300051, Author = {Green, MS and Ball, B and Lutzoni, F and Zi-Min, H and Lopez-Bautista, JM}, Title = {TRENTEPOHLIALES (ULVOPHYCEAE, CHLOROPHYTA) FROM COASTAL SOUTH CAROLINA}, Journal = {JOURNAL OF PHYCOLOGY}, Volume = {48}, Pages = {S15-S15}, Year = {2012}, ISSN = {0022-3646}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000307053000042&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Key = {fds300051} } @article{fds228799, Author = {Schmull, M and Miadlikowska, J and Pelzer, M and Stocker-Wörgötter, E and Hofstetter, V and Fraker, E and Hodkinson, BP and Reeb, V and Kukwa, M and Lumbsch, HT and Kauff, F and Lutzoni, F}, Title = {Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota).}, Journal = {Mycologia}, Volume = {103}, Number = {5}, Pages = {983-1003}, Year = {2011}, Month = {September}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/10-234}, Abstract = {The genus Lecidea Ach. sensu lato (sensu Zahlbruckner) includes almost 1200 species, out of which only 100 species represent Lecidea sensu stricto (sensu Hertel). The systematic position of the remaining species is mostly unsettled but anticipated to represent several unrelated lineages within Lecanoromycetes. This study attempts to elucidate the phylogenetic placement of members of this heterogeneous group of lichen-forming fungi and to improve the classification and phylogeny of Lecanoromycetes. Twenty-five taxa of Lecidea sensu lato and 22 putatively allied species were studied in a broad selection of 268 taxa, representing 48 families of Lecanoromycetes. Six loci, including four ribosomal and two protein-coding genes for 315- and 209-OTU datasets were subjected to maximum likelihood and Bayesian analyses. The resulting well supported phylogenetic relationships within Lecanoromycetes are in agreement with published phylogenies, but the addition of new taxa revealed putative rearrangements of several families (e.g. Catillariaceae, Lecanoraceae, Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae). As expected, species of Lecidea sensu lato and putatively related taxa are scattered within Lecanoromycetidae and beyond, with several species nested in Lecanoraceae and Pilocarpaceae and others placed outside currently recognized families in Lecanorales and orders in Lecanoromycetidae. The phylogenetic affiliations of Schaereria and Strangospora are outside Lecanoromycetidae, probably with Ostropomycetidae. All species referred to as Lecidea sensu stricto based on morphology (including the type species, Lecidea fuscoatra [L.] Ach.) form, with Porpidia species, a monophyletic group with high posterior probability outside Lecanorales, Peltigerales and Teloschistales, in Lecanoromycetidae, supporting the recognition of order Lecideales Vain. in this subclass. The genus name Lecidea must be redefined to apply only to Lecidea sensu stricto and to include at least some members of the genus Porpidia. Based on morphological and chemical similarities, as well as the phylogenetic relationship of Lecidea pullata sister to Frutidella caesioatra, the new combination Frutidella pullata is proposed here.}, Doi = {10.3852/10-234}, Key = {fds228799} } @article{fds228798, Author = {Fernández-Brime, S and Llimona, X and Molnar, K and Stenroos, S and Högnabba, F and Björk, C and Lutzoni, F and Gaya, E}, Title = {Expansion of the Stictidaceae by the addition of the saxicolous lichen-forming genus Ingvariella.}, Journal = {Mycologia}, Volume = {103}, Number = {4}, Pages = {755-763}, Year = {2011}, Month = {July}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/10-287}, Abstract = {The monotypic, lichen-forming genus Ingvariella originally was segregated from Diploschistes and placed within the Thelotremataceae (Ostropales) based on aspects of exciple morphology. However, the I+ hymenium and amyloid ascus wall suggest affinities to families other than the Thelotremataceae. To assess the identity of Ingvariella and to investigate its placement within the Ostropales, we inferred phylogenetic relationships of I. bispora by comparison of mtSSU rDNA and nuLSU rDNA sequences for 59 species encompassing a broad array of ostropalean fungi by means of Bayesian, maximum likelihood and weighted maximum parsimony methods. Here we report that Ingvariella is a member of the Stictidaceae, sister to the mainly saprotrophic genus Cryptodiscus. The inclusion of the first saxicolous lichen-forming fungus within this family expands the broad ecological diversity of the Stictidaceae, where saprotrophic fungi, corticicolous lichen-forming fungi and lichenized and non-lichenized conspecific taxa have been described previously. We also present new insights into the relationships among other families within the Ostropales.}, Doi = {10.3852/10-287}, Key = {fds228798} } @article{fds228804, Author = {Miadlikowska, J and Schoch, CL and Kageyama, SA and Molnar, K and Lutzoni, F and McCune, B}, Title = {Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure}, Journal = {Bryologist}, Volume = {114}, Number = {2}, Pages = {392-400}, Publisher = {American Bryological and Lichenological Society}, Year = {2011}, Month = {June}, ISSN = {0007-2745}, url = {http://dx.doi.org/10.1639/0007-2745-114.2.392}, Abstract = {We inferred phylogenetic relationships using Bayesian and maximum likelihood approaches for two genera of lichenized fungi, Hypogymnia and Cavernularia (Parmeliaceae). Based on the combined ITS and GPD1 dataset from 23 species (49 specimens) of Hypogymnia and two species (8 specimens) of Cavernularia, we conclude that Hypogymnia is paraphyletic, and that it should include Cavernularia to retain its monophyly. Hypogymnia hultenii (= Cavernularia hultenii) and H. lophyrea (= C. lophyrea) are accepted here. Five species of Hypogymnia represented by more than a single individual were found to be monophyletic and significantly supported. The phylogeny reflects a statistically significant biogeographic pattern where continental-scale endemic taxa tend to occur within the same phylogenetic group. Sorediate taxa, which have worldwide or broader geographical ranges than affiliated species lacking soredia, are spread across the phylogenetic tree. Hypogymnia contains three species pairs: H. krogiae and the sorediate counterpart H. incurvoides, H. minilobata and the sorediate H. mollis, and H. lophyrea and the sorediate H. hultenii. In the case of H. minilobata, both members of the pair are restricted to a small area in southern California. In the other two cases, the fertile counterpart occurs only in North America, while the sorediate species occurs in both North America and Fennoscandia. This suggests but not proves an origin of each species pair in North America, with migration of the sorediate member to Fennoscandia following the prevailing wind direction. © 2011 The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745-114.2.392}, Key = {fds228804} } @article{fds331044, Author = {Arnold, AE and Carbone, I and Lutzoni, F and May, G}, Title = {A multidimensional study of endophytic fungal diversity}, Journal = {IMA Fungus}, Volume = {2}, Number = {1}, Pages = {2-4}, Year = {2011}, Month = {June}, Key = {fds331044} } @article{fds228802, Author = {Joneson, S and Armaleo, D and Lutzoni, F}, Title = {Fungal and algal gene expression in early developmental stages of lichen-symbiosis.}, Journal = {Mycologia}, Volume = {103}, Number = {2}, Pages = {291-306}, Year = {2011}, Month = {March}, ISSN = {0027-5514}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20943535}, Abstract = {How plants and microbes recognize each other and interact to form long-lasting relationships remains one of the central questions in cellular communication. The symbiosis between the filamentous fungus Cladonia grayi and the single-celled green alga Asterochloris sp. was used to determine fungal and algal genes upregulated in vitro in early lichen development. cDNA libraries of upregulated genes were created with suppression subtractive hybridization in the first two stages of lichen development. Quantitative PCR subsequently was used to verify the expression level of 41 and 33 candidate fungal and algal genes respectively. Induced fungal genes showed significant matches to genes putatively encoding proteins involved in self and non-self recognition, lipid metabolism, and negative regulation of glucose repressible genes, as well as to a putative d-arabitol reductase and two dioxygenases. Upregulated algal genes included a chitinase-like protein, an amino acid metabolism protein, a dynein-related protein and a protein arginine methyltransferase. These results also provided the first evidence that extracellular communication without cellular contact can occur between lichen symbionts. Many genes showing slight variation in expression appear to direct the development of the lichen symbiosis. The results of this study highlight future avenues of investigation into the molecular biology of lichen symbiosis.}, Doi = {10.3852/10-064}, Key = {fds228802} } @article{fds228803, Author = {Gaya, E and Redelings, BD and Navarro-Rosinés, P and Llimona, X and De Cáceres, M and Lutzoni, F}, Title = {Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.}, Journal = {Mycologia}, Volume = {103}, Number = {2}, Pages = {361-378}, Year = {2011}, Month = {March}, ISSN = {0027-5514}, url = {http://www.mycologia.org/papbyrecent.dtl}, Abstract = {The Caloplaca saxicola group is the main group of saxicolous, lobed-effigurate species within genus Caloplaca (Teloschistaceae, lichen-forming Ascomycota). A recent monographic revision by the first author detected a wide range of morphological variation. To confront the phenotypically based circumscription of these taxa and to resolve their relationships morphological and ITS rDNA data were obtained for 56 individuals representing eight Caloplaca species belonging to the C. saxicola group. We tested the monophyly of these eight morphospecies by performing maximum parsimony, maximum likelihood and two different types of Bayesian analyses (with and without a priori alignments). Restricting phylogenetic analyses to unambiguously aligned portions of ITS was sufficient to resolve, with high bootstrap support, five of the eight previously recognized species within the C. saxicola group. However, phylogenetic resolution of all or most of the eight species currently included as two distinct subgroups within the C. saxicola group was possible only by combining morphological characters and signal from ambiguously aligned regions with the unambiguously aligned ITS sites or when the entire ITS1 and 2 regions were not aligned a priori and included as an integral component of a Bayesian analysis (BAli-Phy). The C. arnoldii subgroup includes C. arnoldii, comprising four subspecies, and the C. saxicola subgroup encompasses seven species. Contrary to the C. saxicola subgroup, monophyly of taxa included within the C. arnoldii subgroup and their relationships could not be resolved with combined ITS and morphological data. Unequivocal morphological synapomorphies for all species except C. arnoldii and C. pusilla are recognized and presented.}, Doi = {10.3852/10-120}, Key = {fds228803} } @article{fds228800, Author = {Thüs, H and Muggia, L and Pérez-Ortega, S and Favero-Longo, SE and Joneson, S and O’Brien, H and Nelsen, MP and Duque-Thüs, R and Grube, M and Friedl, T and Brodie, J and Andrew, CJ and Lücking, R and Lutzoni, F and Gueidan, C}, Title = {Revisiting photobiont diversity in the lichen family verrucariaceae (ascomycota)}, Journal = {European Journal of Phycology}, Volume = {46}, Number = {4}, Pages = {399-415}, Publisher = {Informa UK Limited}, Year = {2011}, Month = {January}, ISSN = {0967-0262}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000299417800006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {The Verrucariaceae (Ascomycota) is a family of mostly lichenized fungi with a unique diversity of algal symbionts, including some algae that are rarely or never associated with other lichens. The phylogenetic position of most of these algae has not yet been studied and, because morphology-based identifications can often be misleading, molecular data is necessary to revisit their identity and to explore patterns of association between fungal and algal partners. For this reason, the diversity of photobionts in this lichen family was investigated using molecular markers (rbcL and nuSSU) amplified from DNA extracts of lichen thalli and cultured isolates. Although a single algal genus, Diplosphaera (Trebouxiophyceae), was associated with 12 out of the 17 sampled genera of Verrucariaceae, representatives of eight other genera in five orders of the Chlorophyta and one genus in the Xanthophyceae also form lichen associations with members of the family. Fungal genera with simple crustose thalli (e.g. Hydropunctaria, Wahlenbergiella, Bagliettoa) use a high diversity and unusual selection of photobionts. In contrast, fungal genera with more complex thalli (e.g. Placidium, Dermatocarpon) tend to have lower photobiont diversity. Habitat requirements and phylogenetic histories are both partly reflected in the observed patterns of associations between lichenized fungi from the family Verrucariaceae and their photobionts. © 2011 Taylor & Francis Group, LLC.}, Doi = {10.1080/09670262.2011.629788}, Key = {fds228800} } @article{fds228801, Author = {Hestmark, G and Miadlikowska, J and Kauff, F and Fraker, E and Molnar, K and Lutzoni, F}, Title = {Single origin and subsequent diversification of central Andean endemic Umbilicaria species.}, Journal = {Mycologia}, Volume = {103}, Number = {1}, Pages = {45-56}, Year = {2011}, Month = {January}, ISSN = {0027-5514}, url = {http://www.mycologia.org/papbyrecent.dtl}, Abstract = {We studied an Andean endemic group of species of the lichen-forming fungal genus Umbilicaria from the subalpine and low-alpine zone, with their biogeographic center in Bolivia and Peru. A number of species and varieties have been described from this element, but apparent instability in several morphological traits has made it difficult to precisely delimit taxa. Based on DNA sequences of nuclear ITS, LSU and mitochondrial SSU from extensive collections from Argentina, Bolivia, Chile, Colombia, Ecuador and Peru, we present here a molecular phylogenetic analysis of this Andean endemic element within genus Umbilicaria. All analyses (MP, ML and Bayesian) support a single origin for the element and a division into two major groups characterized by different apothecium types: the Umbilicaria dichroa group and U. calvescens group. Taxa U. krempelhuberi, U. peruviana and U. subcalvescens are nested withinn U. calvescens and are treated as conspecific with the latter species. The endemic element shares a most recent common ancestor with the Umbilicaria vellea group, which has a worldwide distribution and contains several asexually reproducing (sorediate) species. Independent reversals to sexual reproduction might explain the evolution of two types of apothecia in this monophyletic endemic lineage. A number of cosmopolitan, mostly high-alpine, species of Umbilicaria also present in the central Andes are related only remotely to the endemic element and do not exhibit speciation into endemics. Because the An-dean element dominates the Umbilicaria habitats of the low- and subalpine zones we propose that the founder colonized the Andes at a time when the mountains had not yet reached their current elevation while the high-alpine species arrived more recently.}, Doi = {10.3852/10-012}, Key = {fds228801} } @article{fds228797, Author = {Crespo, A and Kauff, F and Divakar, PK and del Prado, R and Pérez-Ortega, S and de Paz, GA and Ferencova, Z and Blanco, O and Roca-Valiente, B and Núñez-Zapata, J and Cubas, P and Argüello, A and Elix, JA and Esslinger, TL and Hawksworth, DL and Millanes, A and Molina, MC and Wedin, M and Ahti, T and Aptroot, A and Barreno, E and Bungartz, F and Calvelo, S and Candan, M and Cole, M and Ertz, D and Goffinet, B and Lindblom, L and Lücking, R and Lutzoni, F and Mattsson, JE and Messuti, MI and Miadlikowska, J and Piercey-Normore, M and Rico, VJ and Sipman, HJM and Schmitt, I and Spribille, T and Thell, A and Thor, G and Upreti, DK and Thorsten Lumbsch and H}, Title = {Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence}, Journal = {Taxon}, Volume = {59}, Number = {6}, Pages = {1735-1753}, Year = {2010}, Month = {December}, ISSN = {0040-0262}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000285566000008&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.}, Doi = {10.1002/tax.596008}, Key = {fds228797} } @article{fds228808, Author = {Otálora, MAG and Martínez, I and O'Brien, H and Molina, MC and Aragón, G and Lutzoni, F}, Title = {Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes).}, Journal = {Molecular phylogenetics and evolution}, Volume = {56}, Number = {3}, Pages = {1089-1095}, Year = {2010}, Month = {September}, ISSN = {1055-7903}, url = {http://dx.doi.org/10.1016/j.ympev.2010.05.013}, Abstract = {Because the number of fungal species (mycobionts) exceeds the number of algae and cyanobacteria (photobionts) found in lichens by more than two orders of magnitude, reciprocal one-to-one specificity between one fungal species and one photobiont across their entire distribution is not expected in this symbiotic system, and has not previously been observed. The specificity of the cyanobacterium Nostoc found in lichens was evaluated at a broad geographical scale within one of the main families of lichen-forming fungi (Collemataceae) that associate exclusively with this photobiont. A phylogenetic study was conducted using rbcLXS sequences from Nostoc sampled from 79 thalli (representing 24 species within the Collemataceae), and 163 Nostoc sequences gathered from GenBank. Although most of the lichen-forming fungal species belonging to the Collemataceae exhibited the expected generalist pattern of association with multiple distinct lineages of Nostoc, five independent cases of one-to-one reciprocal specificity at the species level, including two that span intercontinental distributions, were discovered. Each of the five distinct monophyletic Nostoc groups, associated with these five highly specific mycobiont species, represent independent transitions from a generalist state during the evolution of both partners, which might be explained by transitions to asexual fungal reproduction, involving vertical photobiont transmission, and narrowing of ecological niches.}, Doi = {10.1016/j.ympev.2010.05.013}, Key = {fds228808} } @article{fds228806, Author = {Otálora, MAG and Aragón, G and Molina, MC and Martínez, I and Lutzoni, F}, Title = {Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota).}, Journal = {Mycologia}, Volume = {102}, Number = {2}, Pages = {279-290}, Year = {2010}, Month = {March}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/09-114}, Abstract = {Family Collemataceae (Peltigerales, Ascomycota) includes species of cyanolichens with foliose to fruticose or crustose thalli, with simple or septate ascospores. The current classification divides this family into two groups on the basis of ascospore types. The objective of this study was to evaluate the phylogenetic relationships within this family. Combined DNA sequence data from the nuclear large subunit and mitochondrial small subunit ribosomal RNA genes were used to evaluate monophyly of the family and the relationships between the largest genera of this family. The results revealed that this family is not monophyletic. Genera Staurolemma and Physma, currently classified within the Collemataceae, were found nested within the Pannariaceae. The second result of this study confirms that the genera Collema and Leptogium, both part of the Collemataceae s. str., are not monophyletic and that the presence of a thallus cortex is not a synapomorphy for Leptogium. The main taxonomic conclusion is that families Collemataceae and Pannariaceae were recircumscribed in light of molecular findings with the latter family now including Staurolemma and Physma. Genera Collema and Leptogium form a single mixed monophyletic group. Inferred ancestral character states within the Collema-Leptogium complex revealed that the ancestor of this family had a thallus without cortex and that a cortex evolved at least twice relatively early in the evolution of the Collemataceae s. str. These independent gains of a thallus cortex seems to be associated with a transition from colonizing bare rocks and soils in semi-arid and exposed habitats to epiphytism in shady humid forests.}, Doi = {10.3852/09-114}, Key = {fds228806} } @article{fds228807, Author = {Prieto, M and Martínez, I and Aragón, G and Otálora, MAG and Lutzoni, F}, Title = {Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis.}, Journal = {Mycologia}, Volume = {102}, Number = {2}, Pages = {291-304}, Year = {2010}, Month = {March}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/09-168}, Abstract = {The current classification of what used to be called Catapyrenium comprises eight genera belonging to distinct lineages in the Verrucariaceae. Previous phylogenetic studies have shown that the redefined genus Catapyrenium (Catapyrenium s. str.) is monophyletic and sister of Placidiopsis within the Staurothele group, but this relationship was based on only two species from each genus. We conducted a phylogenetic study of Catapyrenium and Placidiopsis as currently delimited to evaluate the monophyly of each genus and infer infrageneric relationships. An initial family level phylogenetic analysis based on the nuLSU locus and implementing a backbone constraint tree (with both weighted maximum parsimony and bootstrap maximum likelihood approaches) was performed to infer phylogenetic placements of Catapyrenium and Placidiopsis taxa not included in previous molecular systematic studies. The results of this analysis were used to define the ingroup for a second phylogenetic analysis based on nuITS and nuLSU and centered on Catapyrenium s. str. and Placidiopsis. Placidiopsis was found to be monophyletic, whereas Catapyrenium s. str. was not. Catapyrenium dactylinum was found to be closely related to Placopyrenium caeruleopulvinum and Placopyrenium stanfordii, all of which were closely related to Placocarpus schaereri and Verrucula. In addition we found genus Placopyrenium to be polyphyletic. The resulting trees confirmed that Catapyrenium s. str. (excluding C. dactylinum) and Placidiopsis constitute two sister monophyletic entities. The data do not support Placidiopsis cinerascens and P. tenella as two distinct species because no characters can be used to distinguish them. Thus P. tenella is here reduced to synonymy with P. cinerascens.}, Doi = {10.3852/09-168}, Key = {fds228807} } @article{fds228809, Author = {U'Ren, J and Lutzoni, F and Miadlikowska, J and Arnold, AE}, Title = {Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens}, Journal = {Microbial Ecology}, Volume = {60}, Number = {2}, Pages = {340-353}, Year = {2010}, ISSN = {0095-3628}, url = {http://dx.doi.org/10.1007/s00248-010-9698-2}, Abstract = {Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been "entrapped" by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as endophytes of mosses.}, Doi = {10.1007/s00248-010-9698-2}, Key = {fds228809} } @article{fds228810, Author = {McLaughlin, DJ and Hibbett, DS and Lutzoni, F and Spatafora, JW and Vilgalys, R}, Title = {The search for the fungal tree of life.}, Journal = {Trends in microbiology}, Volume = {17}, Number = {11}, Pages = {488-497}, Year = {2009}, Month = {November}, ISSN = {0966-842X}, url = {http://dx.doi.org/10.1016/j.tim.2009.08.001}, Abstract = {The Fungi comprise a diverse kingdom of eukaryotes that are characterized by a typically filamentous but sometimes unicellular vegetative form, and heterotrophic, absorptive nutrition. Their simple morphologies and variable ecological strategies have confounded efforts to elucidate their limits, phylogenetic relationships, and diversity. Here we review progress in developing a phylogenetic classification of Fungi since Darwin's On the Origin of Species. Knowledge of phylogenetic relationships has been driven by the available characters that have ranged from morphological and ultrastructural to biochemical and genomic. With the availability of multiple gene phylogenies a well-corroborated phylogenetic classification has now begun to emerge. In the process some fungus-like heterotrophs have been shown to belong elsewhere, and several groups of enigmatic eukaryotic microbes have been added to the Fungi.}, Doi = {10.1016/j.tim.2009.08.001}, Key = {fds228810} } @article{fds228818, Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F}, Title = {Assessing reproductive isolation in highly diverse communities of the lichen-forming fungal genus peltigera.}, Journal = {Evolution; international journal of organic evolution}, Volume = {63}, Number = {8}, Pages = {2076-2086}, Year = {2009}, Month = {August}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19453383}, Abstract = {The lichen-forming fungal genus Peltigera includes a number of species that are extremely widespread, both geographically and ecologically. However, morphological variability has lead to doubts about the distinctness of some species, and it has been suggested that hybridization is common in nature. We examined species boundaries by looking for evidence of hybridization and gene flow among seven described species collected at five sites in British Columbia, Canada. We found no evidence of gene flow or hybridization between described species, with fixed differences between species for two or more of the three loci examined. Reproductive isolation did not reflect a solely clonal mode of reproduction as there was evidence of ongoing gene flow within species. In addition, we found five undescribed species that were reproductively isolated, although there was evidence of ongoing or historical gene flow between two of the new species. These results indicate that the genus Peltigera is more diverse in western North America than originally perceived, and that morphological variability is due largely to the presence of undescribed species rather than hybridization or intraspecific variation.}, Doi = {10.1111/j.1558-5646.2009.00685.x}, Key = {fds228818} } @article{fds228815, Author = {Lutzoni, F and Miadlikowska, J}, Title = {Lichens.}, Journal = {Current biology : CB}, Volume = {19}, Number = {13}, Pages = {R502-R503}, Year = {2009}, Month = {July}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19602407}, Doi = {10.1016/j.cub.2009.04.034}, Key = {fds228815} } @article{fds228811, Author = {Arnold, AE and Miadlikowska, J and Higgins, KL and Sarvate, SD and Gugger, P and Way, A and Hofstetter, V and Kauff, F and Lutzoni, F}, Title = {A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?}, Journal = {Systematic biology}, Volume = {58}, Number = {3}, Pages = {283-297}, Year = {2009}, Month = {June}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20525584}, Abstract = {Fungi associated with photosynthetic organisms are major determinants of terrestrial biomass, nutrient cycling, and ecosystem productivity from the poles to the equator. Whereas most fungi are known because of their fruit bodies (e.g., saprotrophs), symptoms (e.g., pathogens), or emergent properties as symbionts (e.g., lichens), the majority of fungal diversity is thought to occur among species that rarely manifest their presence with visual cues on their substrate (e.g., the apparently hyperdiverse fungal endophytes associated with foliage of plants). Fungal endophytes are ubiquitous among all lineages of land plants and live within overtly healthy tissues without causing disease, but the evolutionary origins of these highly diverse symbionts have not been explored. Here, we show that a key to understanding both the evolution of endophytism and the diversification of the most species-rich phylum of Fungi (Ascomycota) lies in endophyte-like fungi that can be isolated from the interior of apparently healthy lichens. These "endolichenic" fungi are distinct from lichen mycobionts or any other previously recognized fungal associates of lichens, represent the same major lineages of Ascomycota as do endophytes, largely parallel the high diversity of endophytes from the arctic to the tropics, and preferentially associate with green algal photobionts in lichen thalli. Using phylogenetic analyses that incorporate these newly recovered fungi and ancestral state reconstructions that take into account phylogenetic uncertainty, we show that endolichenism is an incubator for the evolution of endophytism. In turn, endophytism is evolutionarily transient, with endophytic lineages frequently transitioning to and from pathogenicity. Although symbiotrophic lineages frequently give rise to free-living saprotrophs, reversions to symbiosis are rare. Together, these results provide the basis for estimating trophic transition networks in the Ascomycota and provide a first set of hypotheses regarding the evolution of symbiotrophy and saprotrophy in the most species-rich fungal phylum. [Ancestral state reconstruction; Ascomycota; Bayesian analysis; endolichenic fungi; fungal endophytes; lichens; pathogens; phylogeny; saprotrophy; symbiotrophy; trophic transition network.].}, Doi = {10.1093/sysbio/syp001}, Key = {fds228811} } @article{fds228813, Author = {Schoch, CL and Sung, G-H and López-Giráldez, F and Townsend, JP and Miadlikowska, J and Hofstetter, V and Robbertse, B and Matheny, PB and Kauff, F and Wang, Z and Gueidan, C and Andrie, RM and Trippe, K and Ciufetti, LM and Wynns, A and Fraker, E and Hodkinson, BP and Bonito, G and Groenewald, JZ and Arzanlou, M and de Hoog, GS and Crous, PW and Hewitt, D and Pfister, DH and Peterson, K and Gryzenhout, M and Wingfield, MJ and Aptroot, A and Suh, S-O and Blackwell, M and Hillis, DM and Griffith, GW and Castlebury, LA and Rossman, AY and Lumbsch, HT and Lücking, R and Büdel, B and Rauhut, A and Diederich, P and Ertz, D and Geiser, DM and Hosaka, K and Inderbitzin, P and Kohlmeyer, J and Volkmann-Kohlmeyer, B and Mostert, L and O'Donnell, K and Sipman, H and Rogers, JD and Shoemaker, RA and Sugiyama, J and Summerbell, RC and Untereiner, W and Johnston, PR and Stenroos, S and Zuccaro, A and Dyer, PS and Crittenden, PD and Cole, MS and Hansen, K and Trappe, JM and Yahr, R and Lutzoni, F and Spatafora, JW}, Title = {The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.}, Journal = {Systematic biology}, Volume = {58}, Number = {2}, Pages = {224-239}, Year = {2009}, Month = {April}, ISSN = {1063-5157}, url = {http://dx.doi.org/10.1093/sysbio/syp020}, Abstract = {We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.}, Doi = {10.1093/sysbio/syp020}, Key = {fds228813} } @article{fds228805, Author = {Ruibal, C and Gueidan, C and Selbmann, L and Gorbushina, AA and Crous, PW and Groenewald, JZ and Muggia, L and Grube, M and Isola, D and Schoch, CL and Staley, JT and Lutzoni, F and de Hoog, GS}, Title = {Phylogeny of rock-inhabiting fungi related to Dothideomycetes.}, Journal = {Studies in mycology}, Volume = {64}, Pages = {123-133S7}, Publisher = {Elsevier BV}, Year = {2009}, Month = {January}, ISSN = {0166-0616}, url = {http://dx.doi.org/10.3114/sim.2009.64.06}, Abstract = {The class Dothideomycetes (along with Eurotiomycetes) includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that tolerates surprisingly well harsh conditions prevailing on rock surfaces. Despite their convergent morphology and physiology, RIF are phylogenetically highly diverse in Dothideomycetes. However, the positions of main groups of RIF in this class remain unclear due to the lack of a strong phylogenetic framework. Moreover, connections between rock-dwelling habit and other lifestyles found in Dothideomycetes such as plant pathogens, saprobes and lichen-forming fungi are still unexplored. Based on multigene phylogenetic analyses, we report that RIF belong to Capnodiales (particularly to the family Teratosphaeriaceae s.l.), Dothideales, Pleosporales, and Myriangiales, as well as some uncharacterised groups with affinities to Dothideomycetes. Moreover, one lineage consisting exclusively of RIF proved to be closely related to Arthoniomycetes, the sister class of Dothideomycetes. The broad phylogenetic amplitude of RIF in Dothideomycetes suggests that total species richness in this class remains underestimated. Composition of some RIF-rich lineages suggests that rock surfaces are reservoirs for plant-associated fungi or saprobes, although other data also agree with rocks as a primary substrate for ancient fungal lineages. According to the current sampling, long distance dispersal seems to be common for RIF. Dothideomycetes lineages comprising lichens also include RIF, suggesting a possible link between rock-dwelling habit and lichenisation.}, Doi = {10.3114/sim.2009.64.06}, Key = {fds228805} } @article{fds228812, Author = {Gueidan, C and Savić, S and Thüs, H and Roux, C and Keller, C and Tibell, L and Prieto, M and Heiomarsson, S and Breuss, O and Orange, A and Fröberg, L and Wynns, AA and Navarro-Rosinés, P and Krzewicka, B and Pykälä, J and Grube, M and Lutzoni, F}, Title = {Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: Recent progress and remaining challenges}, Journal = {Taxon}, Volume = {58}, Number = {1}, Pages = {184-208}, Year = {2009}, Month = {January}, ISSN = {0040-0262}, url = {http://dx.doi.org/10.1002/tax.581019}, Abstract = {Recent molecular phylogenetic analyses and morphological studies have shown that it is necessary to revise the present morphology-based generic delineation of the lichen family Verrucariaceae in order to account for evolutionary relatedness between species. Consequently, several genera were recently described or resurrected, and others were re-circumscribed. As an additional step toward this generic revision, three new genera (Hydropunctaria, Parabagliettoa, Wahlenbergiella) and eleven new combinations are proposed here. A summary of the current taxonomic and morphological circumscription of all genera investigated so far is also presented. Several monophyletic groups are identified for which further taxonomical changes will be required, but for which taxon and gene sampling is presently viewed as insufficient. Clear morphological synapomorphies were found to be rare for newly delimited genera. In some cases (reduced morphology or plesiomorphism), even the combinations of slightly homoplasious phenotypic characters do not allow a clear morphological generic circumscription. Molecular features are envisioned as characters for delimiting these taxa.}, Doi = {10.1002/tax.581019}, Key = {fds228812} } @article{fds228814, Author = {Ertz, D and Miadlikowska, J and Lutzoni, F and Dessein, S and Raspé, O and Vigneron, N and Hofstetter, V and Diederich, P}, Title = {Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha.}, Journal = {Mycological research.}, Volume = {113}, Number = {Pt 1}, Pages = {141-152}, Year = {2009}, Month = {January}, ISSN = {0953-7562}, url = {http://dx.doi.org/10.1016/j.mycres.2008.09.002}, Abstract = {A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha. With the inclusion of sequences from GenBank, ten genera and 35 species are included in this study, representing about 18% of the genera and ca 3% of the species of this order. Our study revealed the homoplastic nature of morphological characters traditionally used to circumscribe genera within the Arthoniales, such as exciple carbonization and ascomatal structure. The genus Opegrapha appears polyphyletic, species of that genus being nested in all the major clades identified within Arthoniales. The transfer of O. atra and O. calcarea to the genus Arthonia will allow this genus and family Arthoniaceae to be recognized as monophyletic. The genus Enterographa was also found to be polyphyletic. Therefore, the following new combinations are needed: Arthonia calcarea (basionym: O. calcarea), and O. anguinella (basionym: Stigmatidium anguinellum); and the use of the names A. atra and Enterographa zonata are proposed here. The simultaneous use of a mitochondrial gene and two nuclear genes led to the detection of what seems to be a case of introgression of a mitochondrion from one species to another (mitochondrion capture; cytoplasmic gene flow) resulting from hybridization.}, Doi = {10.1016/j.mycres.2008.09.002}, Key = {fds228814} } @article{fds228816, Author = {Hodkinson, BP and Lutzoni, F}, Title = {A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales}, Journal = {Symbiosis}, Volume = {49}, Number = {3}, Pages = {163-180}, Publisher = {Springer Nature}, Year = {2009}, Month = {January}, ISSN = {0334-5114}, url = {http://dx.doi.org/10.1007/s13199-009-0049-3}, Abstract = {This study uses a set of PCR-based methods to examine the putative microbiota associated with lichen thalli. In initial experiments, generalized oligonucleotide-primers for the 16S rRNA gene resulted in amplicon pools populated almost exclusively with fragments derived from lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This effectively masked the presence of other lichen-associated prokaryotes. In order to facilitate the study of the lichen microbiota, 16S ribosomal oligonucleotide-primers were developed to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria. A preliminary microbiotic survey of lichen thalli using these new primers has revealed the identity of several bacterial associates, including representatives of the extremophilic Acidobacteria, bacteria in the families Acetobacteraceae and Brucellaceae, strains belonging to the genus Methylobacterium, and members of an undescribed lineage in the Rhizobiales. This new lineage was investigated and characterized through molecular cloning, and was found to be present in all examined lichens that are associated with green algae. There is evidence to suggest that members of this lineage may both account for a large proportion of the lichen-associated bacterial community and assist in providing the lichen thallus with crucial nutrients such as fixed nitrogen. ©Springer Science+Business Media B.V. 2009.}, Doi = {10.1007/s13199-009-0049-3}, Key = {fds228816} } @article{fds304276, Author = {Joneson, S and Lutzoni, F}, Title = {Compatibility and thigmotropism in the lichen symbiosis: A reappraisal}, Journal = {Symbiosis}, Volume = {47}, Number = {2}, Pages = {109-115}, Publisher = {Springer Nature}, Year = {2009}, Month = {January}, ISSN = {0334-5114}, url = {http://dx.doi.org/10.1007/BF03182294}, Abstract = {The development of many complex stratified lichen thalli is made through stages of complex phenotypic interactions between a filamentous fungus (the mycobiont), and a trebouxioid alga (the photobiont). Typically, the second stage of this symbiotic development is marked by the envelopment of the photobiont by the mycobiont through increased lateral hyphal branching and the formation of appressoria. Previously, the mycobiont's envelopment of photobiont cells was considered thigmotropic (a growth response due to shape) as a mycobiont can envelop algal sized objects in its environment. However, after growing the mycobiont Cladonia grayi with various phototrophs and glass beads, we conclude that the mycobiont does not show this characteristic second stage morphological response when grown in non-compatible pairings. Instead, C. grayi displays a distinctive morphological growth response only in compatible symbiotic pairings, such as with its natural photobiont Asterochloris sp. © 2009 Balaban.}, Doi = {10.1007/BF03182294}, Key = {fds304276} } @article{fds228819, Author = {Joneson, S and Lutzoni, F}, Title = {Revisiting compatibility and thigmotropism in the lichen symbiosis}, Journal = {Symbiosis}, Volume = {47}, Number = {2}, Pages = {109-115}, Year = {2009}, ISSN = {0334-5114}, Abstract = {The development of many complex stratified lichen thalli is made through stages of complex phenotypic interactions between a filamentous fungus (the mycobiont), and a trebouxioid alga (the photobiont). Typically, the second stage of this symbiotic development is marked by the envelopment of the photobiont by the mycobiont through increased lateral hyphal branching and the formation of appressoria. Previously, the mycobiont's envelopment of photobiont cells was considered thigmotropic (a growth response due to shape) as a mycobiont can envelop algal sized objects in its environment. However, after growing the mycobiont Cladonia grayi with various phototrophs and glass beads, we conclude that the mycobiont does not show this characteristic second stage morphological response when grown in non-compatible pairings. Instead, C. grayi displays a distinctive morphological growth response only in compatible symbiotic pairings, such as with its natural photobiont Asterochloris sp. © 2009 Balaban.}, Key = {fds228819} } @article{fds228820, Author = {Savić, S and Tibell, L and Gueidan, C and Lutzoni, F}, Title = {Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera.}, Journal = {Mycological research.}, Volume = {112}, Number = {Pt 11}, Pages = {1307-1318}, Year = {2008}, Month = {November}, ISSN = {0953-7562}, url = {http://dx.doi.org/10.1016/j.mycres.2008.05.002}, Abstract = {Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A-D), including 129 newly generated sequences, were analysed. Phylogenetic relationships were inferred using a Bayesian approach based on two datasets. A first analysis of a larger, two-locus dataset (nuLSU and RPB1) for 128 members of the Verrucariaceae, confirmed the polyphyly of Polyblastia, Thelidium, Staurothele, and Verrucaria, as currently construed. The second analysis focused on 56 Polyblastia and allied taxa, but using an additional locus (nuITS rDNA) and two closely related outgroup taxa. The latter analysis revealed strongly supported groups, such as Polyblastia s. str., the Thelidium group (a mixture of Polyblastia, Thelidium, Staurothele and Verrucaria species). The genus Sporodictyon, which is here accepted, also accommodates Sporodictyon terrestre comb. nov. Morphological features traditionally used for characterizing Polyblastia, Thelidium, Staurothele and Verrucaria, such as spore septation and colour, occurrence of hymenial photobiont, involucrellum structure, and substrate preference, were found to be only partially consistent within the strongly supported clades, and thus are not always reliable features for characterizing natural groups.}, Doi = {10.1016/j.mycres.2008.05.002}, Key = {fds228820} } @article{fds228822, Author = {Gaya, E and Navarro-Rosinés, P and Llimona, X and Hladun, N and Lutzoni, F}, Title = {Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes).}, Journal = {Mycological research.}, Volume = {112}, Number = {Pt 5}, Pages = {528-546}, Year = {2008}, Month = {May}, ISSN = {0953-7562}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18406120}, Abstract = {The Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of Teloschistaceae. Our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in Caloplaca subgenus Gasparrinia do not form a monophyletic entity. Caloplaca aurantia, C. carphinea and C. saxicola s. str. groups were recovered as monophyletic. The subgenera Caloplaca and Pyrenodesmia were also polyphyletic. In the subgenus Caloplaca, the traditionally recognized C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.}, Doi = {10.1016/j.mycres.2007.11.005}, Key = {fds228822} } @article{fds228827, Author = {Amtoft, A and Lutzoni, F and Miadlikowska, J}, Title = {Dermatocarpon (Verrucariaceae) in the Ozark Highlands, North America}, Journal = {Bryologist}, Volume = {111}, Number = {1}, Pages = {1-40}, Publisher = {American Bryological and Lichenological Society}, Year = {2008}, Month = {March}, ISSN = {0007-2745}, url = {http://dx.doi.org/10.1639/0007-2745(2008)111[1:DVITOH]2.0.CO;2}, Abstract = {Dermatocarpon, a saxicolous lichen, is common throughout the Ozarks Highlands of North America where exposed rock is abundant. Dermatocarpon is an understudied genus. Species delimitation is difficult because of a paucity of morphological characters and a large degree of variation within this genus. The taxonomy of Dermatocarpon in North America was recently thrown into flux because of a molecular study which limited the use of a once widely applied name, D. miniatum. The Melzer's reagent test, currently used for identifying members of the miniatum-complex in North America, is not useful for identifying Ozark specimens. A revision of Dermatocarpon for the Ozark Highlands of North America is presented based on morphological, molecular and ecological studies. The results of these studies indicate that eight taxa are present in the Ozarks. Four taxa are described new to science: D. arenosaxi, D. dolomiticum, D. luridum var. xerophilum and D. multifolium. Copyright ©2008 by The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745(2008)111[1:DVITOH]2.0.CO;2}, Key = {fds228827} } @article{fds228782, Author = {Gueidan, C and Villaseñor, CR and de Hoog, GS and Gorbushina, AA and Untereiner, WA and Lutzoni, F}, Title = {A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages.}, Journal = {Studies in mycology}, Volume = {61}, Pages = {111-119}, Year = {2008}, Month = {January}, ISSN = {0166-0616}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19287533}, Abstract = {Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare rocks. Multigene phylogenetic analyses were used to study relationships of ascomycetes from a variety of substrates, with a dataset including a broad sampling of rock dwellers from different geographical locations. Rock-inhabiting fungi appear particularly diverse in the early diverging lineages of the orders Chaetothyriales and Verrucariales. Although these orders share a most recent common ancestor, their lifestyles are strikingly different. Verrucariales are mostly lichen-forming fungi, while Chaetothyriales, by contrast, are best known as opportunistic pathogens of vertebrates (e.g. Cladophialophora bantiana and Exophiala dermatitidis, both agents of fatal brain infections) and saprophytes. The rock-dwelling habit is shown here to be key to the evolution of these two ecologically disparate orders. The most recent common ancestor of Verrucariales and Chaetothyriales is reconstructed as a non-lichenised rock-inhabitant. Ancestral state reconstructions suggest Verrucariales as one of the independent ascomycetes group where lichenisation has evolved on a hostile rock surface that might have favored this shift to a symbiotic lifestyle. Rock-inhabiting fungi are also ancestral to opportunistic pathogens, as they are found in the early diverging lineages of Chaetothyriales. In Chaetothyriales and Verrucariales, specific morphological and physiological traits (here referred to as extremotolerance) evolved in response to stresses in extreme conditions prevailing on rock surfaces. These factors facilitated colonisation of various substrates including the brains of vertebrates by opportunistic fungal pathogens, as well as helped establishment of a stable lichen symbiosis.}, Doi = {10.3114/sim.2008.61.11}, Key = {fds228782} } @article{fds228821, Author = {Otálora, MAG and Martínez, I and Molina, MC and Aragón, G and Lutzoni, F}, Title = {Phylogenetic relationships and taxonomy of the Leptogium lichenoides group (Collemataceae, Ascomycota) in Europe}, Journal = {Taxon}, Volume = {57}, Number = {3}, Pages = {907-921}, Year = {2008}, Month = {January}, ISSN = {0040-0262}, url = {http://dx.doi.org/10.1002/tax.573019}, Abstract = {The taxonomy of the Leptogium lichenoides complex is revised here based on a morphological, ecological and molecular phylogenetic study. A phylogenetic analysis of phenotypic characters was compared to a phylogeny based on nrITS and β-tubulin data. Using these phylogenies, we concluded that what was commonly recognized as Leptogium lichenoides s.l. encompasses three distinct species. Leptogium lichenoides var. pulvinatum is now recognized as a separate species L. pulvinatum comb. nov. Leptogium aragonii sp. nov., a non-isidiate species with large thalli, is the second species part of this complex, and L. lichenoides s.str., as redefined here, is the only species of this group with isidia. We also found that Leptogium lichenoides s.l. is polyphyletic. Leptogium pulvinatum and L. lichenoides s.str. are more closely related to L. gelatinosum than to L. aragonii. The taxonomic status of L. quercicola is reduced to a variety of L. pulvinatum. Identification key, descriptions and distribution maps are presented for Leptogium aragonii, L. gelatinosum, L. intermedium, L. lichenoides s.str., L. pulvinatum, and L. pulvinatum var. quercicola.}, Doi = {10.1002/tax.573019}, Key = {fds228821} } @article{fds228817, Author = {Gueidan, C and Ruibal Villasenor and C and de Hoog, S and Gorbushina, A and Untereiner, WA and Lutzoni, F}, Title = {An extremotolerant rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages}, Journal = {Studies in Mycology}, Volume = {61}, Pages = {111-119}, Year = {2008}, Key = {fds228817} } @article{fds228781, Author = {Gueidan, C and Roux, C and Lutzoni, F}, Title = {Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota).}, Journal = {Mycological research.}, Volume = {111}, Number = {Pt 10}, Pages = {1145-1168}, Year = {2007}, Month = {October}, ISSN = {0953-7562}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17981450}, Abstract = {Verrucariaceae are a family of mostly crustose lichenized ascomycetes colonizing various habitats ranging from marine and fresh water to arid environments. Phylogenetic relationships among members of the Verrucariaceae are mostly unknown and the current morphology-based classification has never been confronted to molecular data. A multilocus phylogeny (nuLSU, nuSSU and RPB1) was reconstructed for 83 taxa representing all main genera of this family to provide a molecular phylogenetic framework necessary to assess the current morphology-based classification. Four main well-supported monophyletic groups were recovered, one of which contains seven robust monophyletic subgroups. Most genera, as traditionally delimited, were not monophyletic. A few taxonomic changes are proposed here to reconcile the morphology-based classification with the molecular phylogeny (Endocarpon diffractellum comb. nov., Heteroplacidium fusculum comb. nov., and Bagliettoa marmorea comb. nov.). Ancestral state reconstructions show that the most recent common ancestor of the Verrucariaceae was most likely crustose with a weakly differentiated upper cortex, simple ascospores, and hymenium free of algae. As shown in this study, the use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification based on morphological similarity and a classification using monophyly as a grouping criterion.}, Doi = {10.1016/j.mycres.2007.08.010}, Key = {fds228781} } @article{fds228829, Author = {Hofstetter, V and Miadlikowska, J and Kauff, F and Lutzoni, F}, Title = {Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).}, Journal = {Molecular phylogenetics and evolution}, Volume = {44}, Number = {1}, Pages = {412-426}, Year = {2007}, Month = {July}, ISSN = {1055-7903}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17207641}, Abstract = {The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.}, Doi = {10.1016/j.ympev.2006.10.016}, Key = {fds228829} } @article{fds228832, Author = {Kauff, F and Cox, CJ and Lutzoni, F}, Title = {WASABI: an automated sequence processing system for multigene phylogenies.}, Journal = {Systematic biology}, Volume = {56}, Number = {3}, Pages = {523-531}, Year = {2007}, Month = {June}, ISSN = {1063-5157}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17562476}, Doi = {10.1080/10635150701395340}, Key = {fds228832} } @article{fds228828, Author = {Rydholm, C and Dyer, PS and Lutzoni, F}, Title = {DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri.}, Journal = {Eukaryotic cell}, Volume = {6}, Number = {5}, Pages = {868-874}, Year = {2007}, Month = {May}, ISSN = {1535-9778}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17384199}, Abstract = {Degenerate PCR and chromosome-walking approaches were used to identify mating-type (MAT) genes and flanking regions from the homothallic (sexually self-fertile) euascomycete fungus Neosartorya fischeri, a close relative of the opportunistic human pathogen Aspergillus fumigatus. Both putative alpha- and high-mobility-group-domain MAT genes were found within the same genome, providing a functional explanation for self-fertility. However, unlike those in many homothallic euascomycetes (Pezizomycotina), the genes were not found adjacent to each other and were termed MAT1 and MAT2 to recognize the presence of distinct loci. Complete copies of putative APN1 (DNA lyase) and SLA2 (cytoskeleton assembly control) genes were found bordering the MAT1 locus. Partial copies of APN1 and SLA2 were also found bordering the MAT2 locus, but these copies bore the genetic hallmarks of pseudogenes. Genome comparisons revealed synteny over at least 23,300 bp between the N. fischeri MAT1 region and the A. fumigatus MAT locus region, but no such long-range conservation in the N. fischeri MAT2 region was evident. The sequence upstream of MAT2 contained numerous candidate transposase genes. These results demonstrate a novel means involving the segmental translocation of a chromosomal region by which the ability to undergo self-fertilization may be acquired. The results are also discussed in relation to their significance in indicating that heterothallism may be ancestral within the Aspergillus section Fumigati.}, Doi = {10.1128/ec.00319-06}, Key = {fds228828} } @article{fds228830, Author = {Reeb, V and Haugen, P and Bhattacharya, D and Lutzoni, F}, Title = {Evolution of Pleopsidium (lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease.}, Journal = {Journal of molecular evolution}, Volume = {64}, Number = {3}, Pages = {285-298}, Year = {2007}, Month = {March}, ISSN = {0022-2844}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17294323}, Abstract = {The sporadic distribution of nuclear group I introns among different fungal lineages can be explained by vertical inheritance of the introns followed by successive losses, or horizontal transfers from one lineage to another through intron homing or reverse splicing. Homing is mediated by an intron-encoded homing endonuclease (HE) and recent studies suggest that the introns and their associated HE gene (HEG) follow a recurrent cyclical model of invasion, degeneration, loss, and reinvasion. The purpose of this study was to compare this model to the evolution of HEGs found in the group I intron at position S943 of the nuclear ribosomal DNA of the lichen-forming fungus Pleopsidium. Forty-eight S943 introns were found in the 64 Pleopsidium samples from a worldwide screen, 22 of which contained a full-length HEG that encodes a putative 256-amino acid HE, and 2 contained HE pseudogenes. The HEGs are divided into two closely related types (as are the introns that encode them) that differ by 22.6% in their nucleotide sequences. The evolution of the Pleopsidium intron-HEG element shows strong evidence for a cyclical model of evolution. The intron was likely acquired twice in the genus and then transmitted via two or three interspecific horizontal transfers. Close geographical proximity plays an important role in intron-HEG horizontal transfer because most of these mobile elements were found in Europe. Once acquired in a lineage, the intron-HEG element was also vertically transmitted, and occasionally degenerated or was lost.}, Doi = {10.1007/s00239-005-0179-z}, Key = {fds228830} } @article{fds228831, Author = {Arnold, AE and Lutzoni, F}, Title = {Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?}, Journal = {Ecology}, Volume = {88}, Number = {3}, Pages = {541-549}, Year = {2007}, Month = {March}, ISSN = {0012-9658}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17503580}, Abstract = {Fungal endophytes are found in asymptomatic photosynthetic tissues of all major lineages of land plants. The ubiquity of these cryptic symbionts is clear, but the scale of their diversity, host range, and geographic distributions are unknown. To explore the putative hyperdiversity of tropical leaf endophytes, we compared endophyte communities along a broad latitudinal gradient from the Canadian arctic to the lowland tropical forest of central Panama. Here, we use molecular sequence data from 1403 endophyte strains to show that endophytes increase in incidence, diversity, and host breadth from arctic to tropical sites. Endophyte communities from higher latitudes are characterized by relatively few species from many different classes of Ascomycota, whereas tropical endophyte assemblages are dominated by a small number of classes with a very large number of endophytic species. The most easily cultivated endophytes from tropical plants have wide host ranges, but communities are dominated by a large number of rare species whose host range is unclear. Even when only the most easily cultured species are considered, leaves of tropical trees represent hotspots of fungal species diversity, containing numerous species not yet recovered from other biomes. The challenge remains to recover and identify those elusive and rarely cultured taxa with narrower host ranges, and to elucidate the ecological roles of these little-known symbionts in tropical forests.}, Doi = {10.1890/05-1459}, Key = {fds228831} } @article{fds228833, Author = {Arnold, AE and Henk, DA and Eells, RL and Lutzoni, F and Vilgalys, R}, Title = {Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR.}, Journal = {Mycologia}, Volume = {99}, Number = {2}, Pages = {185-206}, Year = {2007}, Month = {March}, ISSN = {0027-5514}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17682771}, Abstract = {We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, U.S.A., with four goals: (i) to evaluate morphotaxa, BLAST matches and groups based on sequence similarity as functional taxonomic units; (ii) to explore methods to maximize phylogenetic signal for environmental datasets, which typically contain many taxa but few characters; (iii) to compare culturing vs. culture-free methods (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition; and (iv) to investigate the relationships between traditional ecological indices (e.g. Shannon index) and phylogenetic diversity (PD) in estimating endophyte diversity and spatial heterogeneity. Endophytes were recovered in culture from 87 of 90 P. taeda leaves sampled, yielding 439 isolates that represented 24 morphotaxa. Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) for 150 isolates revealed 59 distinct ITS genotypes that represented 24 and 37 unique groups based on 90% and 95% sequence similarity, respectively. By recoding ambiguously aligned regions to extract phylogenetic signal and implementing a conservative phylogenetic backbone constraint, we recovered well supported phylogenies based on ca. 600 bp of the nuclear ribosomal large subunit (LSUrDNA) for 72 Ascomycota and Basidiomycota, 145 cultured endophytes and 33 environmental PCR samples. Comparisons with LSUrDNA-delimited species showed that morphotaxa adequately estimated total species richness but rarely corresponded to biologically meaningful groups. ITS BLAST results were variable in their utility, but ITS genotype groups based on 90% sequence similarity were concordant with LSUrDNA-delimited species. Environmental PCR yielded more genotypes per sampling effort and recovered several distinct clades relative to culturing, but some commonly cultured clades were never found (Sordariomycetes) or were rare relative to their high frequency among cultures (Leotiomycetes). In contrast to traditional indices, PD demonstrated spatial heterogeneity in endophyte assemblages among P. taeda trees and study plots. Our results highlight the need for caution in designating taxonomic units based on gross cultural morphology or ITS BLAST matches, the utility of phylogenetic tools for extracting robust phylogenies from environmental samples, the complementarity of culturing and environmental PCR, the utility of PD relative to traditional ecological indices, and the remarkably high diversity of foliar fungal endophytes in this simplified temperate ecosystem.}, Doi = {10.3852/mycologia.99.2.185}, Key = {fds228833} } @article{fds228839, Author = {Higgins, KL and Arnold, AE and Miadlikowska, J and Sarvate, SD and Lutzoni, F}, Title = {Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages.}, Journal = {Molecular phylogenetics and evolution}, Volume = {42}, Number = {2}, Pages = {543-555}, Year = {2007}, Month = {February}, ISSN = {1055-7903}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17005421}, Abstract = {Although associated with all plants, fungal endophytes (microfungi that live within healthy plant tissues) represent an unknown proportion of fungal diversity. While there is a growing appreciation of their ecological importance and human uses, little is known about their host specificity, geographic structure, or phylogenetic relationships. We surveyed endophytic Ascomycota from healthy photosynthetic tissues of three plant species (Huperzia selago, Picea mariana, and Dryas integrifolia, representing lycophytes, conifers, and angiosperms, respectively) in northern and southern boreal forest (Québec, Canada) and arctic tundra (Nunavut, Canada). Endophytes were recovered from all plant species surveyed, and were present in <1-41% of 2 mm2 tissue segments examined per host species. Sequence data from the nuclear ribosomal internal transcribed spacer region (ITS) were obtained for 280 of 558 isolates. Species-accumulation curves based on ITS genotypes remained non-asymptotic, and bootstrap analyses indicated that a large number of genotypes remain to be found. The majority of genotypes were recovered from only a single host species, and only 6% of genotypes were shared between boreal and arctic communities. Two independent Bayesian analyses and a neighbor-joining bootstrapping analysis of combined data from the nuclear large and small ribosomal subunits (LSUrDNA, SSUrDNA; 2.4 kb) showed that boreal and arctic endophytes represent Dothideomycetes, Sordariomycetes, Chaetothyriomycetidae, Leotiomycetes, and Pezizomycetes. Many well-supported phylotypes contained only endophytes despite exhaustive sampling of available sequences of Ascomycota. Together, these data demonstrate greater than expected diversity of endophytes at high-latitude sites and provide a framework for assessing the evolution of these poorly known but ubiquitous symbionts of living plants.}, Doi = {10.1016/j.ympev.2006.07.012}, Key = {fds228839} } @article{fds228826, Author = {Hibbett, DS and Binder, M and Bischoff, JF and Blackwell, M and Cannon, PF and Eriksson, O and Huhndorf, S and James, T and Kirk, PM and Lücking, R and Lumbsch, T and Lutzoni, F and Matheny, PB and McLaughlin, DJ and Powell, MJ and Redhead, S and Schoch, CL and Spatafora, JW and Stalpers, JA and Vilgalys, R and Aime, MC and Aptroot, A and Bauer, R and Begerow, D and Benny, GL and Castlebury, LA and Crous, PW and Dai, YC and Gams, W and Geiser, DM and Griffith, GW and Gueidan, C and Hawksworth, DL and Hestmark, G and Hosaka, K and Humber, RA and Hyde, K and Koljalg, U and Kurtzman, CP and Larsson, KH and Lichtward, R and Longcore, J and Miadlikowska, J and Miller, A and Monclavo, JM and Mozley Standridge, S and Oberwinkler, F and Parmasto, E and Reeb, V and Rogers, JD and Roux, C and Ryvarden, L and Sampaio, JP and Schuessler, A and Sugiyama, J and Thorn, RG and Tibell, L and Untereiner, WA and Walker, C and Wang, Z and Weir, A and Weiss, M and White, M and Winka, K and Yao, YJ and Zhang, N}, Title = {A higher-level phylogenetic classification of the Fungi}, Journal = {Mycological Research}, Volume = {111}, Number = {Pt 5}, Pages = {509-547}, Year = {2007}, ISSN = {0953-7562}, url = {http://dx.doi.org/10.1016/j.mycres.2007.03.004}, Abstract = {A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.}, Doi = {10.1016/j.mycres.2007.03.004}, Key = {fds228826} } @article{fds228834, Author = {Gueidan, C and Roux, C and Lutzoni, F}, Title = {Using a multigene analysis to assess generic delineation and character evolution in the Verrucariaceae (Verrucariales, Ascomycota).}, Journal = {Mycological Research}, Volume = {110}, Pages = {1147-1170}, Year = {2007}, Key = {fds228834} } @article{fds228835, Author = {Litaker, RW and Vandersea, MW and Kibler, SR and Reece, KS and Stokes, NA and Lutzoni, FM and Yonish, BA and West, MA and Black, MND and Tester, PA}, Title = {Recognizing dinoglagellate species using ITS rDNA sequences}, Journal = {Journal of Phycology}, Volume = {43}, Number = {2}, Pages = {344-355}, Publisher = {WILEY}, Year = {2007}, ISSN = {0022-3646}, url = {http://dx.doi.org/10.1111/j.1529-8817.2007.00320.x}, Abstract = {Dinoflagellate taxonomy is based primarily on morphology and morphometric data that can be difficult to obtain. In contrast, molecular data can be rapidly and cost-effectively acquired, which has led to a rapid accumulation of sequence data in GenBank. Currently there are no systematic criteria for utilizing taxonomically unassigned sequence data to identify putative species that could in turn serve as a basis for testable hypotheses concerning the taxonomy, diversity, distribution, and toxicity of these organisms. The goal of this research was to evaluate whether simple, uncorrected genetic distances (p) calculated using ITS1/5.8S/ITS2 (ITS region) rDNA sequences could be used to develop criteria for recognizing putative species before formal morphological evaluation and classification. The current analysis used sequences from 81 dinoflagellate species belonging to 14 genera. For this diverse assemblage of dinoflagellate species, the within-species genetic distances between ITS region copies (p=0.000-0.021 substitutions per site) were consistently less than those observed between species (p=0.042-0.580). Our results indicate that a between-species uncorrected genetic distance of p≥0.04 could be used to delineate most free-living dinoflagellate species. Recently evolved species, however, may have ITS p values <0.04 and would require more extensive morphological and genetic analyses to resolve. For most species, the sequence of the dominant ITS region allele has the potential to serve as a unique species-specific "DNA barcode" that could be used for the rapid identification of dinoflagellates in field and laboratory studies. © 2007 No claim to original US government works.}, Doi = {10.1111/j.1529-8817.2007.00320.x}, Key = {fds228835} } @article{fds303157, Author = {Miadlikowska, J and Kauff, F and Hofstetter, V and Fraker, E and Grube, M and Hafellner, J and Reeb, V and Hodkinson, BP and Kukwa, M and Lücking, R and Hestmark, G and Otalora, MG and Rauhut, A and Büdel, B and Scheidegger, C and Timdal, E and Stenroos, S and Brodo, I and Perlmutter, GB and Ertz, D and Diederich, P and Lendemer, JC and May, P and Schoch, CL and Arnold, AE and Gueidan, C and Tripp, E and Yahr, R and Robertson, C and Lutzoni, F}, Title = {New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1088-1103}, Year = {2006}, Month = {November}, ISSN = {0027-5514}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17486983}, Abstract = {The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.}, Doi = {10.1080/15572536.2006.11832636}, Key = {fds303157} } @article{fds304274, Author = {Spatafora, JW and Sung, G-H and Johnson, D and Hesse, C and O'Rourke, B and Serdani, M and Spotts, R and Lutzoni, F and Hofstetter, V and Miadlikowska, J and Reeb, V and Gueidan, C and Fraker, E and Lumbsch, T and Lücking, R and Schmitt, I and Hosaka, K and Aptroot, A and Roux, C and Miller, AN and Geiser, DM and Hafellner, J and Hestmark, G and Arnold, AE and Büdel, B and Rauhut, A and Hewitt, D and Untereiner, WA and Cole, MS and Scheidegger, C and Schultz, M and Sipman, H and Schoch, CL}, Title = {A five-gene phylogeny of Pezizomycotina.}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1018-1028}, Year = {2006}, Month = {November}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/mycologia.98.6.1018}, Abstract = {Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.}, Doi = {10.3852/mycologia.98.6.1018}, Key = {fds304274} } @article{fds304275, Author = {Geiser, DM and Gueidan, C and Miadlikowska, J and Lutzoni, F and Kauff, F and Hofstetter, V and Fraker, E and Schoch, CL and Tibell, L and Untereiner, WA and Aptroot, A}, Title = {Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1053-1064}, Year = {2006}, Month = {November}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/mycologia.98.6.1053}, Abstract = {The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales.}, Doi = {10.3852/mycologia.98.6.1053}, Key = {fds304275} } @article{fds300050, Author = {Arnold, AE and Lutzoni, F}, Title = {From the leaf to the landscape: Endophyte diversity and interactions at small and large spatial scales}, Journal = {PHYTOPATHOLOGY}, Volume = {96}, Number = {6}, Pages = {S136-S137}, Publisher = {AMER PHYTOPATHOLOGICAL SOC}, Year = {2006}, Month = {June}, ISSN = {0031-949X}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000202991501218&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Key = {fds300050} } @article{fds228837, Author = {Rydholm, C and Szakacs, G and Lutzoni, F}, Title = {Low genetic variation and no detectable population structure in aspergillus fumigatus compared to closely related Neosartorya species.}, Journal = {Eukaryotic cell}, Volume = {5}, Number = {4}, Pages = {650-657}, Year = {2006}, Month = {April}, ISSN = {1535-9778}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16607012}, Abstract = {Aspergillus fumigatus is an anamorphic euascomycete mold with a ubiquitous presence worldwide. Despite intensive work to understand its success as a pathogen infecting immunosuppressed patients, the population dynamics and recent evolutionary history of A. fumigatus remain understudied. We examined patterns of genetic variation at three intergenic loci for 70 natural isolates from Europe, North America, South America, Asia, Africa, and Australia. The same loci were used to analyze within-population genetic variation for 33 isolates obtained from five geographic locations. Neither data set detected evidence of population differentiation or found any association between the genetic and geographic distances among these isolates. No evidence for genetic differentiation within the two A. fumigatus mating types was detected. The genetic diversity of A. fumigatus, contrasted with that of its close teleomorphic relatives, Neosartorya fischeri and Neosartorya spinosa, is remarkably low.}, Doi = {10.1128/ec.5.4.650-657.2006}, Key = {fds228837} } @article{fds228838, Author = {Fernández, FA and Miller, AN and Huhndorf, SM and Lutzoni, FM and Zoller, S}, Title = {Systematics of the genus Chaetosphaeria and its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa.}, Journal = {Mycologia}, Volume = {98}, Number = {1}, Pages = {121-130}, Year = {2006}, Month = {January}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/mycologia.98.1.121}, Abstract = {Chaetosphaeria is a common saprobic pyrenomycete genus with simple, homogeneous teleomorphs and complex, diverse anamorphs. As currently circumscribed in the literature, the genus encompasses 30 species distributed in four 'natural groups', and includes morphological entities in 11 anamorphic genera. Species frequently have been defined primarily based on characters of the anamorphs resulting in species with almost indistinguishable teleomorphs. This study aimed to assess the value and significance of morphological characters in resolving phylogenetic relationships in Chaetosphaeria and its allied genera. Phylogenetic relationships of 42 taxa, representing 29 species distributed in Chaetosphaeria and five related genera, were estimated with partial sequences of the nuclear LSU rDNA and beta-tubulin genes. Sequences were analyzed with maximum parsimony, maximum likelihood and Bayesian methods. Phylogenetic analyses of these two genes combined revealed two major lineages. The Chaetosphaeria lineage includes 21 species possessing both typical and new sexual and asexual morphologies. The lineage contains a strongly supported monophyletic clade of 13 species and eight paraphyletic taxa; the latter includes C. innumera, the type species of the genus. The second major lineage includes groupings concordant with the morphological circumscriptions of the genera Melanochaeta, Melanopsammella, Striatosphaeria, Zignoëlla and the new genus Tainosphaeria.}, Doi = {10.3852/mycologia.98.1.121}, Key = {fds228838} } @article{fds228823, Author = {Spatafora, JW and Sung, GH and Johnson, D and O’Rourke, B and Serdani, M and Spotts, R and Lutzoni, F and Hofstetter, V and Aptroot, A and Roux, C and Miller, A and Geiser, D and Hafellner, J and Hestmark, G and Arnold, AE and Büdel, B and Rauhut, A and Untereiner, WA and Cole, MS and Scheidegger, C and Schultz, M and Sipman, H and Schoch, C}, Title = {A five-gene phylogeny of Pezizomycotina}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1020-1030}, Year = {2006}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/mycologia.98.6.1018}, Abstract = {Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results fromweighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-1α) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support. © 2006 by The Mycological Society of America.}, Doi = {10.3852/mycologia.98.6.1018}, Key = {fds228823} } @article{fds228824, Author = {Geiser, DM and Gueidan Miadlikowska and J and Kauff, F and Hofstetter, V and Fraker, E and Schoch, CL and Tibell, L and Untereiner, WA and Aptroot, A and Lutzoni, F}, Title = {Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1055-1066}, Year = {2006}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.3852/mycologia.98.6.1053}, Abstract = {The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales. © 2006 by The Mycological Society of America.}, Doi = {10.3852/mycologia.98.6.1053}, Key = {fds228824} } @article{fds228825, Author = {Miadlikowska, J and Kauff, F and Hofstetter, V and Fraker, E and Grube, M and Hafellner, J and Reeb, V and Hodkinson, BP and Kukwa, M and Lücking, R and Hestmark, G and Otalora, MAG and Rauhut, A and Büdel, B and Scheidegger, C and Timdal, I and Stenroos, S and Brodo, I and Perlmutter, G and Ertz, D and Diederich, P and Lendemer, JC and Tripp, E and Yahr, R and May, P and Gueidan, C and Arnold, AE and Robertson, C and Lutzoni, F}, Title = {New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1090-1103}, Year = {2006}, ISSN = {0027-5514}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17486983}, Abstract = {The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.}, Key = {fds228825} } @article{fds228836, Author = {James, TY and Kauff, F and Schoch, C and Matheny, PB and Hofstetter, V and Cox, CJ and Celio, G and Gueidan, C and Fraker, E and Miadlikowska, J and Lumbsch, T and Rauhut, A and Reeb, V and Arnold, AE and Amtoft, A and Stajich, JE and Hosaka, K and Sung, GH and Johnson, D and O’Rourke, B and Binder, M and Curtis, JM and Slot, JC and Wang, Z and Wilson, AW and Schüßler, A and Longcore, JE and O’Donnell, K and Mozley Standridge, S and Porter, D and Letcher, PM and Powell, MJ and Taylor, JW and White, MM and Griffith, GW and Davies, DR and Sugiyama, J and Rossman, AY and Rogers, JD and Pfister, DH and Hewitt, D and Hansen, K and Hambleton, S and Shoemaker, RA and Kohlmeyer, J and Volkmann Kohlmeyer, B and Spotts, RA and Serdani, M and Crous, PW and Hughes, KW and Matsuura, K and Langer, E and Langer, G and Untereiner, WA and Lücking, R and Büdel, B and Geiser, DM and Aptroot, A and Buck, WR and Cole, MS and Diederich, P and Printzen, C and Schmitt, I and Schultz, M and Yahr, R and Zavarzin, A and Hibbett, DH and Lutzoni, F and McLaughlin, DJ and Spatafora, JW and Vilgalys, R}, Title = {Reconstructing the early evolution of the Fungi using a six-gene phylogeny}, Journal = {Nature}, Volume = {443}, Number = {7113}, Pages = {818-822}, Year = {2006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17051209}, Abstract = {The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.}, Doi = {10.1038/nature05110}, Key = {fds228836} } @article{fds228840, Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F}, Title = {Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungus Peltigera}, Journal = {European Journal of Phycology}, Volume = {40}, Number = {4}, Pages = {363-378}, Publisher = {Informa UK Limited}, Year = {2005}, Month = {November}, ISSN = {0967-0262}, url = {http://dx.doi.org/10.1080/09670260500342647}, Abstract = {Heterocystous cyanobacteria form symbiotic associations with a wide range of plant and fungal hosts. We used a molecular phylogenetic approach to investigate the degree of host specialization of cyanobacteria associated with four closely related species of the lichenized fungus Peltigera, and to compare these strains with other symbiotic cyanobacteria. We conducted phylogenetic analyses on 16S, rbcLX, and trnL sequences from cyanobacteria associated with multiple specimens of each lichen species and from symbionts of other fungi and plants, as well as from free-living strains of Nostoc and related genera of cyanobacteria. The genus Nostoc comprises two divergent lineages, but symbiotic strains occur primarily within a single monophyletic lineage that also includes free-living representatives. Cyanobacteria from the same lichen species were often more closely related to strains from other species or to plant symbionts or free-living strains than to each other. These results indicate that host specialization is low for the genus Nostoc, and suggest that opportunities for coevolution with its partners may be rare. © 2005 British Phycological Society.}, Doi = {10.1080/09670260500342647}, Key = {fds228840} } @article{fds228842, Author = {Bhattacharya, D and Reeb, V and Simon, DM and Lutzoni, F}, Title = {Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA.}, Journal = {BMC evolutionary biology}, Volume = {5}, Number = {68}, Pages = {68}, Year = {2005}, Month = {November}, ISSN = {1471-2148}, url = {http://dx.doi.org/10.1186/1471-2148-5-68}, Abstract = {<h4>Background</h4>Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of fungal group I introns including 9 putatively ancient group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri.<h4>Results</h4>Our analyses reveal a complex evolutionary history of the fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then group I intron loss was widespread in fungal rDNA evolution.<h4>Conclusion</h4>On the basis of these results, we suggest that the extensive distribution of fungal group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.}, Doi = {10.1186/1471-2148-5-68}, Key = {fds228842} } @article{fds228777, Author = {Lutzoni}, Title = {Erratum: (American Journal of Botany (October 2004) 91:10 (1450))}, Journal = {American Journal of Botany}, Volume = {92}, Number = {1}, Pages = {i}, Year = {2005}, Month = {January}, ISSN = {0002-9122}, Key = {fds228777} } @article{fds228841, Author = {Paoletti, M and Rydholm, C and Schwier, E and Anderson, MJ and Szakacs, G and Lutzoni, F and Debeaupuis, JP and Latgé, JP and Denning, DW and Dyer, PS}, Title = {Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus.}, Journal = {Current Biology}, Volume = {15}, Number = {13}, Pages = {1242-1248}, Year = {2005}, url = {http://dx.doi.org/10.1016/j.cub.2005.05.045}, Abstract = {Aspergillus fumigatus is a medically important opportunistic pathogen and a major cause of respiratory allergy. The species has long been considered an asexual organism. However, genome analysis has revealed the presence of genes associated with sexual reproduction, including a MAT-2 high-mobility group mating-type gene and genes for pheromone production and detection (Galagan et al., personal communication; Nierman et al., personal communication). We now demonstrate that A. fumigatus has other key characteristics of a sexual species. We reveal the existence of isolates containing a complementary MAT-1 alpha box mating-type gene and show that the MAT locus has an idiomorph structure characteristic of heterothallic (obligate sexual outbreeding) fungi. Analysis of 290 worldwide clinical and environmental isolates with a multiplex-PCR assay revealed the presence of MAT1-1 and MAT1-2 genotypes in similar proportions (43% and 57%, respectively). Further population genetic analyses provided evidence of recombination across a global sampling and within North American and European subpopulations. We also show that mating-type, pheromone-precursor, and pheromone-receptor genes are expressed during mycelial growth. These results indicate that A. fumigatus has a recent evolutionary history of sexual recombination and might have the potential for sexual reproduction. The possible presence of a sexual cycle is highly significant for the population biology and disease management of the species.}, Doi = {10.1016/j.cub.2005.05.045}, Key = {fds228841} } @article{fds228843, Author = {Lutzoni, F and Kauff, F and Cox, CJ and McLaughlin, D and Celio, G and Dentinger, B and Padamsee, M and Hibbett, D and James, TY and Baloch, E and Grube, M and Reeb, V and Hofstetter, V and Schoch, C and Arnold, AE and Miadlikowska, J and Spatafora, J and Johnson, D and Hambleton, S and Crockett, M and Shoemaker, R and Sung, G-H and Lücking, R and Lumbsch, T and O'Donnell, K and Binder, M and Diederich, P and Ertz, D and Gueidan, C and Hansen, K and Harris, RC and Hosaka, K and Lim, Y-W and Matheny, B and Nishida, H and Pfister, D and Rogers, J and Rossman, A and Schmitt, I and Sipman, H and Stone, J and Sugiyama, J and Yahr, R and Vilgalys, R}, Title = {Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.}, Journal = {American journal of botany}, Volume = {91}, Number = {10}, Pages = {1446-1480}, Year = {2004}, Month = {October}, ISSN = {0002-9122}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21652303}, Abstract = {Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.}, Doi = {10.3732/ajb.91.10.1446}, Key = {fds228843} } @article{fds228844, Author = {Reeb, V and Lutzoni, F and Roux, C}, Title = {Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.}, Journal = {Molecular phylogenetics and evolution}, Volume = {32}, Number = {3}, Pages = {1036-1060}, Year = {2004}, Month = {September}, ISSN = {1055-7903}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15288074}, Abstract = {Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).}, Doi = {10.1016/j.ympev.2004.04.012}, Key = {fds228844} } @article{fds228860, Author = {Miadlikowska, J and Lutzoni, F}, Title = {Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits.}, Journal = {American journal of botany}, Volume = {91}, Number = {3}, Pages = {449-464}, Year = {2004}, Month = {March}, ISSN = {0002-9122}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21653401}, Abstract = {To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup consisted of 59 individuals representing six families, 12 genera, and 54 species potentially part of the Peltigerineae/Peltigerales. Our study revealed that all six families together formed a strongly supported monophyletic group within the Lecanoromycetidae. We propose here a new classification for these lichens consisting of the order Peltigerales and two suborders-Collematineae subordo nov. (Collemataceae, Placynthiaceae, and Pannariaceae) and Peltigerineae (Lobariaceae, Nephromataceae, and Peltigeraceae). To accommodate these new monophyletic groups, we redefined the Lecanorineae, Pertusariales, and Lecanorales sensu Eriksson et al. (Outline of Ascomycota-2003, Myconet 9: 1-103, 2003). Our study confirms the monophyly of the Collemataceae, Lobariaceae, Nephromataceae, and Peltigeraceae, and the genera Nephroma, Sticta, and Peltigera. However, Leptogium, Lobaria, Pseudocyphellaria, and Solorina were found to be nonmonophyletic genera. Reconstruction of ancestral symbiotic states within the Peltigerales, using maximum likelihood (ML) and a Bayesian approach to account for phylogenetic uncertainty, revealed an evolutionary scenario in which bimembered associations with cyanobacteria were ancestral, followed by multiple independent acquisitions of green algae to form tripartite symbioses and rare subsequent losses of the cyanobiont to form bimembered symbioses with green algae.}, Doi = {10.3732/ajb.91.3.449}, Key = {fds228860} } @article{fds304273, Author = {Haugen, P and Reeb, V and Lutzoni, F and Bhattacharya, D}, Title = {The evolution of homing endonuclease genes and group I introns in nuclear rDNA.}, Journal = {Molecular biology and evolution}, Volume = {21}, Number = {1}, Pages = {129-140}, Year = {2004}, Month = {January}, url = {http://dx.doi.org/10.1093/molbev/msh005}, Abstract = {Group I introns are autonomous genetic elements that can catalyze their own excision from pre-RNA. Understanding how group I introns move in nuclear ribosomal (r)DNA remains an important question in evolutionary biology. Two models are invoked to explain group I intron movement. The first is termed homing and results from the action of an intron-encoded homing endonuclease that recognizes and cleaves an intronless allele at or near the intron insertion site. Alternatively, introns can be inserted into RNA through reverse splicing. Here, we present the sequences of two large group I introns from fungal nuclear rDNA, which both encode putative full-length homing endonuclease genes (HEGs). Five remnant HEGs in different fungal species are also reported. This brings the total number of known nuclear HEGs from 15 to 22. We determined the phylogeny of all known nuclear HEGs and their associated introns. We found evidence for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA. These results suggest that nuclear HEGs are frequently mobilized. HEG invasion appears, however, to be limited to existing introns in the same or neighboring sites. To study the intron-HEG relationship in more detail, the S943 group I intron in fungal small-subunit rDNA was used as a model system. The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns.}, Doi = {10.1093/molbev/msh005}, Key = {fds304273} } @article{fds228859, Author = {Haugen, P and Reeb, V and Lutzoni, F and Bhattacharya, D}, Title = {The evolution of homing endonuclease genes and group I introns in nuclear rDNA.}, Journal = {Molecular Biology and Evolution}, Volume = {21}, Number = {1}, Pages = {105-116}, Year = {2004}, url = {http://dx.doi.org/10.1093/molbev/msh005}, Abstract = {Group I introns are autonomous genetic elements that can catalyze their own excision from pre-RNA. Understanding how group I introns move in nuclear ribosomal (r)DNA remains an important question in evolutionary biology. Two models are invoked to explain group I intron movement. The first is termed homing and results from the action of an intron-encoded homing endonuclease that recognizes and cleaves an intronless allele at or near the intron insertion site. Alternatively, introns can be inserted into RNA through reverse splicing. Here, we present the sequences of two large group I introns from fungal nuclear rDNA, which both encode putative full-length homing endonuclease genes (HEGs). Five remnant HEGs in different fungal species are also reported. This brings the total number of known nuclear HEGs from 15 to 22. We determined the phylogeny of all known nuclear HEGs and their associated introns. We found evidence for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA. These results suggest that nuclear HEGs are frequently mobilized. HEG invasion appears, however, to be limited to existing introns in the same or neighboring sites. To study the intron-HEG relationship in more detail, the S943 group I intron in fungal small-subunit rDNA was used as a model system. The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns.}, Doi = {10.1093/molbev/msh005}, Key = {fds228859} } @book{fds14721, Author = {Taylor, J. W. and Spatafora, J. and O’Donnell, K. and Lutzoni, F. and James, T. and Hibbett, D. S. and Geiser, D. and Bruns, T. D. and Blackwell, M.}, Title = {The Fungi}, Pages = {171-194}, Booktitle = {Assembling the Tree of Life}, Publisher = {Oxford University Press, Oxford, UK}, Editor = {J. Cracraft and M. J. Donoghue}, Year = {2004}, Key = {fds14721} } @article{fds228861, Author = {Zoller, S and Lutzoni, F}, Title = {Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa.}, Journal = {Molecular phylogenetics and evolution}, Volume = {29}, Number = {3}, Pages = {629-640}, Year = {2003}, Month = {December}, ISSN = {1055-7903}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14615198}, Abstract = {Omphalina basidiolichens are obligate mutualistic associations of a fungus of the genus Omphalina (the exhabitant) and a unicellular green alga of the genus Coccomyxa (the inhabitant). It has been suggested that symbiotic inhabitants have a lower rate of genetic change compared to exhabitants because the latter are more exposed to abiotic environmental variation and competition from other organisms. In order to test this hypothesis we compared substitution rates in the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S, ITS2) among fungal species with rates among their respective algal symbionts. To ensure valid comparisons, only taxon pairs (12) with a common evolutionary history were used. On average, substitution rates in the ITS1 portion of Omphalina pairs were 27.5 times higher than rates in the corresponding pairs of Coccomyxa since divergence from their respective ancestor at the base of the Omphalina/Coccomyxa lineage. Substitution rates in the 5.8S and the ITS2 portions were 2.4 and 18.0 times higher, respectively. The highest rate difference (43.0) was found in the ITS1 region. These are, to our knowledge, the highest differences of substitution rates reported for symbiotic organisms. We conclude that the Omphalina model system conforms to the proposed hypothesis of lower substitution rates in the inhabitant, but that the mode of transmission of the inhabitant (vertical versus horizontal) could be a prevailing factor in the regulation of unequal rates of nucleotide substitution between co-evolving symbionts. Our phylogenetic study of Coccomyxa revealed three main lineages within this genus, corresponding to free-living Coccomyxa, individuals isolated from basidiolichens Omphalina and Coccomyxa isolated from ascolichens belonging to the Peltigerales.}, Doi = {10.1016/s1055-7903(03)00215-x}, Key = {fds228861} } @article{fds228857, Author = {Miadlikowska, J and Lutzoni, F and Goward, T and Zoller, S and Posada, D}, Title = {New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex.}, Journal = {Mycologia}, Volume = {95}, Number = {6}, Pages = {1181-1203}, Year = {2003}, Month = {November}, ISSN = {0027-5514}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21149020}, Abstract = {The Peltigera canina species complex consists of foliose lichenized bitunicate ascohymenial discomycetes forming section Peltigera within the genus Peltigera (Lecanoromycetes, lichen-forming Ascomycetes). To test the circumscription of highly polymorphic species and to resolve relationships among putative members of the P. canina complex, part of the nuclear ribosomal DNA large subunit (LSU rDNA) and the entire internal-transcribed spacer (ITS rDNA) were sequenced for 84 individuals representing 33 putative Peltigera taxa. Seventeen of the 25 taxa from the P. canina complex are well established and widely accepted. The remaining eight taxa have been proposed recently but are undescribed. A hypervariable region in ITS1 (ITS1-HR, sites 111-237 in our alignment) showed remarkable variation in length, especially in the P. canina complex, ranging from 8 to 126 bp, and contained several microsatellites. We describe here an alignment-free method to code such large gap-rich hypervariable regions for phylogenetic analyses. Variation among ITS1-HR sequences greatly contributed to species delimitation and species identification and can be a major asset to future population studies for specific species within section Peltigera. Sequences of ITS1-HR alone were sufficient to identify all existing species of Peltigera from the P. canina species complex and related sections Retifoveatae and Horizontales included in this study. However, only when INAASE (for short ambiguously aligned regions) and ITS1-HR coded characters were added to the combined analysis of nonambiguous LSU and ITS sites was it possible to reach the level of phylogenetic resolution and support necessary to disentangle the P. canina complex. We report here complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. canina complex (P. canina, P. cinnamomea, P. degenii, P. evansiana, P. frigida, P. kristinssonii, P. laciniata, P. lambinonii, P. lepidophora, P. membranacea, P. monticola, P. ponojensis, P. praetextata, P. rufescens and P. ulcerata). Four of the eight newly proposed but undescribed taxa most likely represent new species (P. "fuscopraetextata", P. "neocanina", P. "neorufescens" and P. "scotteri") within the P. canina complex. We found that morphologically and chemically distinct P. didactyla s. str. and P. didactyla var. extenuata form two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level (P. extenuata). The North American and European populations of the morphologically uniform P. degenii might represent two sibling species because they were found to be genetically distinct and monophyletic. Two major monophyletic groups within the P. canina complex (CICADE = CInnamomea + CAnina + DEgenii group and PORUDI = POnojensis + RUfescens + DIdactyla group) seem to be correlated with different humidity preferences. Although some authors previously have suggested interspecies recombination within the P. canina complex, we did not find statistically significant evidence for this phenomenon based on LSU and ITS sequences.}, Doi = {10.1080/15572536.2004.11833027}, Key = {fds228857} } @article{fds228858, Author = {Søchting, U and Lutzoni, F}, Title = {Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae).}, Journal = {Mycological research.}, Volume = {107}, Number = {Pt 11}, Pages = {1266-1276}, Year = {2003}, Month = {November}, url = {http://dx.doi.org/10.1017/s0953756203008529}, Abstract = {A molecular phylogenetic analysis of rDNA was performed for seven Caloplaca, seven Xanthoria, one Fulgensia and five outgroup species. Phylogenetic hypotheses are constructed based on nuclear small and large subunit rDNA, separately and in combination. Three strongly supported major monophyletic groups were revealed within the Teloschistaceae. One group represents the Xanthoria fallax-group. The second group includes three subgroups: (1) X. parietina and X. elegans; (2) basal placodioid Caloplaca species followed by speciations leading to X. polycarpa and X. candelaria; and (3) a mixture of placodioid and endolithic Caloplaca species. The third main monophyletic group represents a heterogeneous assemblage of Caloplaca and Fulgensia species with a drastically different metabolite content. We report here that the two genera Caloplaca and Xanthoria, as well as the subgenus Gasparrinia, are all polyphyletic. The taxonomic significance of thallus morphology in Teloschistaceae and the current delimitation of the genus Xanthoria is discussed in light of these results.}, Doi = {10.1017/s0953756203008529}, Key = {fds228858} } @article{fds228862, Author = {Gaya, E and Lutzoni, F and Zoller, S and Navarro-Rosinés, P}, Title = {Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming ascomycota).}, Journal = {American journal of botany}, Volume = {90}, Number = {7}, Pages = {1095-1103}, Year = {2003}, Month = {July}, url = {http://dx.doi.org/10.3732/ajb.90.7.1095}, Abstract = {Fulgensia Massal. & De Not. is a widespread genus with considerable morphological and ecological heterogeneity across species. For this reason, the taxonomic delimitation of this genus has been controversial. Relationships among species of Fulgensia, Caloplaca Th. Fr., and Xanthoria (Fr.) Th. Fr. (Lecanorales) were investigated based on a comprehensive phylogenetic analysis of 62 DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region using maximum parsimony (MP) and likelihood (ML). Ambiguously aligned (INAASE coded characters) and unambiguous regions were analyzed separately and combined when using MP as the optimization criterion. All our analyses confirm the polyphyly of this genus as three distinct lineages: Fulgensia sensu stricto, F. australis, and F. schistidii. We report here that Caloplaca, Fulgensia, and Xanthoria together form two main sister lineages. One lineage includes Fulgensia schistidii (part of the C. saxicola group), Xanthoria, and most of the lobed Caloplaca species belonging to the Gasparrinia group. A second main lineage comprises the remaining Caloplaca species, Fulgensia sensu stricto, and F. australis. Therefore, the traditional generic level classification schemes for the family Teloschistaceae appear to be highly artificial. All three genera were found to be nonmonophyletic. We demonstrate here that the ITS is appropriate to resolve relationships across the Teloschistaceae. However, a combination of an MP analysis, in which ambiguously aligned regions are accommodated using INAASE, with an ML analysis, in which phylogenetic confidence is estimated using a Bayesian approach, is needed.}, Doi = {10.3732/ajb.90.7.1095}, Key = {fds228862} } @article{fds228864, Author = {Alfaro, ME and Zoller, S and Lutzoni, F}, Title = {Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.}, Journal = {Molecular biology and evolution}, Volume = {20}, Number = {2}, Pages = {255-266}, Year = {2003}, Month = {February}, url = {http://dx.doi.org/10.1093/molbev/msg028}, Abstract = {Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.}, Doi = {10.1093/molbev/msg028}, Key = {fds228864} } @article{fds228863, Author = {McDonald, T and Miadlikowska, J and Lutzoni, F}, Title = {The lichen genus Sticta in the Great Smoky Mountains: A phylogenetic study of morphological, chemical, and molecular data}, Journal = {Bryologist}, Volume = {106}, Number = {1}, Pages = {61-79}, Publisher = {American Bryological and Lichenological Society}, Year = {2003}, Month = {January}, url = {http://dx.doi.org/10.1639/0007-2745(2003)106[0061:TLGSIT]2.0.CO;2}, Abstract = {In this paper we segregate specimens from the genus Sticta in the Great Smoky Mountains National Park into phenotypic groups corresponding to putative species using traditional taxonomic methods, paying particular attention to specimens from the S. weigelii s. 1. group, then employ phylogenetic analyses and rigorous statistics to test the robustness of these species groups. In order to circumscribe putative species and to resolve the S. weigelii complex, morphological, chemical, and molecular characters from the nuclear ribosomal DNA sequences of the entire Internal Transcribed Spacer region are analyzed separately and simultaneously using maximum parsimony or maximum likelihood. In addition to the bootstrap method, Bayesian statistics with the Markov Chain Monte Carlo algorithm are used to estimate branch robustness on the resulting reconstructed trees. Five out of six analyses recover the same five monophyletic putative species from the genus Sticta, indicating the concordance of DNA-based and morphology-based species delimitation. The phylogenies show that lichens identified as S. weigelii represented S. beauvoisii and the two new species described here - S. carolinensis and S. fragilinata. Sticta weigelii s. s. does not occur in the park. Specimens from Oregon identified as S. weigelii belong to another unnamed Sticta taxon. The remaining two monophyletic groups represent two species well known from the park-S. fuliginosa and S. limbata. Characteristics of secondary compounds detected by Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography (HPLC) in S. fragilinata thalli are provided. Detailed descriptions, including morphology and chemistry, are provided for four Sticta species found in the Smoky Mountains: S. beauvoisii, S. carolinensis, S. fragilinata and S. fuliginosa.}, Doi = {10.1639/0007-2745(2003)106[0061:TLGSIT]2.0.CO;2}, Key = {fds228863} } @article{fds228865, Author = {Kauff, F and Lutzoni, F}, Title = {Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits.}, Journal = {Molecular phylogenetics and evolution}, Volume = {25}, Number = {1}, Pages = {138-156}, Year = {2002}, Month = {October}, ISSN = {1055-7903}, url = {http://dx.doi.org/10.1016/s1055-7903(02)00214-2}, Abstract = {Despite various morphological and anatomical similarities, the two orders Gyalectales (lichenized ascomycetes) and Ostropales (lichenized and non-lichenized ascomycetes) have been considered to be distantly related to each other and their position within the Ascomycota was unsettled. To estimate relationships within these groups and their respective phylogenenetic placement within the Ascomycota, we analyzed DNA sequences from the nuclear small and large subunit ribosomal RNA genes using Maximum Parsimony, Maximum Likelihood, and Bayesian statistics with Markov chain Monte Carlo algorithms. Support for internal branches estimated with bootstrap was compared to Bayesian posterior probabilities. We report here that the Ostropales, in their current circumscription, are paraphyletic, and that the Ostropales s.l. include the Gyalectales and Trapeliaceae. The Unitunicate Ascohymenials are redelineated to include the Ostropales s.l., as defined here, and the Baeomycetaceae. Dimerella and Coenogonium are congeneric, and Petractis thelotremella and P. hypoleuca are reunited with members of the genus Gyalecta. In addition to requiring less computational time, Bayesian inference of phylogeny recovered the same topology as a conventional heuristic search using Maximum Likelihood as the optimization criterion and seems superior to bootstrapping in estimating support for short internal branches.}, Doi = {10.1016/s1055-7903(02)00214-2}, Key = {fds228865} } @article{fds228866, Author = {Barker, FK and Lutzoni, FM}, Title = {The utility of the incongruence length difference test.}, Journal = {Systematic biology}, Volume = {51}, Number = {4}, Pages = {625-637}, Year = {2002}, Month = {August}, url = {http://dx.doi.org/10.1080/10635150290102302}, Doi = {10.1080/10635150290102302}, Key = {fds228866} } @article{fds228876, Author = {Redhead, SA and Lutzoni, F and Moncalvo, JM and Vilgalys, R}, Title = {Phylogeny of agarics: partial systematics solutions for core omphalinoid genera in the agaricales (Euagarics).}, Journal = {Mycotaxon.}, Volume = {83}, Pages = {19-57}, Year = {2002}, Month = {July}, Abstract = {The taxonomy of species previously assigned to Omphalina sensu lato or Clitocybe is reevaluated in light of recent molecularly-based phylogenetic hypotheses. Nomenclatural complications involving generic and specific names, lectotypifications and changes to the Code are analysed. Lichenomphalia gen. nov. (type Hygrophorus hudsonianus, syn. Omphalina hudsoniana) is proposed for lichenized former omphalinas. Ampulloclitocybe gen. nov. (type Agaricus clavipes, syn. Clitocybe clavipes) is erected for its type species. Arrhenia is emended to include greyish species formerly included in Omphalina, but excluding reddish brown species related to Omphalina pyxidada, the conserved lectotype for Omphalina. The genera Cantharellula, Chrysomphalina, Gerronema, Glabrocyphella, Gliophorus, Haasiella, Hygrophorus, Hygrocybe, Pseudoarmillariella, and Rickenella, and the generic names Botrydina, Coriscium, Leptoglossum, Phaeotellus, Phytoconis, and Semiomphalina are discussed.}, Key = {fds228876} } @article{fds228867, Author = {Redhead, SA and Moncalvo, JM and Vilgalys, R and Lutzoni, F}, Title = {Phylogeny of agarics: partial systematics solutions for bryophilous omphalinoid agarics outside of the Agaricales (Euagarics).}, Journal = {Mycotaxon.}, Volume = {82}, Pages = {151-168}, Year = {2002}, Month = {June}, ISSN = {0093-4666}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000177167900010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {The taxonomy of several species previously assigned to Omphalina sensu lato or Gerronema is reevaluated in light of recent molecularly based phylogenetic hypotheses. One surmised clade, herein informally labelled the rickenelloid clade, falls outside of the Agaricales using nLSU data. Analysis of how best to classify these taxa results in the establishment of two new genera, Loreleia (type: Agaricus postii) and Sphagnomphalia (type: Clitocybe brevibasidiata), and the renaming of a later homonym, Jacobia nom. illeg., as Contumyces (type: Clitocybe rosella). New combinations are proposed and an interim key to these genera is provided.}, Key = {fds228867} } @article{fds228775, Author = {O'Donnell, K and Lutzoni, FM and Ward, TJ and Benny, GL}, Title = {Erratum: Evolutionary relationships among mucoralean fungi (zygomycota): Evidence for family polyphyly on a large scale (Mycologia (2001) 93:2)}, Journal = {Mycologia}, Volume = {93}, Number = {4}, Pages = {814}, Year = {2002}, Month = {January}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.1080/00275514.2001.12063214}, Doi = {10.1080/00275514.2001.12063214}, Key = {fds228775} } @article{fds228868, Author = {Miadlikowska, J and McCune, B and Lutzoni, F}, Title = {Pseudocyphellaria perpetua, a new lichen from western North America}, Journal = {Bryologist}, Volume = {105}, Number = {1}, Pages = {1-10}, Publisher = {American Bryological and Lichenological Society}, Year = {2002}, Month = {January}, url = {http://dx.doi.org/10.1639/0007-2745(2002)105[0001:PPANLF]2.0.CO;2}, Abstract = {Pseudocyphellaria perpetua McCune & Miadlikowska is described as a new species of lichenized fungus from Oregon, U.S.A. Morphologically similar to some forms of P. crocata, P. perpetua is separated from that species by a yellow medulla and predominantly marginal soralia. Comparison of ITS and LSU nrDNA sequences support taxonomic distinctness of these two species. Phylogenetic analyses were conducted on LSU and ITS nrDNA data sets separately and simultaneously using maximum parsimony and maximum likelihood as optimization criteria. All analyses except one (maximum parsimony on LSU nrDNA data alone) confirmed the monophyly of P. perpetua. There are two distinct groups within the P. perpetua clade represented by specimens sampled from near the type locality in Oregon, and specimens outside of Oregon (eastern Canada, eastern Russia and eastern U.S.A.). The genus Pseudocyphellaria is very likely polyphyletic, consisting of at least two highly divergent groups.}, Doi = {10.1639/0007-2745(2002)105[0001:PPANLF]2.0.CO;2}, Key = {fds228868} } @book{fds1698, Author = {Lutzoni, F.}, Title = {Lichens}, Volume = {2}, Pages = {618-622}, Booktitle = {Encyclopedia of Evolution}, Publisher = {Oxford University Press, Oxford, UK}, Editor = {M. Pagel}, Year = {2002}, Key = {fds1698} } @book{fds1713, Author = {Pagel, M. and Lutzoni, F.}, Title = {Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation}, Pages = {151-164}, Booktitle = {Biological Evolution and Statistical Physics}, Publisher = {Springer Verlag, Berlin, Germany}, Editor = {M. Laessig and A. Valleriani}, Year = {2002}, Key = {fds1713} } @article{fds228869, Author = {Lutzoni, F and Pagel, M and Reeb, V}, Title = {Major fungal lineages are derived from lichen symbiotic ancestors.}, Journal = {Nature}, Volume = {411}, Number = {6840}, Pages = {937-940}, Year = {2001}, Month = {June}, ISSN = {0028-0836}, url = {http://dx.doi.org/10.1038/35082053}, Abstract = {About one-fifth of all known extant fungal species form obligate symbiotic associations with green algae, cyanobacteria or with both photobionts. These symbioses, known as lichens, are one way for fungi to meet their requirement for carbohydrates. Lichens are widely believed to have arisen independently on several occasions, accounting for the high diversity and mixed occurrence of lichenized and non-lichenized (42 and 58%, respectively) fungal species within the Ascomycota. Depending on the taxonomic classification chosen, 15-18 orders of the Ascomycota include lichen-forming taxa, and 8-11 of these orders (representing about 60% of the Ascomycota species) contain both lichenized and non-lichenized species. Here we report a phylogenetic comparative analysis of the Ascomycota, a phylum that includes greater than 98% of known lichenized fungal species. Using a Bayesian phylogenetic tree sampling methodology combined with a statistical model of trait evolution, we take into account uncertainty about the phylogenetic tree and ancestral state reconstructions. Our results show that lichens evolved earlier than believed, and that gains of lichenization have been infrequent during Ascomycota evolution, but have been followed by multiple independent losses of the lichen symbiosis. As a consequence, major Ascomycota lineages of exclusively non-lichen-forming species are derived from lichen-forming ancestors. These species include taxa with important benefits and detriments to humans, such as Penicillium and Aspergillus.}, Doi = {10.1038/35082053}, Key = {fds228869} } @article{fds228870, Author = {O'Donnell, K and Lutzoni, FM and Ward, TJ and Benny, GL}, Title = {Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale}, Journal = {Mycologia}, Volume = {93}, Number = {2}, Pages = {286-296}, Publisher = {JSTOR}, Year = {2001}, Month = {January}, ISSN = {0027-5514}, url = {http://dx.doi.org/10.2307/3761650}, Abstract = {Mucorales (Zygomycota) are ubiquitous, morphologically simple terrestrial fungi that are united taxonomically by possession of a coenocytic mycelium upon which nonmotile mitotic spores are produced asexually in uni- to multispored sporangia, and zygospores, where known, are produced following fusion of sexually compatible hyphae. Here we report the first comprehensive phylogenetic analysis of essentially all genera of Mucorales (63 species, 54 genera and 13 families) based on partial nucleotide sequence data of nuclear small subunit (18S) ribosomal RNA and nuclear large subunit (28S) ribosomal RNA genes, translation elongation factor-1α gene exons, and a morphological data set consisting of 1826, 389, 1092 and 11 characters, respectively. Individual and combined data sets were analyzed by unequally weighted maximum parsimony (MP) to investigate evolutionary relationships among and within mucoralean families. A Micromucor-Umbelopsis clade, traditionally included in the Mortierellaceae, was identified as the basal sister-group to all other Mucorales. A major discovery of this study is that traditional family-level classification schemes for this order appear to be highly artificial as evidenced by polyphyly of four of the seven families containing two or more genera. As presently circumscribed, these four families include 83% of the Mucorales. In addition, the largest and best known genera, Mucor and Absidia, were resolved as polyphyletic. The results provide a robust phylogenetic framework for additional evolutionary studies of the Mucorales.}, Doi = {10.2307/3761650}, Key = {fds228870} } @article{fds300053, Author = {Alfaro, ME and Zoller, S and Lutzoni, F}, Title = {Comparative performance of the bootstrap and Bayesian MCMC sampling in assessing phylogenetic confidence: a simulation study}, Journal = {AMERICAN ZOOLOGIST}, Volume = {41}, Number = {6}, Pages = {1379-1379}, Year = {2001}, ISSN = {0003-1569}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000174306500021&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Key = {fds300053} } @article{fds228871, Author = {Bhattacharya, D and Lutzoni, F and Reeb, V and Simon, D and Nason, J and Fernandez, F}, Title = {Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes.}, Journal = {Molecular biology and evolution}, Volume = {17}, Number = {12}, Pages = {1971-1984}, Year = {2000}, Month = {December}, ISSN = {0737-4038}, url = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a026298}, Abstract = {Spliceosomal (pre-mRNA) introns have previously been found in eukaryotic protein-coding genes, in the small nuclear RNAs of some fungi, and in the small- and large-subunit ribosomal DNA genes of a limited number of ascomycetes. How the majority of these introns originate remains an open question because few proven cases of recent and pervasive intron origin have been documented. We report here the widespread occurrence of spliceosomal introns (69 introns at 27 different sites) in the small- and large-subunit nuclear-encoded rDNA of lichen-forming and free-living members of the Ascomycota. Our analyses suggest that these spliceosomal introns are of relatively recent origin, i.e., within the Euascomycetes, and have arisen through aberrant reverse-splicing (in trans) of free pre-mRNA introns into rRNAs. The spliceosome itself, and not an external agent (e.g., transposable elements, group II introns), may have given rise to these introns. A nonrandom sequence pattern was found at sites flanking the rRNA spliceosomal introns. This pattern (AG-intron-G) closely resembles the proto-splice site (MAG-intron-R) postulated for intron insertions in pre-mRNA genes. The clustered positions of spliceosomal introns on secondary structures suggest that particular rRNA regions are preferred sites for insertion through reverse-splicing.}, Doi = {10.1093/oxfordjournals.molbev.a026298}, Key = {fds228871} } @article{fds228872, Author = {Lutzoni, F and Wagner, P and Reeb, V and Zoller, S}, Title = {Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.}, Journal = {Systematic biology}, Volume = {49}, Number = {4}, Pages = {628-651}, Year = {2000}, Month = {December}, url = {http://dx.doi.org/10.1080/106351500750049743}, Abstract = {Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony.}, Doi = {10.1080/106351500750049743}, Key = {fds228872} } @article{fds228874, Author = {Wu, QX and Mueller, GM and Lutzoni, FM and Huang, YQ and Guo, SY}, Title = {Phylogenetic and biogeographic relationships of eastern Asian and eastern North American disjunct Suillus species (fungi) as inferred from nuclear ribosomal RNA ITS sequences.}, Journal = {Molecular phylogenetics and evolution}, Volume = {17}, Number = {1}, Pages = {37-47}, Year = {2000}, Month = {October}, ISSN = {1055-7903}, url = {http://dx.doi.org/10.1006/mpev.2000.0812}, Abstract = {Species of Suillus produce fleshy, pored mushrooms. They are important symbiotic (ectomycorrhizal) partners of many coniferous trees. The genus includes several putative eastern Asian and eastern North American disjunct species, i.e., the S. americanus-S. sibiricus and S. decipiens-S. spraguei complexes. Phylogenetic relationships among the groups were determined to further understand the biogeographic pattern. Analyses were based on 40 sequences of the ITS region of the nuclear ribosomal RNA tandem repeats, representing 18 distinct species/populations. Our phylogenetic analyses suggested that: (1) Chinese and United States' (U.S.) S. spraguei plus S. decipiens form a strongly supported monophyletic group, with North American S. decipiens and Chinese S. spraguei being sister taxa; (2) S. americanus, Asian and U.S. S. sibiricus, plus S. umbonatus form a clade supported by a high bootstrap value; and (3) little ITS sequence divergence exists within the latter group compared to the S. decipiens-S. spraguei clade. Phylogenetic patterns revealed by this study imply a close phylogenetic relationship between eastern Asian and eastern North American disjunct population/species of Suillus. These fungi display relatively high host fidelity (at least to the host subgenus level), suggesting potential coevolutionary/comigratory trends.}, Doi = {10.1006/mpev.2000.0812}, Key = {fds228874} } @article{fds228875, Author = {Moncalvo, JM and Lutzoni, FM and Rehner, SA and Johnson, J and Vilgalys, R}, Title = {Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.}, Journal = {Systematic biology}, Volume = {49}, Number = {2}, Pages = {278-305}, Year = {2000}, Month = {June}, ISSN = {1063-5157}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12118409}, Abstract = {Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.}, Doi = {10.1093/sysbio/49.2.278}, Key = {fds228875} } @article{fds228873, Author = {Miadlikowska, J and Lutzoni, F}, Title = {Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA data}, Journal = {International Journal of Plant Sciences}, Volume = {161}, Number = {6}, Pages = {925-958}, Publisher = {University of Chicago Press}, Year = {2000}, Month = {January}, url = {http://dx.doi.org/10.1086/317568}, Abstract = {Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi- and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra- and inter-specific levels is present in this genus. Compared to many other genera of macrolichens: its taxonomy, including chemotaxonomy, still remains poorly understood. Existing infrageneric classifications of Peltigera are almost exclusively based on photobiont composition of the thallus. These classifications assumed that bi- and trimembered taxa were distinct monophyletic entities. The genus Peltigera has never been the focus of a comprehensive phylogenetic study. The most recent and widely accepted subdivision of the genus into seven groups is based mainly on morphological and chemical characters. Relationships among species of Peltigera are investigated here using chemical, morphological, and large subunit nuclear ribosomal DNA (LSU nrDNA) data. We test the monophyly of these seven morpho-chemical Peltigera groups and propose a classification based on a phylogenetic approach. Data sets of 42 chemical characters (terpenoids), 31 morphological characters, and 1135 LSU nrDNA characters for 96 samples representing 38 Peltigera species, eight undescribed putative Peltigera species, and nine species from seven potentially closely related genera from Peltigerineae were subjected to maximum parsimony analyses. Morphological, chemical, and molecular analyses were carried out independently and on a combined data set. Monophyly of Peltigera, including Hydrothyria, was confirmed. The genus Hydrothyria is transferred to Peltigera and a new combination Peltigera hydrothyria Miadlikowska and Lutzoni is proposed. Eight monophyletic sections within the genus Peltigera, with high bootstrap support, are circumscribed: sections Peltigera, Polydactylon Miadlikowska and Lutzoni, Chloropeltigera Gyeln., Peltidea (Ach.) Vain., Horizontales Miadlikowska and Lutzoni, Retifoveatae Miadlikowska and Lutzoni, Phlebia Wallr., and Hydrothyriae Miadlikowska and Lutzoni. Unequivocal morphological and chemical synapomorphies for all sections except section Peltidea are recognized and presented. A key for identification of the sections is provided. In addition, a key based on four main terpenoids for determination of the chemotypes and species within section Polydactylon is included. Five terpenoids (50-54) identified on thin-layer chromatography plates for P. elisabethae and P. horizontalis chemotype I are added to the list of substances found in Peltigera. Five chemotypes, mainly from Poland and Norway, are reported from Peltigera thalli for the first time: P. malacea chemotype V, P. leucophlebia chemotype II, P. hymenina chemotypes II and III, and P. collina chemotype IV. Three main types of vein structure in Peltigera were recognized based on SEM studies.}, Doi = {10.1086/317568}, Key = {fds228873} } @article{fds228774, Author = {Zoller, S and Lutzoni, F and Scheidegger, C}, Title = {Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation.}, Journal = {Molecular ecology}, Volume = {8}, Number = {12}, Pages = {2049-2059}, Year = {1999}, Month = {December}, ISSN = {0962-1083}, url = {http://dx.doi.org/10.1046/j.1365-294x.1999.00820.x}, Abstract = {The foliose epiphytic lichen Lobaria pulmonaria has suffered a significant decline in European lowlands during the last decades and therefore is considered as endangered throughout Europe. An assessment of the genetic variability is necessary to formulate biologically sound conservation recommendations for this species. We investigated the genetic diversity of the fungal symbiont of L. pulmonaria using 143 specimens sampled from six populations (two small, one medium, three large) in the lowland, the Jura Mountains, the pre-Alps and the Alps of Switzerland. Among all nuclear and mitochondrial regions sequenced for this study, variability was found only in the internal transcribed spacer (ITS I), with three polymorphic sites, and in the nuclear ribosomal large subunit (nrLSU), with four polymorphic sites. The variable sites in the nrLSU are all located within a putative spliceosomal intron. We sequenced these two regions for 81 specimens and detected six genotypes. Two genotypes were common, two were found only in the more diverse populations and two were found only in one population each. There was no correlation between population size and genetic diversity. The highest genetic diversity was found in populations where the fungal symbiont is reproducing sexually. Populations with low genetic diversity included only the two same common genotypes. Our study provides evidence suggesting that L. pulmonaria is self-incompatible and heterothallic. Based on our results we give populations with sexually reproducing individuals a higher rank in terms of conservation priority than strictly asexual populations. The remaining lowland populations are so small, that one single catastrophic event such as a windthrow might destroy the entire population. Hence we suggest augmenting such populations in size and genetic diversity using small thallus fragments or vegetative diaspores collected in other populations. As we did not detect any locally adapted genotypes, these transplants can be taken from any other genetically diverse population in Switzerland.}, Doi = {10.1046/j.1365-294x.1999.00820.x}, Key = {fds228774} } @article{fds228855, Author = {Lutzoni, F and Barker, FK}, Title = {Sampling confidence envelopes of phylogenetic trees for combinability testing: a reply to Rodrigo.}, Journal = {Systematic biology}, Volume = {48}, Number = {3}, Pages = {596-603}, Year = {1999}, Month = {September}, url = {http://dx.doi.org/10.1080/106351599260166}, Doi = {10.1080/106351599260166}, Key = {fds228855} } @article{fds228854, Author = {Fernández, FA and Lutzoni, FM and Huhndorf, SM}, Title = {Teleomorph-anamorph connections: The new pyrenomycetous genus Carpoligna and its Pleurothecium anamorph}, Journal = {Mycologia}, Volume = {91}, Number = {2}, Pages = {251-262}, Publisher = {JSTOR}, Year = {1999}, Month = {January}, url = {http://dx.doi.org/10.2307/3761370}, Abstract = {Several collections of a pyrenomycete identified as Chaetosphaeria were made from decorticated wood of twigs and branches in Costa Rica, Panama, Puerto Rico and continental USA. Discrete and continuous characters of the ascomata, asci and ascospores in these collections show that they are very similar morphologically and represent populations of the same species. However, culturing of single ascospore isolates from these collections yielded an anamorph unlike the typical phialidic anamorphs of Chaetosphaeria. This anamorph fits the description of Pleurothecium recurvatum, for which a teleomorph connection has not been yet established. Sequences of the ITS region of the nuclear ribosomal DNA of three collections from Costa Rica, Puerto Rico and USA were compared and found to be 98% similar. Parsimony and maximum likelihood analyses of sequences of the large subunit nuclear-encoded ribosomal DNA from representative taxa of eight ascomycetous orders show this ascomycete as a monophyletic group distinct from Chaetosphaeria. Statistical analyses of hypothetical trees based on the most parsimonious and the most likely trees rule out phylogenetic affinities of this pyrenomycete to Chaetosphaeria. These analyses suggest possible affinities to the Hypocreales and/or the Microascales. Based on morphology of the anamorph and analyses of ribosomal DNA sequence data, Carpoligna pleurothecii gen. et sp. nov. are described. The implications of the phylogenetic relationships of Carpoligna in the practical identification of morphologically similar pyrenomycetes are discussed.}, Doi = {10.2307/3761370}, Key = {fds228854} } @book{fds20844, Author = {Kranner, I. and Lutzoni, F.}, Title = {Evolutionary consequences of transition to a lichen symbiotic state and physiological adaptation to oxidative damage associated with poikilohydry}, Pages = {591-698}, Booktitle = {Plant response to environmental stresses: From phytohormones to genome reorganization.}, Publisher = {Marcel Dekker, New York}, Editor = {H. R. Lerner}, Year = {1999}, Key = {fds20844} } @article{fds31593, Author = {Lutzoni, F. [Review] Stefan Ekman in Opera Botanica 127 and 148 pp., 1996.}, Title = {The corticolous and lignicolous species of Bacidia and Bacidina in North America}, Journal = {The Bryologist}, Volume = {102}, Pages = {165-166}, Year = {1999}, Key = {fds31593} } @article{fds228856, Author = {Zoller, S and Lutzoni, F and Scheidegger, C}, Title = {Genetic variability within and among populations of the threatened foliose lichen Lobaria pulmonaria (L.)}, Journal = {Molecular Ecology}, Volume = {8}, Pages = {2049-2060}, Publisher = {Hoffm. in Switzerland.}, Year = {1999}, Key = {fds228856} } @article{fds228853, Author = {Lutzoni, F and Pagel, M}, Title = {Accelerated evolution as a consequence of transitions to mutualism.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {94}, Number = {21}, Pages = {11422-11427}, Year = {1997}, Month = {October}, ISSN = {0027-8424}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11038586}, Abstract = {Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.}, Doi = {10.1073/pnas.94.21.11422}, Key = {fds228853} } @article{fds228852, Author = {Lutzoni, FM}, Title = {Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets.}, Journal = {Systematic biology}, Volume = {46}, Number = {3}, Pages = {373-406}, Year = {1997}, Month = {September}, ISSN = {1063-5157}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11975328}, Abstract = {As an initial step toward developing a model system to study requirements for and consequences of transitions to mutualism, the phylogeny of a group of closely related lichenized and nonlichenized basidiomycetes (Omphalina) was reconstructed. The phylogenetic analyses are based on four data sets representing different regions of the nuclear ribosomal repeat unit (ITS1, 5.8S, ITS2, and 25S) obtained from 30 species of Omphalina and related genera. The resulting phylogenetic trees from each of these four data sets, when analyzed separately, were not identical. Testing for the combinability of these four data sets suggested that they could not be combined in their entirety. The removal of ambiguous alignments and saturated sites was sufficient, after reapplying the combinability test on the pruned data sets, to explain the topological discrepancies. In this process, the first of two complementary tests developed by Rodrigo et al. (1993, N.Z. J. Bot. 31:257-268) to assess whether two data sets are the result of the same phylogenetic history was found to be biased, rejecting the combinability of two data sets even when they are samples of the same phylogenetic history. Combining the four pruned data sets yielded phylogenies that suggest the five lichen-forming species of Omphalina form a monophyletic group. The sister group to this symbiotic clade consists mostly of dark brown Omphalina species intermixed with species from the genera Arrhenia and Phaeothellus. The genera Omphalina and Gerronema are shown to be polyphyletic. The lichen-forming species O. ericetorum and the nonmutualistic species O. velutipes, O. epichysium, and O. sphagnicola are the best candidates for experimental work designed to gain a better understanding of mechanisms involved in symbiotic interactions and the role symbiosis has played in the evolution of fungi.}, Doi = {10.1093/sysbio/46.3.373}, Key = {fds228852} } @misc{fds300052, Author = {Lutzoni, F and Vilgalys, R}, Title = {Integration of morphological and molecular data sets in estimating fungal phytogenies}, Journal = {Canadian Journal of Botany}, Volume = {73}, Number = {S1}, Pages = {649-659}, Publisher = {Canadian Science Publishing}, Year = {1995}, Month = {December}, ISSN = {0008-4026}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1995TC46300001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {<jats:p> To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA. </jats:p>}, Doi = {10.1139/b95-307}, Key = {fds300052} } @article{fds228850, Author = {Lutzoni, FM and Brodo, IM}, Title = {A generic redelimitation of the Ionaspis-Hymenelia complex (lichenized ascomycotina)}, Journal = {Systematic Botany}, Volume = {20}, Number = {3}, Pages = {224-258}, Publisher = {JSTOR}, Year = {1995}, Month = {January}, url = {http://dx.doi.org/10.2307/2419494}, Doi = {10.2307/2419494}, Key = {fds228850} } @article{fds228845, Author = {Lutzoni, F and Vilgalys, R}, Title = {ntegration of morphological and molecular datasets in estimating fungal phylogenies}, Journal = {Canadian Journal of Botany}, Volume = {73(Suppl. 1)}, Pages = {S649-S659}, Year = {1995}, Key = {fds228845} } @article{fds228851, Author = {Lutzoni, F and Vilgalys, R}, Title = {Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichenized fungi}, Journal = {Special Issue of Cryptogamic Botany}, Volume = {5}, Pages = {82-97}, Year = {1995}, Key = {fds228851} } @article{fds228848, Author = {Lutzoni, FM and Brodo, IM}, Title = {Proposal to conserve the name Gyalecta suaveolens Fr. (lichenized Ascomycota) with a conserved type}, Journal = {Taxon}, Volume = {43}, Number = {4}, Pages = {657-659}, Year = {1994}, Month = {January}, url = {http://dx.doi.org/10.2307/1223556}, Doi = {10.2307/1223556}, Key = {fds228848} } @article{fds228849, Author = {Lutzoni, FM}, Title = {Ionaspis alba (Ascomycotina, Hymeneliaceae), a new lichen species from eastern North America}, Journal = {Bryologist}, Volume = {97}, Number = {4}, Pages = {393-395}, Publisher = {JSTOR}, Year = {1994}, Month = {January}, url = {http://dx.doi.org/10.2307/3243904}, Doi = {10.2307/3243904}, Key = {fds228849} } @article{fds228847, Author = {Grandtner, MM and Lutzoni, F}, Title = {References on the vegetation of Québec}, Journal = {Excerpta Botanica Sec. B. Bd}, Volume = {29}, Number = {1}, Pages = {1-24}, Year = {1991}, Key = {fds228847} } @article{fds304272, Author = {Sirois, L and Lutzoni, F and Grandtner, MM}, Title = {Lichens on serpentine and amphibolite on the plateau of Mt. Albert, Gaspesie, Quebec}, Journal = {Canadian Journal of Botany}, Volume = {66}, Number = {5}, Pages = {851-862}, Publisher = {Canadian Science Publishing}, Year = {1988}, Month = {January}, url = {http://dx.doi.org/10.1139/b88-124}, Abstract = {At Mount Albert, many taxa are found exclusively on either serpentine or amphibolite contiguous formations, and are exclusively more noticeable within saxicolous lichens. There are more infrequent taxa on serpentine than on amphibolite. The saxicolous, muscicolous, and terricolous lichen flora and the lichenicolous fungi of the plateau include 202 taxa, most of which have an arctic affinity. Of these taxa, 36 are recorded for the first time in Quebec, 16 in Canada and 11 in North America. -from English summary}, Doi = {10.1139/b88-124}, Key = {fds304272} } @article{fds228846, Author = {Sirois, L and Lutzoni, F and Grandtner, MM}, Title = {Les lichens sur serpentine et amphibolite du plateau du mont Albert, Gaspésie, Québec}, Journal = {Canadian Journal of Botany}, Volume = {66}, Number = {5}, Pages = {851-862}, Year = {1988}, Abstract = {At Mount Albert, many taxa are found exclusively on either serpentine or amphibolite contiguous formations, and are exclusively more noticeable within saxicolous lichens. There are more infrequent taxa on serpentine than on amphibolite. The saxicolous, muscicolous, and terricolous lichen flora and the lichenicolous fungi of the plateau include 202 taxa, most of which have an arctic affinity. Of these taxa, 36 are recorded for the first time in Quebec, 16 in Canada and 11 in North America. -from English summary}, Key = {fds228846} } %% Miadlikowska, Jolanta M. @article{fds376709, Author = {U'Ren, JM and Oita, S and Lutzoni, F and Miadlikowska, J and Ball, B and Carbone, I and May, G and Zimmerman, NB and Valle, D and Trouet, V and Arnold, AE}, Title = {Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth's largest terrestrial biome.}, Journal = {Current biology : CB}, Volume = {34}, Number = {5}, Pages = {1148-1156.e7}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1016/j.cub.2024.01.063}, Abstract = {Understanding how symbiotic associations differ across environmental gradients is key to predicting the fate of symbioses as environments change, and it is vital for detecting global reservoirs of symbiont biodiversity in a changing world.<sup>1</sup><sup>,</sup><sup>2</sup><sup>,</sup><sup>3</sup> However, sampling of symbiotic partners at the full-biome scale is difficult and rare. As Earth's largest terrestrial biome, boreal forests influence carbon dynamics and climate regulation at a planetary scale. Plants and lichens in this biome host the highest known phylogenetic diversity of fungal endophytes, which occur within healthy photosynthetic tissues and can influence hosts' resilience to stress.<sup>4</sup><sup>,</sup><sup>5</sup> We examined how communities of endophytes are structured across the climate gradient of the boreal biome, focusing on the dominant plant and lichen species occurring across the entire south-to-north span of the boreal zone in eastern North America. Although often invoked for understanding the distribution of biodiversity, neither a latitudinal gradient nor mid-domain effect<sup>5</sup><sup>,</sup><sup>6</sup><sup>,</sup><sup>7</sup> can explain variation in endophyte diversity at this trans-biome scale. Instead, analyses considering shifts in forest characteristics, Picea biomass and age, and nutrients in host tissues from 46° to 58° N reveal strong and distinctive signatures of climate in defining endophyte assemblages in each host lineage. Host breadth of endophytes varies with climate factors, and biodiversity hotspots can be identified at plant-community transitions across the boreal zone at a global scale. Placed against a backdrop of global circumboreal sampling,<sup>4</sup> our study reveals the sensitivity of endophytic fungi, their reservoirs of biodiversity, and their important symbiotic associations, to climate.}, Doi = {10.1016/j.cub.2024.01.063}, Key = {fds376709} } @article{fds375869, Author = {Magain, N and Miadlikowska, J and Goffinet, B and Goward, T and Pardo-De la Hoz, CJ and Jüriado, I and Simon, A and Mercado-Díaz, JA and Barlow, T and Moncada, B and Lücking, R and Spielmann, A and Canez, L and Wang, LS and Nelson, P and Wheeler, T and Lutzoni, F and Sérusiaux, E}, Title = {High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science}, Journal = {Persoonia: Molecular Phylogeny and Evolution of Fungi}, Volume = {51}, Pages = {1-88}, Year = {2023}, Month = {December}, url = {http://dx.doi.org/10.3767/persoonia.2023.51.01}, Abstract = {Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification.}, Doi = {10.3767/persoonia.2023.51.01}, Key = {fds375869} } @article{fds373352, Author = {Miadlikowska, J and Magain, N and Medeiros, ID and Pardo-De La Hoz, CJ and Carbone, I and Lagreca, S and Barlow, T and Myllys, L and Schmull, M and Lutzoni, F}, Title = {Towards a nomenclatural clarification of the Peltigera ponojensis/monticola clade including metagenomic sequencing of type material and the introduction of P. globulata Miadl. & Magain sp. nov.}, Journal = {Lichenologist}, Volume = {55}, Number = {5}, Pages = {315-324}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1017/S0024282923000373}, Abstract = {Peltigera globulata Miadl. & Magain, a new species in the P. ponojensis/monticola species complex of section Peltigera, is formally described. This clade was previously given the interim designation Peltigera sp. 17. It is found in sun-exposed and xeric habitats at high altitudes in Peru and Ecuador. Peltigera globulata can be easily recognized by its irregularly globulated margins covered mostly by thick, white pruina, somewhat resembling the sorediate thallus margins of P. soredians, another South American species from section Peltigera. The hypervariable region of ITS1 (ITS1-HR), which is in general highly variable among species of section Peltigera, does not have diagnostic value for species identification within the P. ponojensis/monticola complex. Nevertheless, no significant level of gene flow was detected among eight lineages representing a clade of putative species (including P. globulata) within this complex. ITS sequences from the holotype specimens of P. monticola Vitik. (collected in 1979) and P. soredians Vitik. (collected in 1981) and lectotype specimens of P. antarctica C. W. Dodge (collected in 1941) and P. aubertii C. W. Dodge (collected in 1952) were successfully obtained through Sanger and Illumina metagenomic sequencing. BLAST results of these sequences revealed that the type specimen of P. monticola falls within the P. monticola/ponojensis 7 clade, which represents P. monticola s. str., and confirmed that the type specimen of P. aubertii falls within a clade identified previously as P. aubertii based on morphology. The ITS sequence from the type specimen of P. soredians, which superficially resembles P. globulata, confirms its placement in the P. rufescens clade. Finally, we discovered that the name P. antarctica was erroneously applied to a lineage in the P. ponojensis/monticola clade. The ITS sequence from the type specimen of P. antarctica represents a lineage within the P. rufescens clade, which is sister to the P. ponojensis/monticola clade.}, Doi = {10.1017/S0024282923000373}, Key = {fds373352} } @article{fds371578, Author = {Pardo-De la Hoz and CJ and Magain, N and Piatkowski, B and Cornet, L and Dal Forno and M and Carbone, I and Miadlikowska, J and Lutzoni, F}, Title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria.}, Journal = {Systematic biology}, Volume = {72}, Number = {3}, Pages = {694-712}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1093/sysbio/syad008}, Abstract = {Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].}, Doi = {10.1093/sysbio/syad008}, Key = {fds371578} } @article{fds365220, Author = {McMullin, RT and Miadlikowska, J}, Title = {Two rare Peltigera species new to the Canadian Arctic, P. islandica and P. lyngei}, Journal = {Plant and Fungal Systematics}, Volume = {67}, Number = {1}, Pages = {17-23}, Year = {2022}, Month = {July}, url = {http://dx.doi.org/10.35535/pfsyst-2022-0002}, Abstract = {Peltigera islandica and P. lyngei are rarely reported lichens. Previously, P. islandica was known from British Columbia, Estonia, and Iceland, and P. lyngei from Amchitka Island (Alaska), Gough Island (South Atlantic), Iceland, Siberia and Svalbard. Both species are reported here for the first time from the Canadian Arctic and from the second localities in North America. Peltigera lyngei is also reported for the first time from Canada. The identities of these species are confirmed morphologically, chemically, and with molecular data. Phylogenetic relationships are inferred using the ITS region. The widespread, but scattered, distribution of both species suggests that they may be underreported throughout their range.}, Doi = {10.35535/pfsyst-2022-0002}, Key = {fds365220} } @article{fds360545, Author = {Franco, MEE and Wisecaver, JH and Arnold, AE and Ju, Y-M and Slot, JC and Ahrendt, S and Moore, LP and Eastman, KE and Scott, K and Konkel, Z and Mondo, SJ and Kuo, A and Hayes, RD and Haridas, S and Andreopoulos, B and Riley, R and LaButti, K and Pangilinan, J and Lipzen, A and Amirebrahimi, M and Yan, J and Adam, C and Keymanesh, K and Ng, V and Louie, K and Northen, T and Drula, E and Henrissat, B and Hsieh, H-M and Youens-Clark, K and Lutzoni, F and Miadlikowska, J and Eastwood, DC and Hamelin, RC and Grigoriev, IV and U'Ren, JM}, Title = {Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes.}, Journal = {The New phytologist}, Volume = {233}, Number = {3}, Pages = {1317-1330}, Year = {2022}, Month = {February}, url = {http://dx.doi.org/10.1111/nph.17873}, Abstract = {Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.}, Doi = {10.1111/nph.17873}, Key = {fds360545} } @article{fds362657, Author = {Pardo-De la Hoz and CJ and Medeiros, ID and Gibert, JP and Chagnon, P-L and Magain, N and Miadlikowska, J and Lutzoni, F}, Title = {Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks.}, Journal = {Ecology and evolution}, Volume = {12}, Number = {3}, Pages = {e8649}, Year = {2022}, Month = {February}, url = {http://dx.doi.org/10.1002/ece3.8649}, Abstract = {Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α-diversity. To calculate the PSS index, we then compare observed partner phylogenetic α-diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host-parasite, avian seed-dispersal, lichenized fungi-cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much-needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss.}, Doi = {10.1002/ece3.8649}, Key = {fds362657} } @article{fds357292, Author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan, DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, EÁ and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni, FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux, J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao, LL and Groenewald, JZ}, Title = {New and Interesting Fungi. 4.}, Journal = {Fungal systematics and evolution}, Volume = {7}, Pages = {255-343}, Year = {2021}, Month = {June}, url = {http://dx.doi.org/10.3114/fuse.2021.07.13}, Abstract = {An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: <i>Superstratomycetales</i> and <i>Superstratomycetaceae</i> (based on <i>Superstratomyces</i> <i>)</i>. New genera: <i>Haudseptoria</i> (based on <i>Haudseptoria typhae</i>); <i>Hogelandia</i> (based on <i>Hogelandia lambearum</i>); <i>Neoscirrhia</i> (based on <i>Neoscirrhia osmundae</i>); <i>Nothoanungitopsis</i> (based on <i>Nothoanungitopsis urophyllae</i>); <i>Nothomicrosphaeropsis</i> (based on <i>Nothomicrosphaeropsis welwitschiae</i>); <i>Populomyces</i> (based on <i>Populomyces zwinianus</i>); <i>Pseudoacrospermum</i> (based on <i>Pseudoacrospermum goniomae</i>). New species: <i>Apiospora sasae</i> on dead culms of <i>Sasa veitchii</i> (Netherlands); <i>Apiospora stipae</i> on dead culms of <i>Stipa gigantea</i> (Spain); <i>Bagadiella eucalyptorum</i> on leaves of <i>Eucalyptus</i> sp. (Australia); <i>Calonectria singaporensis</i> from submerged leaf litter (Singapore); <i>Castanediella neomalaysiana</i> on leaves of <i>Eucalyptus</i> sp. (Malaysia); <i>Colletotrichum pleopeltidis</i> on leaves of <i>Pleopeltis</i> sp. (South Africa); <i>Coniochaeta deborreae</i> from soil (Netherlands); <i>Diaporthe durionigena</i> on branches of <i>Durio zibethinus</i> (Vietnam); <i>Floricola juncicola</i> on dead culm of <i>Juncus</i> sp. (France); <i>Haudseptoria typhae</i> on leaf sheath of <i>Typha</i> sp. (Germany); <i>Hogelandia lambearum</i> from soil (Netherlands); <i>Lomentospora valparaisensis</i> from soil (Chile); <i>Neofusicoccum mystacidii</i> on dead stems of <i>Mystacidium capense</i> (South Africa); <i>Neomycosphaerella guibourtiae</i> on leaves of <i>Guibourtia</i> sp. (Angola); <i>Niesslia neoexosporioides</i> on dead leaves of <i>Carex paniculata</i> (Germany); <i>Nothoanungitopsis urophyllae</i> on seed capsules of <i>Eucalyptus urophylla</i> (South Africa); <i>Nothomicrosphaeropsis welwitschiae</i> on dead leaves of <i>Welwitschia mirabilis</i> (Namibia); <i>Paracremonium bendijkiorum</i> from soil (Netherlands); <i>Paraphoma ledniceana</i> on dead wood of <i>Buxus sempervirens</i> (Czech Republic); <i>Paraphoma salicis</i> on leaves of <i>Salix cf. alba</i> (Ukraine); <i>Parasarocladium wereldwijsianum</i> from soil (Netherlands); <i>Peziza ligni</i> on masonry and plastering (France); <i>Phyllosticta phoenicis</i> on leaves of <i>Phoenix reclinata</i> (South Africa); <i>Plectosphaerella slobbergiarum</i> from soil (Netherlands); <i>Populomyces zwinianus</i> from soil (Netherlands); <i>Pseudoacrospermum goniomae</i> on leaves of <i>Gonioma kamassi</i> (South Africa); <i>Pseudopyricularia festucae</i> on leaves of <i>Festuca californica</i> (USA); <i>Sarocladium sasijaorum</i> from soil (Netherlands); <i>Sporothrix hypoxyli</i> in sporocarp of <i>Hypoxylon petriniae</i> on <i>Fraxinus</i> wood (Netherlands); <i>Superstratomyces albomucosus</i> on <i>Pycnanthus angolensis</i> (Netherlands); <i>Superstratomyces atroviridis</i> on <i>Pinus sylvestris</i> (Netherlands); <i>Superstratomyces flavomucosus</i> on leaf of <i>Hakea multilinearis</i> (Australia); <i>Superstratomyces tardicrescens</i> from human eye specimen (USA); <i>Taeniolella platani</i> on twig of <i>Platanus hispanica</i> (Germany), and <i>Tympanis pini</i> on twigs of <i>Pinus sylvestris</i> (Spain). <b>Citation:</b> Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. <i>Fungal Systematics and Evolution</i> <b>7:</b> 255-343. doi: 10.3114/fuse.2021.07.13.}, Doi = {10.3114/fuse.2021.07.13}, Key = {fds357292} } @article{fds355540, Author = {Oita, S and Ibáñez, A and Lutzoni, F and Miadlikowska, J and Geml, J and Lewis, LA and Hom, EFY and Carbone, I and U'Ren, JM and Arnold, AE}, Title = {Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale.}, Journal = {Communications biology}, Volume = {4}, Number = {1}, Pages = {313}, Year = {2021}, Month = {March}, url = {http://dx.doi.org/10.1038/s42003-021-01826-7}, Abstract = {Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves-fungal endophytes-that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.}, Doi = {10.1038/s42003-021-01826-7}, Key = {fds355540} } @article{fds355689, Author = {Stone, DF and Mccune, B and Pardo-De La Hoz and CJ and Magain, N and Miadlikowska, J}, Title = {Sinuicella denisonii, a new genus and species in the Peltigeraceae from western North America}, Journal = {Lichenologist}, Volume = {53}, Number = {2}, Pages = {185-192}, Year = {2021}, Month = {March}, url = {http://dx.doi.org/10.1017/S0024282920000584}, Abstract = {The new genus Sinuicella, an early successional lichen, was found on bare soil in Oregon, USA. The thallus is minute fruticose, grey to nearly black, branching isotomic dichotomous, branches round, 20-90 μm wide in water mount. The cortex is composed of interlocking cells shaped like jigsaw puzzle pieces. Spores are hyaline, 1-septate, 25-40(-50) × 6.5-9(-11) μm. Maximum likelihood phylogenetic analyses on multilocus data sets, first spanning the entire order Peltigerales and then restricted to Peltigeraceae with extended sampling from Solorina and Peltigera, revealed the placement of Sinuicella outside of currently recognized genera, sister to Peltigera, with high support. Based on the phylogenetic, morphological and ecological distinctness of Sinuicella, we formally introduce a new genus represented by the single species S. denisonii. The cyanobiont of S. denisonii is Nostoc from phylogroup XL, Clade 2, Subclade 3 based on the rbcLX marker.}, Doi = {10.1017/S0024282920000584}, Key = {fds355689} } @article{fds361299, Author = {Medeiros, ID and Mazur, E and Miadlikowska, J and Flakus, A and Rodriguez-Flakus, P and Pardo-De la Hoz and CJ and Cieślak, E and Śliwa, L and Lutzoni, F}, Title = {Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis.}, Journal = {Frontiers in microbiology}, Volume = {12}, Pages = {774839}, Year = {2021}, Month = {January}, url = {http://dx.doi.org/10.3389/fmicb.2021.774839}, Abstract = {Shifts in climate along elevation gradients structure mycobiont-photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (<i>Trebouxia</i> alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, <i>RPB1</i>, <i>RPB2</i>, and <i>MCM7</i>) and two photobiont loci (ITS, <i>rbc</i>L); we designed new primers to amplify Lecanoraceae <i>RPB1</i> and <i>RPB2</i> with a nested PCR approach. Mycobionts belonged to <i>Lecanora</i> s.lat., <i>Bryonora</i>, <i>Myriolecis</i>, <i>Protoparmeliopsis</i>, the "<i>Lecanora</i>" <i>polytropa</i> group, and the "<i>L</i>." saligna group. All of these clades except for <i>Lecanora</i> s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. <i>Trebouxia</i> clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from <i>Trebouxia</i> clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while <i>Trebouxia</i> clades A and S dominate open habitats at high elevation. We did not find <i>Trebouxia</i> clade D. Several putative new species were found in <i>Trebouxia</i> clades A, C, and I. These included one putative species in clade A associated with <i>Myriolecis</i> species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with <i>Lecanora</i> on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with <i>Trebouxia</i> from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and <i>Trebouxia</i> photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of <i>Trebouxia</i> diversity and distribution.}, Doi = {10.3389/fmicb.2021.774839}, Key = {fds361299} } @article{fds357529, Author = {McCune, B and Arup, U and Breuss, O and Di Meglio and E and Di Meglio and J and Esslinger, TL and Miadlikowska, J and Miller, AE and Rosentreter, R and Schultz, M and Sheard, J and Tønsberg, T and Walton, J}, Title = {Biodiversity and ecology of lichens of Kenai Fjords National Park, Alaska}, Journal = {Plant and Fungal Systematics}, Volume = {65}, Number = {2}, Pages = {586-619}, Year = {2020}, Month = {December}, url = {http://dx.doi.org/10.35535/pfsyst-2020-0032}, Abstract = {We inventoried lichens in Kenai Fjords National Park in Alaska, USA We assembled the known information on occurrence and ecology of lichens in this park by combining field, herbarium, and literature studies. Our results provide baseline data on lichen occurrence that may be used in resource condition assessments, vulnerability assessments, long-term ecological monitoring, and resource management. We report a total of 616 taxa of lichenized fungi from the Park, plus an additional five subspecies and three varieties, all of which are new additions to the National Park Service database for this park unit. An additional five species of nonlichenized lichenicolous fungi are reported here. Eight non-lichenized fungi that are traditionally treated with lichens are also included, most of these associated with bark of particular host species. Four taxa new to North America are reported here (Arctomia delicatula var. acutior, Aspicilia dudinensis, Myriospora myochroa, and Ochrolechia bahusiensis), along with 44 species new to Alaska. Numerous species have been confirmed using ITS barcoding sequences. Also several records assigned to the genus level are reported, many of those are likely new species.}, Doi = {10.35535/pfsyst-2020-0032}, Key = {fds357529} } @article{fds357530, Author = {Miadlikowska, J and Magain, N and Buck, WR and Castillo, RV and Barlow, GT and Pardo-De la Hoz and CJ and LaGreca, S and Lutzoni, F}, Title = {Peltigera hydrophila (Lecanoromycetes, Ascomycota), a new semi-aquatic cyanolichen species from Chile}, Journal = {Plant and Fungal Systematics}, Volume = {65}, Number = {1}, Pages = {210-218}, Year = {2020}, Month = {June}, url = {http://dx.doi.org/10.35535/pfsyst-2020-0016}, Abstract = {Peltigera hydrophila, a new species from Chile tentatively distinguished based on phylogenetic evidence but not yet named, is formally described here. Morphological differences (e.g., non-tomentose thallus) and habitat preferences (semi-aquatic) corroborate molecular and phylogenetic distinctiveness of this early diverging lineage in section Peltigera. Due to overlapping ecological ranges, P. hydrophila shares some morphological traits with aquatic species from the phylogenetically unrelated section Hydrothyriae.}, Doi = {10.35535/pfsyst-2020-0016}, Key = {fds357530} } @article{fds357531, Author = {Magain, N and Goffinet, B and Simon, A and Seelan, JSS and Medeiros, ID and Lutzoni, F and Miadlikowska, J}, Title = {Peltigera serusiauxii (Lecanoromycetes, Ascomycota), a new species from Papua New Guinea and Malaysia}, Journal = {Plant and Fungal Systematics}, Volume = {65}, Number = {1}, Pages = {139-146}, Year = {2020}, Month = {June}, url = {http://dx.doi.org/10.35535/pfsyst-2020-0009}, Abstract = {Peltigera serusiauxii is proposed here as a new species from Papua New Guinea and Sabah, northern Borneo (Malaysia). The species belongs to the polydactyloid clade of section Polydactylon. Because of its large thalli with a glabrous upper surface, this species was previously identified as P. dolichorhiza, but it differs by its polydactylon-type lower surface and the high amount of dolichorrhizin. It appears to be a strict specialist in its association with Nostoc phylogroup IX throughout its known distribution. This is one of many undescribed species remaining to be formally described within the genus Peltigera, especially in Asia and Australasia.}, Doi = {10.35535/pfsyst-2020-0009}, Key = {fds357531} } @article{fds348830, Author = {Magain, N and Spribille, T and Dimeglio, J and Nelson, PR and Miadlikowska, J and Sérusiaux, E}, Title = {Phylogenetic evidence for an expanded circumscription of Gabura (Arctomiaceae)}, Journal = {Lichenologist}, Volume = {52}, Number = {1}, Pages = {3-15}, Year = {2020}, Month = {January}, url = {http://dx.doi.org/10.1017/S0024282919000471}, Abstract = {Since the advent of molecular taxonomy, numerous lichen-forming fungi with homoiomerous thalli initially classified in the family Collemataceae Zenker have been transferred to other families, highlighting the extent of morphological convergence within Lecanoromycetes O. E. Erikss. & Winka. While the higher level classification of these fungi might be clarified by such transfers, numerous specific and generic classifications remain to be addressed. We examined the relationships within the broadly circumscribed genus Arctomia Th. Fr., which has been the recipient of several transfers from Collemataceae. We demonstrated that Arctomia insignis (P. M. Jorg. & Tonsberg) Ertz does not belong to Arctomia s. str. but forms a strong monophyletic group with Gabura fascicularis (L.) P. M. Jorg. We also confirmed that Arctomia borbonica Magain & Sérus. and the closely related Arctomia insignis represent two species. We formally transferred A. insignis and A. borbonica to the genus Gabura Adans. and introduced two new combinations: Gabura insignis and Gabura borbonica. We reported Gabura insignis from Europe (Scotland and Ireland) for the first time. While material from Europe and North America is genetically almost identical, specimens from Madagascar, South Africa and Reunion Island belong to three distinct phylogenetic lineages, all of which are present in the latter area and may represent distinct species. In its current circumscription, the genus Gabura may contain up to six species, whereas Arctomia s. str. includes only two species (A. delicatula Th. Fr. and A. teretiuscula P. M. Jorg.). The Gabura insignis group is shown to have an unexpectedly large, subcosmopolitan distribution. With the extended sampling from Arctomiaceae Th. Fr., the placement of Steinera sorediata P. James & Henssen in the genus Steinera Zahlbr. is confirmed and the presence of a new Steinera species from Chile is highlighted.}, Doi = {10.1017/S0024282919000471}, Key = {fds348830} } @article{fds366475, Author = {Flakus, A and Etayo, J and Miadlikowska, J and Lutzoni, F and Kukwa, M and Matura, N and Rodriguez-Flakus, P}, Title = {Biodiversity assessment of ascomycetes inhabiting Lobariella lichens in Andean cloud forests led to one new family, three new genera and 13 new species of lichenicolous fungi}, Journal = {Plant and Fungal Systematics}, Volume = {64}, Number = {2}, Pages = {283-344}, Year = {2019}, Month = {December}, url = {http://dx.doi.org/10.2478/pfs-2019-0022}, Abstract = {Neotropical mountain forests are characterized by having hyperdiverse and unusual fungi inhabiting lichens. The great majority of these lichenicolous fungi (i.e., detectable by light microscopy) remain undescribed and their phylogenetic relationships are mostly unknown. This study focuses on lichenicolous fungi inhabiting the genus Lobariella (Peltigerales), one of the most important lichen hosts in the Andean cloud forests. Based on molecular and morphological data, three new genera are introduced: Lawreyella gen. nov. (Cordieritidaceae, for Unguiculariopsis lobariella), Neobaryopsis gen. nov. (Cordycipitaceae), and Pseudodidymocyrtis gen. nov. (Didymosphaeriaceae). Nine additional new species are described (Abrothallus subhalei sp. nov., Atronectria lobariellae sp. nov., Corticifraga microspora sp. nov., Epithamnolia rugosopycnidiata sp. nov., Lichenotubeufia cryptica sp. nov., Neobaryopsis andensis sp. nov., Pseudodidymocyrtis lobariellae sp. nov., Rhagadostomella hypolobariella sp. nov., and Xylaria lichenicola sp. nov.). Phylogenetic placements of 13 lichenicolous species are reported here for Abrothallus, Arthonia, Globonectria, Lawreyella, Monodictys, Neobaryopsis, Pseudodidymocyrtis, Sclerococcum, Trichonectria and Xylaria. The name Sclerococcum ricasoliae comb. nov. is reestablished for the neotropical populations formerly named S. lobariellum (Sclerococcales). A key to sexual and asexual states of 40 species of lobariellicolous ascomycetous fungi is provided. Teleomorph-anamorph connections were established for several species using molecular methods and/or visual observations in nature. Additionally, we found that the anamorphic species Cornutispora ophiurospora inhabiting Lobariella was often accompanied by ascomata of Spirographa. Results of phylogenetic analyses, including newly generated sequences of several Cornutispora and Spirographa species inhabiting various host lichens, support the conclusion that Cornutispora is a synonym of Spirographa. Our Maximum Likelihood inference based on multiple loci show that all studied Spirographa (including Cornutispora) belong to a new lineage within Ostropales. Based on these highly supported phylogenetic placements and the distinct character states of their conidiomata, in comparison with other Lecanoromycetes, a new family is proposed - Spirographaceae fam. nov. This new lineage includes broadly distributed mycoparasites, inhabiting various lichen and fungal hosts, and representing an early diversification event preceding the lichen-forming clade of Fissurinaceae, Gomphillaceae and Graphidaceae. Two lichenicolous species, Asteroglobulus giselae and Pleoscutula arsenii, were found to be nested within the Spirographa clade, and their teleomorph-anamorph connections were confirmed based on genotypic and phenotypic data. This phylogenetic result is corroborated by their highly similar ascomata anatomy. Together these results strongly indicate that both species are congeneric with Spirographa. As a result, four new species (S. aggregata sp. nov., S. galligena sp. nov., S. maroneae sp. nov., and S. parmotrematis sp. nov.) and 15 new combinations are proposed (Spirographa ascaridiella comb. nov., S. arsenii comb. nov., S. ciliata comb. nov., S. giselae comb. nov., S. herteliana comb. nov., S. hypotrachynae comb. nov., S. intermedia comb. nov., S. lichenicola comb. nov., S. limaciformis comb. nov., S. ophiurospora comb. nov., S. pittii comb. nov., S. pyramidalis comb. nov., S. triangularis comb. nov., S. tricupulata comb. nov., and S. vermiformis comb. nov.). Species of the genus Spirographa, as outlined here, are strongly host-specific, mainly at the generic level of their host. Some host genera can harbour more than one Spirographa species.}, Doi = {10.2478/pfs-2019-0022}, Key = {fds366475} } @article{fds346584, Author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Zimmerman, NB and Carbone, I and May, G and Arnold, AE}, Title = {Host availability drives distributions of fungal endophytes in the imperilled boreal realm.}, Journal = {Nature ecology & evolution}, Volume = {3}, Number = {10}, Pages = {1430-1437}, Year = {2019}, Month = {October}, url = {http://dx.doi.org/10.1038/s41559-019-0975-2}, Abstract = {Boreal forests represent the world's largest terrestrial biome and provide ecosystem services of global importance. Highly imperilled by climate change, these forests host Earth's greatest phylogenetic diversity of endophytes, a hyperdiverse group of symbionts that are defined by their occurrence within living, symptomless plant and lichen tissues. Endophytes shape the ecological and evolutionary trajectories of plants and are therefore key to the function and resilience of terrestrial ecosystems. A critical step in linking the ecological functions of endophytes with those of their hosts is to understand the distributions of these symbionts at the global scale; however, turnover in host taxa with geography and climate can confound insights into endophyte biogeography. As a result, global drivers of endophyte diversity and distributions are not known. Here, we leverage sampling from phylogenetically diverse boreal plants and lichens across North America and Eurasia to show that host filtering in distinctive environments, rather than turnover with geographical or environmental distance, is the main determinant of the community composition and diversity of endophytes. We reveal the distinctiveness of boreal endophytes relative to soil fungi worldwide and endophytes from diverse temperate biomes, highlighting a high degree of global endemism. Overall, the distributions of endophytes are directly linked to the availability of compatible hosts, highlighting the role of biotic interactions in shaping fungal communities across large spatial scales, and the threat that climate change poses to biological diversity and function in the imperilled boreal realm.}, Doi = {10.1038/s41559-019-0975-2}, Key = {fds346584} } @article{fds344599, Author = {Chagnon, PL and Magain, N and Miadlikowska, J and Lutzoni, F}, Title = {Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera}, Journal = {Journal of Ecology}, Volume = {107}, Number = {4}, Pages = {1645-1661}, Year = {2019}, Month = {July}, url = {http://dx.doi.org/10.1111/1365-2745.13207}, Abstract = {Ecological interactions range from purely specialized to extremely generalized in nature. Recent research has showed very high levels of specialization in the cyanolichens involving Peltigera (mycobionts) and their Nostoc photosynthetic partners (cyanobionts). Yet, little is known about the mechanisms contributing to the establishment and maintenance of such high specialization levels. Here, we characterized interactions between Peltigera and Nostoc partners at a global scale, using more than one thousand thalli. We used tools from network theory, community phylogenetics and biogeographical history reconstruction to evaluate how these symbiotic interactions may have evolved. After splitting the interaction matrix into modules of preferentially interacting partners, we evaluated how module membership might have evolved along the mycobionts’ phylogeny. We also teased apart the contributions of geographical overlap vs phylogeny in driving interaction establishment between Peltigera and Nostoc taxa. Module affiliation rarely evolves through the splitting of large ancestral modules. Instead, new modules appear to emerge independently, which is often associated with a fungal speciation event. We also found strong phylogenetic signal in these interactions, which suggests that partner switching is constrained by conserved traits. Therefore, it seems that a high rate of fungal diversification following a switch to a new cyanobiont can lead to the formation of large modules, with cyanobionts associating with multiple closely retated Peltigera species. Finally, when restricting our analyses to Peltigera sister species, the latter differed more through partner acquisition/loss than replacement (i.e., switching). This pattern vanishes as we look at sister species that have diverged longer ago. This suggests that fungal speciation may be accompanied by a stepwise process of (a) novel partner acquisition and (b) loss of the ancestral partner. This could explain the maintenance of high specialization levels in this symbiotic system where the transmission of the cyanobiont to the next generation is assumed to be predominantly horizontal. Synthesis. Overall, our study suggests that oscillation between generalization and ancestral partner loss may maintain high specialization within the lichen genus Peltigera, and that partner selection is not only driven by partners’ geographical overlap, but also by their phylogenetically conserved traits.}, Doi = {10.1111/1365-2745.13207}, Key = {fds344599} } @article{fds345378, Author = {Carbone, I and White, JB and Miadlikowska, J and Arnold, AE and Miller, MA and Magain, N and U'Ren, JM and Lutzoni, F}, Title = {T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.}, Journal = {Microbiology resource announcements}, Volume = {8}, Number = {29}, Pages = {e00328-e00319}, Year = {2019}, Month = {July}, url = {http://dx.doi.org/10.1128/mra.00328-19}, Abstract = {The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.}, Doi = {10.1128/mra.00328-19}, Key = {fds345378} } @article{fds340996, Author = {Miadlikowska, J and Magain, N and Pardo-De La Hoz and CJ and Niu, D and Goward, T and Sérusiaux, E and Lutzoni, F}, Title = {Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision}, Journal = {Plant and Fungal Systematics}, Volume = {63}, Number = {2}, Pages = {45-64}, Year = {2018}, Month = {December}, url = {http://dx.doi.org/10.2478/pfs-2018-0007}, Abstract = {Closely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.}, Doi = {10.2478/pfs-2018-0007}, Key = {fds340996} } @article{fds340628, Author = {Lutzoni, F and Nowak, MD and Alfaro, ME and Reeb, V and Miadlikowska, J and Krug, M and Arnold, AE and Lewis, LA and Swofford, DL and Hibbett, D and Hilu, K and James, TY and Quandt, D and Magallón, S}, Title = {Contemporaneous radiations of fungi and plants linked to symbiosis.}, Journal = {Nature communications}, Volume = {9}, Number = {1}, Pages = {5451}, Year = {2018}, Month = {December}, url = {http://dx.doi.org/10.1038/s41467-018-07849-9}, Abstract = {Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous.}, Doi = {10.1038/s41467-018-07849-9}, Key = {fds340628} } @article{fds339811, Author = {Hoz, CJPDL and Magain, N and Lutzoni, F and Goward, T and Restrepo, S and Miadlikowska, J}, Title = {Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera}, Journal = {Frontiers in Microbiology}, Volume = {9}, Number = {NOV}, Publisher = {FRONTIERS MEDIA SA}, Year = {2018}, Month = {November}, url = {http://dx.doi.org/10.3389/fmicb.2018.02770}, Abstract = {Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.}, Doi = {10.3389/fmicb.2018.02770}, Key = {fds339811} } @article{fds339620, Author = {Magain, N and Truong, C and Goward, T and Niu, D and Goffinet, B and Sérusiaux, E and Vitikainen, O and Lutzoni, F and Miadlikowska, J}, Title = {Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in peltigera section peltigera (Lichenized ascomycota: Lecanoromycetes)}, Journal = {Taxon}, Volume = {67}, Number = {5}, Pages = {836-870}, Publisher = {WILEY}, Year = {2018}, Month = {October}, url = {http://dx.doi.org/10.12705/675.3}, Abstract = {This comprehensive phylogenetic revision of sections Peltigera and Retifoveatae of the cyanolichen genus Peltigera is based on DNA sequences from more than 500 specimens from five continents. We amplified five loci (nrITS, β-tubulin and three intergenic spacers part of colinear orthologous regions [COR]) for the mycobiont, and the rbcLX locus for the cyanobacterial partner Nostoc. Phylogenetic inferences (RAxML, BEAST) and species delimitation methods (bGMYC, bPTP, bPP) suggest the presence of 88 species in section Peltigera, including 50 species new to science, hence uncovering a surprisingly high proportion of previously unnoticed biodiversity. The hypervariable region in ITS1 (ITS1-HR) is a powerful marker to identify species within sections Peltigera and Retifoveatae. Most newly delimited species are restricted to a single biogeographic region, however, up to ten species have a nearly cosmopolitan distribution. The specificity of mycobionts in their association with Nostoc cyanobionts ranges from strict specialists (associate with only one Nostoc phylogroup) to broad generalists (up to eight Nostoc phylogroups uncovered), with widespread species recruiting a broader selection of Nostoc phylogroups than species with limited distributions. In contrast, species from the P. didactyla clade characterized by small thalli and asexual vegetative propagules (soredia) associate with fewer Nostoc phylogroups (i.e., are more specialized) despite their broad distributions, and show significantly higher rates of nucleotide substitutions.}, Doi = {10.12705/675.3}, Key = {fds339620} } @article{fds337995, Author = {Lu, J and Magain, N and Miadlikowska, J and Coyle, JR and Truong, C and Lutzoni, F}, Title = {Bioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen-forming genus Peltigera.}, Journal = {American journal of botany}, Volume = {105}, Number = {7}, Pages = {1198-1211}, Year = {2018}, Month = {July}, url = {http://dx.doi.org/10.1002/ajb2.1119}, Abstract = {<h4>Premise of the study</h4>Factors shaping spatiotemporal patterns of associations in mutualistic systems are poorly understood. We used the lichen-forming fungi Peltigera and their cyanobacterial partners Nostoc to investigate the spatial structure of this symbiosis at an intrabiome scale and to identify potential factors shaping these associations.<h4>Methods</h4>Ninety-three thalli were sampled in Québec, Canada, along a south-north and an east-west transect of ~1300 km each. We identified the two main partners (Peltigera species and Nostoc phylogroups) using molecular markers and modeled the effects of environmental variables and partner occurrence on Peltigera-Nostoc distributions.<h4>Key results</h4>Peltigera species showed a high degree of specialization toward cyanobionts, whereas two Nostoc phylogroups dominated both transects by associating with several Peltigera species. Peltigera species had narrower ranges than these two main cyanobionts. Distributions of three Peltigera species were highly associated with precipitation and temperature variables, which was not detected for Nostoc phylogroups at this spatial scale.<h4>Conclusions</h4>For these cyanolichens, factors driving patterns of symbiotic associations are scale dependent. Contrary to global-scale findings, generalist Peltigera species were not more widespread within the boreal biome than specialists. Nostoc availability was not the only driver of Peltigera species' geographic ranges; environmental factors also contributed to their intrabiome distributions. Climatic conditions (especially precipitation) limited the range of some Peltigera species more than the range of their cyanobacterial partners at an intrabiome (boreal) scale.}, Doi = {10.1002/ajb2.1119}, Key = {fds337995} } @article{fds337996, Author = {Chagnon, PL and Magain, N and Miadlikowska, J and Lutzoni, F}, Title = {Strong specificity and network modularity at a very fine phylogenetic scale in the lichen genus Peltigera.}, Journal = {Oecologia}, Volume = {187}, Number = {3}, Pages = {767-782}, Publisher = {Springer Nature}, Year = {2018}, Month = {July}, url = {http://dx.doi.org/10.1007/s00442-018-4159-6}, Abstract = {Identifying the drivers and evolutionary consequences of species interactions is a major goal of community ecology. Network-based analyses can provide mathematical tools to detect non-random patterns of interactions, and potentially help predicting the consequences of such patterns on evolutionary dynamics of symbiotic systems. Here, we characterize the structure of a lichen network at a very fine phylogenetic scale, by identifying the photosynthetic partners (i.e., cyanobacteria of the genus Nostoc) of lichenized fungi belonging to a monophyletic section of a single genus (i.e., section Polydactylon of the genus Peltigera), worldwide. Even at such a fine phylogenetic scale, we found that interactions were highly modular and anti-nested, indicating strong preferences in interactions. When considering local Peltigera communities, i.e., datasets at small spatial scales with only a slightly broader phylogenetic range, interactions remained modular but were asymmetric, with generalist Nostoc partners interacting with specialized Peltigera species. This asymmetry was not detected with our global spatial scale dataset. We discuss these results in the light of lichen community assembly, and explore how such interaction patterns may influence coevolution in lichens and the evolutionary stability of the mutualism in general.}, Doi = {10.1007/s00442-018-4159-6}, Key = {fds337996} } @article{fds352215, Author = {McCune, B and Arup, U and Breuss, O and Di Meglio and ED and Di Meglio and JD and Esslinger, TL and Magain, N and Miadlikowska, J and Miller, AE and Muggia, L and Nelson, PR and Rosentreter, R and Schultz, M and Sheard, JW and Tønsberg, T and Walton, J}, Title = {Biodiversity and ecology of lichens of Katmai and Lake Clark National Parks and Preserves, Alaska}, Journal = {Mycosphere}, Volume = {9}, Number = {4}, Pages = {859-930}, Year = {2018}, Month = {January}, url = {http://dx.doi.org/10.5943/mycosphere/9/4/10}, Abstract = {We inventoried lichens in Lake Clark (LACL) and Katmai (KATM) National Parks and Preserves. We assembled the known information on lichens in these parks by combining field, herbarium, and literature studies. Our results provide baseline data on lichen occurrence that may be used in resource condition assessments, vulnerability assessments, long-term ecological monitoring, and resource management. We report a total of 896 taxa of lichenized fungi from the Parks, adding 889 taxa to the total of seven taxa reported for the Parks by the National Park Service database and including ten new species first published elsewhere. An additional 15 lichenicolous fungi are reported here. Seven non-lichenized fungi associated with young living twigs of particular host species are also included. Sixteen species are new to Alaska, and six species new to North America (Caloplaca fuscorufa, Lecanora leucococca s.l., Ochrolechia brodoi, Protoparmelia memnonia, and Rhizocarpon leptolepis). Four new combinations are made, Cetraria minuscula, Enchylium millegranum var. bachmanianum, Lathagrium undulatum var. granulosum, and Protomicarea alpestris. Additional new species based on collections from the Parks have been described in separate publications.}, Doi = {10.5943/mycosphere/9/4/10}, Key = {fds352215} } @article{fds329418, Author = {Magain, N and Miadlikowska, J and Mueller, O and Gajdeczka, M and Truong, C and Salamov, AA and Dubchak, I and Grigoriev, IV and Goffinet, B and Sérusiaux, E and Lutzoni, F}, Title = {Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon.}, Journal = {Molecular phylogenetics and evolution}, Volume = {117}, Pages = {10-29}, Year = {2017}, Month = {December}, url = {http://dx.doi.org/10.1016/j.ympev.2017.08.013}, Abstract = {Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. Asa proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) - a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.}, Doi = {10.1016/j.ympev.2017.08.013}, Key = {fds329418} } @article{fds328939, Author = {Heiđmarsson, S and Gueidan, C and Miadlikowska, J and Lutzoni, F}, Title = {Multi-locus phylogeny supports the placement of endocarpon pulvinatum within staurothele s. Str. (lichenised ascomycetes, eurotiomycetes, verrucariaceae)}, Journal = {Phytotaxa}, Volume = {306}, Number = {1}, Pages = {37-48}, Publisher = {MAGNOLIA PRESS}, Year = {2017}, Month = {May}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Within the lichen family Verrucariaceae, the genera Endocarpon, Willeya and Staurothele are characterised by muriform ascospores and the presence of algal cells in the hymenium. Endocarpon thalli are squamulose to subfruticose, whereas Willeya and Staurothele include only crustose species. Endocarpon pulvinatum, an arctic-alpine species newly reported for Iceland, is one of the few Endocarpon with a subfruticose thallus formed by long and narrow erected squamules. Molecular phylogenetic analyses of four loci (ITS, nrLSU, mtSSU, and mcm7) newly obtained from E. pulvinatum specimens from Iceland, Finland and North America does not confirm its current classification within the mostly squamulose genus Endocarpon, but instead supports its placement within the crustose genus Staurothele. The new combination Staurothele pulvinata is therefore proposed here. It includes also E. tortuosum, which was confirmed as a synonym of E. pulvinatum based on a single sequence.}, Doi = {10.11646/phytotaxa.306.1.3}, Key = {fds328939} } @article{fds328940, Author = {Carbone, I and White, JB and Miadlikowska, J and Arnold, AE and Miller, MA and Kauff, F and U'Ren, JM and May, G and Lutzoni, F}, Title = {T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.}, Journal = {Bioinformatics (Oxford, England)}, Volume = {33}, Number = {8}, Pages = {1160-1168}, Year = {2017}, Month = {April}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {<h4>Motivation</h4>High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades.<h4>Results</h4>In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree.<h4>Availability and implementation</h4>T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources.<h4>Contact</h4>icarbon@ncsu.edu.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.}, Doi = {10.1093/bioinformatics/btw808}, Key = {fds328940} } @article{fds332336, Author = {Magain, N and Miadlikowska, J and Goffinet, B and Sérusiaux, E and Lutzoni, F}, Title = {Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota).}, Journal = {Systematic biology}, Volume = {66}, Number = {1}, Pages = {74-99}, Year = {2017}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here, we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred from five nuclear loci and the rbcLX region, respectively. These sequences were obtained from 206 lichen thalli, representing ca. 40 closely related Peltigera species sampled worldwide, doubling the number of known species in this group. We found a broad spectrum of specificity for both partners ranging from strict specialists to generalists. Overall, mycobionts are more specialized than cyanobionts by associating mostly with one or a few Nostoc phylogroups, whereas most cyanobionts associate frequently with several Peltigera species. Specialist mycobionts are older than generalists, supporting the hypothesis that specialization of mycobionts to one or few cyanobionts, is favored through time in geographic areas where species have been established for long periods of time. The relatively recent colonization of a new geographic area (Central and South America) by members of section Polydactylon is associated with a switch to a generalist pattern of association and an increased diversification rate by the fungal partner, suggesting that switches to generalism are rare events that are advantageous in new environments. We detected higher genetic diversity in generalist mycobionts. We also found that Peltigera species specialized on a single Nostoc phylogroup have narrower geographical distributions compared with generalist species.}, Doi = {10.1093/sysbio/syw065}, Key = {fds332336} } @article{fds329419, Author = {Darnajoux, R and Zhang, X and McRose, DL and Miadlikowska, J and Lutzoni, F and Kraepiel, AML and Bellenger, J-P}, Title = {Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates.}, Journal = {The New phytologist}, Volume = {213}, Number = {2}, Pages = {680-689}, Year = {2017}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Cryptogamic species and their associated cyanobacteria have attracted the attention of biogeochemists because of their critical roles in the nitrogen cycle through symbiotic and asymbiotic biological fixation of nitrogen (BNF). BNF is mediated by the nitrogenase enzyme, which, in its most common form, requires molybdenum at its active site. Molybdenum has been reported as a limiting nutrient for BNF in many ecosystems, including tropical and temperate forests. Recent studies have suggested that alternative nitrogenases, which use vanadium or iron in place of molybdenum at their active site, might play a more prominent role in natural ecosystems than previously recognized. Here, we studied the occurrence of vanadium, the role of molybdenum availability on vanadium acquisition and the contribution of alternative nitrogenases to BNF in the ubiquitous cyanolichen Peltigera aphthosa s.l. We confirmed the use of the alternative vanadium-based nitrogenase in the Nostoc cyanobiont of these lichens and its substantial contribution to BNF in this organism. We also showed that the acquisition of vanadium is strongly regulated by the abundance of molybdenum. These findings show that alternative nitrogenase can no longer be neglected in natural ecosystems, particularly in molybdenum-limited habitats.}, Doi = {10.1111/nph.14166}, Key = {fds329419} } @article{fds327998, Author = {Gryganskyi, A. P. and Humber, R. A. and Miadlikowska, J. and Smith, M. and Wu, S. and Rubinstein, N. and Voigt, K. and Walter, G. and Anihchenko, I. M. and Vilgalys, R.}, Title = {Molecular Phylogeny of Entomophthoralean Fungi.}, Journal = {Molecular Phylogenetics and Evolution}, Volume = {65}, Pages = {682-694}, Year = {2017}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds327998} } @article{fds328021, Author = {Miadlikowska, J. and Lutzoni, F.}, Title = {Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits.}, Journal = {American Journal of Botany}, Volume = {91}, Pages = {449–464}, Year = {2017}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds328021} } @article{fds329500, Author = {Manoharan-Basil, SS and Miadlikowska, J and Goward, T and Andrésson, ÓS and Miao, VPW}, Title = {Peltigera islandica, a new cyanolichen species in section Peltigera ('P. canina group')}, Journal = {Lichenologist}, Volume = {48}, Number = {5}, Pages = {451-467}, Publisher = {Cambridge University Press (CUP)}, Year = {2016}, Month = {September}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {A new cyanolichen, Peltigera islandica sp. nov. in the section Peltigera ('P. canina group') is described from Iceland. This species is similar in general appearance to P. rufescens and P. membranacea, but may be recognized by its downturned lobe tips and narrow lobes, respectively. Most thalli are bright emerald green in colour when moist, although a dark khaki green colourmorph is also documented. Monophyly of P. islandica s. lat. (i.e. including P. sp. A sensu O'Brien et al., from Canada) is significantly supported based on ITS sequences and corroborated by molecular synapomorphy (absence of the ITS1 hypervariable region). Analysis of the rbcLX locus indicates the cyanobiont of P. islandica (Nostoc sp.) comprises strains belonging to a pool of Icelandic genotypes, some of which are present in other Peltigera species, including P. neorufescens, another taxon new to Iceland collected during this study. Association with photobionts that are shared by other local species suggests P. islandica may be well established in Iceland, but a review of herbarium collections as well as broader field surveys are needed to better characterize its geographical distribution.}, Doi = {10.1017/S0024282916000414}, Key = {fds329500} } @article{fds329420, Author = {Hestmark, G and Lutzoni, F and Miadlikowska, J}, Title = {Photobiont associations in co-occurring umbilicate lichens with contrasting modes of reproduction in coastal Norway}, Journal = {Lichenologist}, Volume = {48}, Number = {5}, Pages = {545-557}, Publisher = {Cambridge University Press (CUP)}, Year = {2016}, Month = {September}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The identity and phylogenetic placement of photobionts associated with two lichen-forming fungi, Umbilicaria spodochroa and Lasallia pustulata were examined. These lichens commonly grow together in high abundance on coastal cliffs in Norway, Sweden and Finland. The mycobiont of U. spodochroa reproduces sexually through ascospores, and must find a suitable algal partner in the environment to re-establish the lichen symbiosis. Lasallia pustulata reproduces mainly vegetatively using symbiotic propagules (isidia) containing both symbiotic partners (photobiont and mycobiont). Based on DNA sequences of the internal transcribed spacer region (ITS) we detected seven haplotypes of the green-algal genus Trebouxia in 19 pairs of adjacent thalli of U. spodochroa and L. pustulata from five coastal localities in Norway. As expected, U. spodochroa associated with a higher diversity of photobionts (seven haplotypes) than the mostly asexually reproducing L. pustulata (four haplotypes). The latter was associated with the same haplotype in 15 of the 19 thalli sampled. Nine of the lichen pairs examined share the same algal haplotype, supporting the hypothesis that the mycobiont of U. spodochroa might associate with the photobiont 'pirated' from the abundant isidia produced by L. pustulata that are often scattered on the cliff surfaces. Up to six haplotypes of Trebouxia were found within a single sampling site, indicating a low level of specificity of both mycobionts for their algal partner. Most photobiont strains associated with species of Umbilicaria and Lasallia, including samples from this study, represent phylogenetically closely related taxa of Trebouxia grouped within a small number of main clades (Trebouxia sp., T. simplex/T. jamesii, and T. incrustata+T. gigantea). Three of the photobiont haplotypes were found only in U. spodochroa thalli.}, Doi = {10.1017/S0024282916000232}, Key = {fds329420} } @article{fds329421, Author = {van Nieuwenhuijzen, EJ and Miadlikowska, JM and Houbraken, JAMP and Adan, OCG and Lutzoni, FM and Samson, RA}, Title = {Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni.}, Journal = {Studies in mycology}, Volume = {85}, Pages = {107-124}, Year = {2016}, Month = {September}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {A culture-based survey of staining fungi on oil-treated timber after outdoor exposure in Australia and the Netherlands uncovered new taxa in <i>Pezizomycotina</i>. Their taxonomic novelty was confirmed by phylogenetic analyses of multi-locus sequences (ITS, nrSSU, nrLSU, mitSSU, <i>RPB1</i>, <i>RPB2</i>, and <i>EF-1α</i>) using multiple reference data sets. These previously unknown taxa are recognised as part of a new order (<i>Superstratomycetales</i>) potentially closely related to <i>Trypetheliales</i> (<i>Dothideomycetes</i>), and as a new species of <i>Cyanodermella</i>, <i>C. oleoligni</i> in <i>Stictidaceae</i> (<i>Ostropales</i>) part of the mostly lichenised class <i>Lecanoromycetes</i>. Within <i>Superstratomycetales</i> a single genus named <i>Superstratomyces</i> with three putative species: <i>S. flavomucosus</i>, <i>S. atroviridis</i>, and <i>S. albomucosus</i> are formally described. Monophyly of each circumscribed <i>Superstratomyces</i> species was highly supported and the intraspecific genetic variation was substantially lower than interspecific differences detected among species based on the ITS, nrLSU, and <i>EF-1α</i> loci. Ribosomal loci for all members of <i>Superstratomyces</i> were noticeably different from all fungal sequences available in GenBank. All strains from this genus grow slowly in culture, have darkly pigmented mycelia and produce pycnidia. The strains of <i>C. oleoligni</i> form green colonies with slimy masses and develop green pycnidia on oatmeal agar. These new taxa could not be classified reliably at the class and lower taxonomic ranks by sequencing from the substrate directly or based solely on culture-dependent morphological investigations. Coupling phenotypic observations with multi-locus sequencing of fungi isolated in culture enabled these taxonomic discoveries. Outdoor situated timber provides a great potential for culturable undescribed fungal taxa, including higher rank lineages as revealed by this study, and therefore, should be further explored.}, Doi = {10.1016/j.simyco.2016.11.008}, Key = {fds329421} } @article{fds329422, Author = {Chagnon, P-L and U'Ren, JM and Miadlikowska, J and Lutzoni, F and Arnold, AE}, Title = {Erratum to: Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.}, Journal = {Oecologia}, Volume = {181}, Number = {2}, Pages = {633}, Publisher = {Springer Nature}, Year = {2016}, Month = {June}, url = {http://dx.doi.org/10.1007/s00442-016-3589-2}, Doi = {10.1007/s00442-016-3589-2}, Key = {fds329422} } @article{fds329423, Author = {U'Ren, JM and Miadlikowska, J and Zimmerman, NB and Lutzoni, F and Stajich, JE and Arnold, AE}, Title = {Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).}, Journal = {Molecular phylogenetics and evolution}, Volume = {98}, Pages = {210-232}, Year = {2016}, Month = {May}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.}, Doi = {10.1016/j.ympev.2016.02.010}, Key = {fds329423} } @article{fds329424, Author = {Chagnon, P-L and U'Ren, JM and Miadlikowska, J and Lutzoni, F and Arnold, AE}, Title = {Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.}, Journal = {Oecologia}, Volume = {180}, Number = {1}, Pages = {181-191}, Year = {2016}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Understanding the factors that shape community assembly remains one of the most enduring and important questions in modern ecology. Network theory can reveal rules of community assembly within and across study systems and suggest novel hypotheses regarding the formation and stability of communities. However, such studies generally face the challenge of disentangling the relative influence of factors such as interaction type and environmental conditions on shaping communities and associated networks. Endophytic and endolichenic symbioses, characterized by microbial species that occur within healthy plants and lichen thalli, represent some of the most ubiquitous interactions in nature. Fungi that engage in these symbioses are hyperdiverse, often horizontally transmitted, and functionally beneficial in many cases, and they represent the diversification of multiple phylogenetic groups. We evaluated six measures of ecological network structure for >4100 isolates of endophytic and endolichenic fungi collected systematically from five sites across North America. Our comparison of these co-occurring interactions in biomes ranging from tundra to subtropical forest showed that the type of interactions (i.e., endophytic vs. endolichenic) had a much more pronounced influence on network structure than did environmental conditions. In particular, endophytic networks were less nested, less connected, and more modular than endolichenic networks in all sites. The consistency of the network structure within each interaction type, independent of site, is encouraging for current efforts devoted to gathering metadata on ecological network structure at a global scale. We discuss several mechanisms potentially responsible for such patterns and draw attention to knowledge gaps in our understanding of networks for diverse interaction types.}, Doi = {10.1007/s00442-015-3457-5}, Key = {fds329424} } @article{fds327983, Author = {Magain, N. and Sérusiaux, E. and Zhurbenko, M. P. and Lutzoni, F. and Miadlikowska, J.}, Title = {Disentangling the Peltigera polydactylon species complex by recognizing two new taxa, P. polydactylon subsp. udeghe and P. seneca.}, Journal = {Herzogia}, Volume = {29}, Pages = {514-528}, Year = {2016}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds327983} } @article{fds329501, Author = {Divakar, PK and Crespo, A and Wedin, M and Leavitt, SD and Hawksworth, DL and Myllys, L and McCune, B and Randlane, T and Bjerke, JW and Ohmura, Y and Schmitt, I and Boluda, CG and Alors, D and Roca-Valiente, B and Del-Prado, R and Ruibal, C and Buaruang, K and Núñez-Zapata, J and Amo de Paz, G and Rico, VJ and Molina, MC and Elix, JA and Esslinger, TL and Tronstad, IKK and Lindgren, H and Ertz, D and Gueidan, C and Saag, L and Mark, K and Singh, G and Dal Grande and F and Parnmen, S and Beck, A and Benatti, MN and Blanchon, D and Candan, M and Clerc, P and Goward, T and Grube, M and Hodkinson, BP and Hur, J-S and Kantvilas, G and Kirika, PM and Lendemer, J and Mattsson, J-E and Messuti, MI and Miadlikowska, J and Nelsen, M and Ohlson, JI and Pérez-Ortega, S and Saag, A and Sipman, HJM and Sohrabi, M and Thell, A and Thor, G and Truong, C and Yahr, R and Upreti, DK and Cubas, P and Lumbsch, HT}, Title = {Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.}, Journal = {The New phytologist}, Volume = {208}, Number = {4}, Pages = {1217-1226}, Year = {2015}, Month = {December}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.}, Doi = {10.1111/nph.13553}, Key = {fds329501} } @article{fds329425, Author = {Darnajoux, R and Lutzoni, F and Miadlikowska, J and Bellenger, J-P}, Title = {Determination of elemental baseline using peltigeralean lichens from Northeastern Canada (Québec): Initial data collection for long term monitoring of the impact of global climate change on boreal and subarctic area in Canada.}, Journal = {The Science of the total environment}, Volume = {533}, Pages = {1-7}, Year = {2015}, Month = {November}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Northeastern Canada is mostly free of anthropogenic activities. The extent to which this territory has been impacted by anthropogenic atmospheric depositions remains to be studied. The main goal of our study was to establish background levels for metals in boreal muscicolous/terricolous macrolichens over non-urbanized areas of northeastern Canada (Québec). Concentrations of 18 elements (Na, Mg, Al, P, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Cd, and Pb) were determined for three species of the genus Peltigera (Peltigera aphthosa (L.) Willd. s.l., Peltigera neopolydactyla (Gyeln.) Gyeln. s.l., Peltigera scabrosa Th. Fr. s.l.), and Nephroma arcticum (L.) Torss., along a 1080 km south-north transect and along a of 730 km west-east transect. We report that elemental contents in the sampled lichen thalli are very low and similar to background levels found in other studies performed in pristine places (high elevation or remote ecosystems) throughout the world. Overall, our results demonstrate that most of the boreal and subarctic zone of Québec (northeastern Canada) is still pristine. The elemental baseline established in these lichen populations will contribute to monitor metal pollution in boreal and sub-polar ecosystems due to global climate change and future industrial expansion.}, Doi = {10.1016/j.scitotenv.2015.06.030}, Key = {fds329425} } @article{fds329426, Author = {Chen, K-H and Miadlikowska, J and Molnár, K and Arnold, AE and U'Ren, JM and Gaya, E and Gueidan, C and Lutzoni, F}, Title = {Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.}, Journal = {Molecular phylogenetics and evolution}, Volume = {85}, Pages = {117-130}, Year = {2015}, Month = {April}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.}, Doi = {10.1016/j.ympev.2015.01.008}, Key = {fds329426} } @article{fds329427, Author = {Gueidan, C and Hill, DJ and Miadlikowska, J and Lutzoni, F}, Title = {Pezizomycotina: Lecanoromycetes}, Pages = {89-120}, Publisher = {Springer Berlin Heidelberg}, Year = {2015}, Month = {January}, url = {http://dx.doi.org/10.1007/978-3-662-46011-5_4}, Abstract = {Lecanoromycetes is the class of Ascomycota with the largest number of lichen-forming fungi. Members of this class are important components of most terrestrial ecosystems and occur in various habitats and on different substrates, from tropical to polar regions. Morphological, anatomical, and chemical characters have traditionally been used to classify orders, families, and genera within Lecanoromycetes. In the last two decades, molecular phylogenies have shown that traditional classification systems were not always consistent with the evolutionary history of this fungal class, resulting in changes in the delimitation of orders and families. Here, we revisit the taxonomic value of the main characters traditionally used for classification in light of current molecular phylogenies. The current delimitation of the 14 orders of Lecanoromycetes is also discussed, and recent changes in classification are highlighted.}, Doi = {10.1007/978-3-662-46011-5_4}, Key = {fds329427} } @article{fds327990, Author = {Gueidan, C. and Hill, D. J. and Miadlikowska, J. and Lutzoni, F.}, Title = {Chapter 4. Pezizomycotina: Lecanoromycetes.}, Volume = {VIIB}, Pages = {89–120 }, Booktitle = {The Mycota, Systematics and Evolution }, Publisher = {Springer Verlag,}, Address = {Berlin, Germany}, Editor = {D. J. McLaughlin and J. W. Spatafora}, Year = {2015}, Key = {fds327990} } @article{fds324524, Author = {Miadlikowska, J and Kauff, F and Högnabba, F and Oliver, JC and Molnár, K and Fraker, E and Gaya, E and Hafellner, J and Hofstetter, V and Gueidan, C and Otálora, MAG and Hodkinson, B and Kukwa, M and Lücking, R and Björk, C and Sipman, HJM and Burgaz, AR and Thell, A and Passo, A and Myllys, L and Goward, T and Fernández-Brime, S and Hestmark, G and Lendemer, J and Lumbsch, HT and Schmull, M and Schoch, CL and Sérusiaux, E and Maddison, DR and Arnold, AE and Lutzoni, F and Stenroos, S}, Title = {A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.}, Journal = {Molecular phylogenetics and evolution}, Volume = {79}, Pages = {132-168}, Year = {2014}, Month = {October}, url = {http://dx.doi.org/10.1016/j.ympev.2014.04.003}, Abstract = {The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.}, Doi = {10.1016/j.ympev.2014.04.003}, Key = {fds324524} } @article{fds329502, Author = {U'Ren, JM and Riddle, JM and Monacell, JT and Carbone, I and Miadlikowska, J and Arnold, AE}, Title = {Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi.}, Journal = {Molecular ecology resources}, Volume = {14}, Number = {5}, Pages = {1032-1048}, Year = {2014}, Month = {September}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best-practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness c. 15-fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artefacts.}, Doi = {10.1111/1755-0998.12252}, Key = {fds329502} } @article{fds329428, Author = {Miadlikowska, J and Richardson, D and Magain, N and Ball, B and Anderson, F and Cameron, R and Lendemer, J and Truong, C and Lutzoni, F}, Title = {Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).}, Journal = {American journal of botany}, Volume = {101}, Number = {7}, Pages = {1141-1156}, Year = {2014}, Month = {July}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {• Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.• Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria.• Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes.• Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America.}, Doi = {10.3732/ajb.1400267}, Key = {fds329428} } @article{fds329429, Author = {Darnajoux, R and Constantin, J and Miadlikowska, J and Lutzoni, F and Bellenger, J-P}, Title = {Is vanadium a biometal for boreal cyanolichens?}, Journal = {The New phytologist}, Volume = {202}, Number = {3}, Pages = {765-771}, Year = {2014}, Month = {May}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Molybdenum (Mo) nitrogenase has long been considered the predominant isoenzyme responsible for dinitrogen fixation worldwide. Recent findings have challenged the paradigm of Mo hegemony, and highlighted the role of alternative nitrogenases, such as the vanadium-nitrogenase. Here, we first characterized homeostasis of vanadium (V) along with other metals in situ in the dinitrogen fixing cyanolichen Peltigera aphthosa. These lichens were sampled in natural sites exposed to various levels of atmospheric metal deposition. These results were compared with laboratory experiments where Anabaena variabilis, which is also hosting the V-nitrogenase, and a relatively close relative of the lichen cyanobiont Nostoc, was subjected to various levels of V. We report here that V is preferentially allocated to cephalodia, specialized structures where dinitrogen fixation occurs in tri-membered lichens. This specific allocation is biologically controlled and tightly regulated. Vanadium homeostasis in lichen cephalodia exposed to various V concentrations is comparable to the one observed in Anabaena variabilis and other dinitrogen fixing organisms using V-nitrogenase. Overall, our findings support current hypotheses that V could be a more important factor in mediating nitrogen input in high latitude ecosystems than previously recognized. They invite the reassessment of current theoretical models linking metal dynamics and dinitrogen fixation in boreal and subarctic ecosystems.}, Doi = {10.1111/nph.12777}, Key = {fds329429} } @article{fds329430, Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F}, Title = {Assessing population structure and host specialization in lichenized cyanobacteria.}, Journal = {The New phytologist}, Volume = {198}, Number = {2}, Pages = {557-566}, Year = {2013}, Month = {April}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Coevolutionary theory predicts that the distribution of obligately symbiotic organisms will be determined by the dispersal ability and ecological range of both partners. We examined this prediction for lichen-forming fungi that form obligate symbioses with cyanobacteria. We compared genotypes of both partners of 250 lichens collected at multiple spatial scales in British Columbia, Canada. Multilocus sequence data collected from a subset of 128 of the specimens were used to determine the degree of recombination within the cyanobacterial populations. We found that six distinct clusters of cyanobacterial genotypes are distributed throughout the known global phylogeny of the genus Nostoc, and that each appears to be evolving clonally. Fungal specialization is high, with each species associating with either one or two of the cyanobacterial clusters, while cyanobacterial specialization varies, with clusters associating with between one and 12 different fungal species. Specialization also varies geographically, with some combinations restricted to a single site despite the availability of both partners elsewhere. Photobiont association patterns are determined by a combination of genetically based specificity, spatial population structure, and ecological factors and cannot be easily predicted by photobiont dispersal syndromes.}, Doi = {10.1111/nph.12165}, Key = {fds329430} } @article{fds329432, Author = {Gazis, R and Miadlikowska, J and Lutzoni, F and Arnold, AE and Chaverri, P}, Title = {Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes.}, Journal = {Molecular phylogenetics and evolution}, Volume = {65}, Number = {1}, Pages = {294-304}, Year = {2012}, Month = {October}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Through a culture-based survey of living sapwood and leaves of rubber trees (Hevea spp.) in remote forests of Peru, we discovered a new major lineage of Ascomycota, equivalent to a class rank. Multilocus phylogenetic analyses reveal that this new lineage originated during the radiation of the 'Leotiomyceta', which resulted not only in the evolution of the Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, and Sordariomycetes, but also of the majority of hyperdiverse foliar endophytes. Because its origin is nested within this major burst of fungal diversification, we could not recover strong support for its phylogenetic relationship within the 'Leotiomyceta'. Congruent with their long phylogenetic history and distinctive preference for growing in sapwood, this new lineage displays unique morphological, physiological, and ecological traits relative to known endophytes and currently described members of the 'Leotiomyceta'. In marked contrast to many foliar endophytes, the strains we isolated fail to degrade cellulose and lignin in vitro. Discovery of the new class, herein named Xylonomycetes and originally mis-identified by ITSrDNA sequencing alone, highlights the importance of inventorying tropical endophytes from unexplored regions, using multilocus data sets to infer the phylogenetic placement of unknown strains, and the need to sample diverse plant tissues using traditional methods to enhance efforts to discover the evolutionary, taxonomic, and functional diversity of symbiotrophic fungi.}, Doi = {10.1016/j.ympev.2012.06.019}, Key = {fds329432} } @article{fds329431, Author = {Liwa, L and Miadlikowska, J and Redelings, BD and Molnar, K and Lutzoni, F}, Title = {Are widespread morphospecies from the Lecanora dispersa group (lichen-forming Ascomycota) monophyletic?}, Journal = {Bryologist}, Volume = {115}, Number = {2}, Pages = {265-277}, Publisher = {American Bryological and Lichenological Society}, Year = {2012}, Month = {June}, url = {http://dx.doi.org/10.1639/0007-2745-115.2.265}, Abstract = {To evaluate the current delimitation of broadly distributed morphospecies from the Lecanora dispersa group, the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S and ITS2) was analyzed phylogenetically and compared to phenotypic data variation within and among species. Phylogenetic relationships among 34 individuals representing eight species from the L. dispersa group, collected mainly from Poland and other European countries, were inferred using two types of Bayesian analyses (with and without a priori alignments), maximum likelihood and maximum parsimony approaches. The highest phylogenetic resolution and the largest number of significantly supported internodes resulted from the Bayesian analysis without a priori alignment. Inferred phylogenies confirmed a broader delimitation of the L. dispersa group, to include four additional lobate taxa: L. contractula, L. pruinosa, L. reuteri, and L. thuleana ( Arctopeltis thuleana). Lecanora crenulata, L. dispersa, L. reuterii, and the core of L. albescens and L. semipallida were all found to be monophyletic with high support (by at least one phylogenetic analysis) except the first species. Based on the ITS region, phenotypically similar individuals, thought to belong to one monophyletic group, were found to belong to multiple distantly related groups (e.g., members of L. albescens and L. hagenii), suggesting that morphological, anatomical and chemical characters may not be consistent in predicting species boundaries within the L. dispersa group. Potential undescribed species were found within phenotypically defined L. albescens and L. semipallida. Phylo-taxonomic studies of the L. dispersa group with more loci and a more extensive taxon sampling are urgently needed. © 2012 The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745-115.2.265}, Key = {fds329431} } @article{fds329433, Author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Laetsch, AD and Arnold, AE}, Title = {Host and geographic structure of endophytic and endolichenic fungi at a continental scale.}, Journal = {American journal of botany}, Volume = {99}, Number = {5}, Pages = {898-914}, Year = {2012}, Month = {May}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {<h4>Premise of the study</h4>Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities.<h4>Methods</h4>Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of five North American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska).<h4>Key results</h4>Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, reflecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences reflected climate factors more strongly than geographic distance alone.<h4>Conclusions</h4>Our study provides a first evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition reflect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specificity, metabolic capability, and comparative genomics.}, Doi = {10.3732/ajb.1100459}, Key = {fds329433} } @article{fds329503, Author = {McCune, B and Schoch, C and Root, HT and Kageyama, SA and Miadlikowska, J}, Title = {Geographic, climatic, and chemical differentiation in the Hypogymnia imshaugii species complex (Lecanoromycetes, Parmeliaceae) in North America}, Journal = {Bryologist}, Volume = {114}, Number = {3}, Pages = {526-544}, Publisher = {American Bryological and Lichenological Society}, Year = {2011}, Month = {September}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Hypogymnia imshaugii is one of the most common, conspicuous and morphologically variable epiphytic lichens of the Pacific coastal states and provinces. The species varies greatly in morphology and chemistry, suggesting multiple closely related species or one or more phenotypically plastic species. We sought to determine whether additional ecologically meaningful species might be present within the H. imshaugii complex. Improving our species concepts could potentially improve ecological inferences based on community sampling. Three relatively well-defined genetic groups and one residual group in the H. imshaugii complex were detected with haplotype networks based on the ITS locus; however, phylogenetic reconstructions on combined ITS, mtSSU, GPD1 and TEF1 loci did not reflect this pattern. At present, we have insufficient evidence to support defining any of these groups as new taxa. The four major chemotypes in H. imshaugii differed in frequency among the genetic groups. None of the genetic groups was, however, qualitatively uniform in chemotype. Only one chemotype occurred in a single genetic group, but several chemotypes occurred in that group. While broadly sympatric, each chemotype had a distinct geographic distribution, and each chemotype showed its own relationship to climate, as shown by regression of occurrences of chemotypes against climatic variables. The genetic variation detected within H. imshaugii did not correspond to geographic variation in morphology, chemistry, or climate. Within the broader H. imshaugii complex, we recommend treating H. amplexa as a synonym of H. imshaugii unless it can be more distinctly separated from the clinal variation in morphology, chemistry, or DNA sequences. In contrast to H. amplexa, however, H. inactiva and H. gracilis are both easily separated morphologically from H. imshaugii and do not intergrade with it. © 2011 The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745-114.3.526}, Key = {fds329503} } @article{fds329436, Author = {Schmull, M and Miadlikowska, J and Pelzer, M and Stocker-Wörgötter, E and Hofstetter, V and Fraker, E and Hodkinson, BP and Reeb, V and Kukwa, M and Lumbsch, HT and Kauff, F and Lutzoni, F}, Title = {Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota).}, Journal = {Mycologia}, Volume = {103}, Number = {5}, Pages = {983-1003}, Year = {2011}, Month = {September}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The genus Lecidea Ach. sensu lato (sensu Zahlbruckner) includes almost 1200 species, out of which only 100 species represent Lecidea sensu stricto (sensu Hertel). The systematic position of the remaining species is mostly unsettled but anticipated to represent several unrelated lineages within Lecanoromycetes. This study attempts to elucidate the phylogenetic placement of members of this heterogeneous group of lichen-forming fungi and to improve the classification and phylogeny of Lecanoromycetes. Twenty-five taxa of Lecidea sensu lato and 22 putatively allied species were studied in a broad selection of 268 taxa, representing 48 families of Lecanoromycetes. Six loci, including four ribosomal and two protein-coding genes for 315- and 209-OTU datasets were subjected to maximum likelihood and Bayesian analyses. The resulting well supported phylogenetic relationships within Lecanoromycetes are in agreement with published phylogenies, but the addition of new taxa revealed putative rearrangements of several families (e.g. Catillariaceae, Lecanoraceae, Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae). As expected, species of Lecidea sensu lato and putatively related taxa are scattered within Lecanoromycetidae and beyond, with several species nested in Lecanoraceae and Pilocarpaceae and others placed outside currently recognized families in Lecanorales and orders in Lecanoromycetidae. The phylogenetic affiliations of Schaereria and Strangospora are outside Lecanoromycetidae, probably with Ostropomycetidae. All species referred to as Lecidea sensu stricto based on morphology (including the type species, Lecidea fuscoatra [L.] Ach.) form, with Porpidia species, a monophyletic group with high posterior probability outside Lecanorales, Peltigerales and Teloschistales, in Lecanoromycetidae, supporting the recognition of order Lecideales Vain. in this subclass. The genus name Lecidea must be redefined to apply only to Lecidea sensu stricto and to include at least some members of the genus Porpidia. Based on morphological and chemical similarities, as well as the phylogenetic relationship of Lecidea pullata sister to Frutidella caesioatra, the new combination Frutidella pullata is proposed here.}, Doi = {10.3852/10-234}, Key = {fds329436} } @article{fds329434, Author = {Miadlikowska, J and Schoch, CL and Kageyama, SA and Molnar, K and Lutzoni, F and McCune, B}, Title = {Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure}, Journal = {Bryologist}, Volume = {114}, Number = {2}, Pages = {392-400}, Publisher = {American Bryological and Lichenological Society}, Year = {2011}, Month = {June}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {We inferred phylogenetic relationships using Bayesian and maximum likelihood approaches for two genera of lichenized fungi, Hypogymnia and Cavernularia (Parmeliaceae). Based on the combined ITS and GPD1 dataset from 23 species (49 specimens) of Hypogymnia and two species (8 specimens) of Cavernularia, we conclude that Hypogymnia is paraphyletic, and that it should include Cavernularia to retain its monophyly. Hypogymnia hultenii (= Cavernularia hultenii) and H. lophyrea (= C. lophyrea) are accepted here. Five species of Hypogymnia represented by more than a single individual were found to be monophyletic and significantly supported. The phylogeny reflects a statistically significant biogeographic pattern where continental-scale endemic taxa tend to occur within the same phylogenetic group. Sorediate taxa, which have worldwide or broader geographical ranges than affiliated species lacking soredia, are spread across the phylogenetic tree. Hypogymnia contains three species pairs: H. krogiae and the sorediate counterpart H. incurvoides, H. minilobata and the sorediate H. mollis, and H. lophyrea and the sorediate H. hultenii. In the case of H. minilobata, both members of the pair are restricted to a small area in southern California. In the other two cases, the fertile counterpart occurs only in North America, while the sorediate species occurs in both North America and Fennoscandia. This suggests but not proves an origin of each species pair in North America, with migration of the sorediate member to Fennoscandia following the prevailing wind direction. © 2011 The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745-114.2.392}, Key = {fds329434} } @article{fds329435, Author = {Hestmark, G and Miadlikowska, J and Kauff, F and Fraker, E and Molnar, K and Lutzoni, F}, Title = {Single origin and subsequent diversification of central Andean endemic Umbilicaria species.}, Journal = {Mycologia}, Volume = {103}, Number = {1}, Pages = {45-56}, Year = {2011}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {We studied an Andean endemic group of species of the lichen-forming fungal genus Umbilicaria from the subalpine and low-alpine zone, with their biogeographic center in Bolivia and Peru. A number of species and varieties have been described from this element, but apparent instability in several morphological traits has made it difficult to precisely delimit taxa. Based on DNA sequences of nuclear ITS, LSU and mitochondrial SSU from extensive collections from Argentina, Bolivia, Chile, Colombia, Ecuador and Peru, we present here a molecular phylogenetic analysis of this Andean endemic element within genus Umbilicaria. All analyses (MP, ML and Bayesian) support a single origin for the element and a division into two major groups characterized by different apothecium types: the Umbilicaria dichroa group and U. calvescens group. Taxa U. krempelhuberi, U. peruviana and U. subcalvescens are nested withinn U. calvescens and are treated as conspecific with the latter species. The endemic element shares a most recent common ancestor with the Umbilicaria vellea group, which has a worldwide distribution and contains several asexually reproducing (sorediate) species. Independent reversals to sexual reproduction might explain the evolution of two types of apothecia in this monophyletic endemic lineage. A number of cosmopolitan, mostly high-alpine, species of Umbilicaria also present in the central Andes are related only remotely to the endemic element and do not exhibit speciation into endemics. Because the An-dean element dominates the Umbilicaria habitats of the low- and subalpine zones we propose that the founder colonized the Andes at a time when the mountains had not yet reached their current elevation while the high-alpine species arrived more recently.}, Doi = {10.3852/10-012}, Key = {fds329435} } @article{fds327999, Author = {Sliwa, L. and Miadlikowska, J. and Redelings, B. D. and Molnar, K. and Lutzoni, F.}, Title = {Are morphospecies from the Lecanora dispersa group (lichenized Lecanoromycetes, Pezizomycotina) monophyletic?}, Journal = {The Bryologist}, Volume = {115}, Pages = {265–277}, Year = {2011}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds327999} } @article{fds329437, Author = {Crespo, A and Kauff, F and Divakar, PK and del Prado, R and Pérez-Ortega, S and de Paz, GA and Ferencova, Z and Blanco, O and Roca-Valiente, B and Núñez-Zapata, J and Cubas, P and Argüello, A and Elix, JA and Esslinger, TL and Hawksworth, DL and Millanes, A and Molina, MC and Wedin, M and Ahti, T and Aptroot, A and Barreno, E and Bungartz, F and Calvelo, S and Candan, M and Cole, M and Ertz, D and Goffinet, B and Lindblom, L and Lücking, R and Lutzoni, F and Mattsson, JE and Messuti, MI and Miadlikowska, J and Piercey-Normore, M and Rico, VJ and Sipman, HJM and Schmitt, I and Spribille, T and Thell, A and Thor, G and Upreti, DK and Thorsten Lumbsch and H}, Title = {Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence}, Journal = {Taxon}, Volume = {59}, Number = {6}, Pages = {1735-1753}, Year = {2010}, Month = {December}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.}, Doi = {10.1002/tax.596008}, Key = {fds329437} } @article{fds329438, Author = {U'Ren, J and Lutzoni, F and Miadlikowska, J and Arnold, AE}, Title = {Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens}, Journal = {Microbial Ecology}, Volume = {60}, Number = {2}, Pages = {340-353}, Year = {2010}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been "entrapped" by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as endophytes of mosses.}, Doi = {10.1007/s00248-010-9698-2}, Key = {fds329438} } @article{fds329439, Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F}, Title = {Assessing reproductive isolation in highly diverse communities of the lichen-forming fungal genus peltigera.}, Journal = {Evolution; international journal of organic evolution}, Volume = {63}, Number = {8}, Pages = {2076-2086}, Year = {2009}, Month = {August}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The lichen-forming fungal genus Peltigera includes a number of species that are extremely widespread, both geographically and ecologically. However, morphological variability has lead to doubts about the distinctness of some species, and it has been suggested that hybridization is common in nature. We examined species boundaries by looking for evidence of hybridization and gene flow among seven described species collected at five sites in British Columbia, Canada. We found no evidence of gene flow or hybridization between described species, with fixed differences between species for two or more of the three loci examined. Reproductive isolation did not reflect a solely clonal mode of reproduction as there was evidence of ongoing gene flow within species. In addition, we found five undescribed species that were reproductively isolated, although there was evidence of ongoing or historical gene flow between two of the new species. These results indicate that the genus Peltigera is more diverse in western North America than originally perceived, and that morphological variability is due largely to the presence of undescribed species rather than hybridization or intraspecific variation.}, Doi = {10.1111/j.1558-5646.2009.00685.x}, Key = {fds329439} } @article{fds329440, Author = {Lutzoni, F and Miadlikowska, J}, Title = {Lichens.}, Journal = {Current biology : CB}, Volume = {19}, Number = {13}, Pages = {R502-R503}, Year = {2009}, Month = {July}, url = {http://lutzonilab.org/publications-datasets/}, Doi = {10.1016/j.cub.2009.04.034}, Key = {fds329440} } @article{fds329441, Author = {Arnold, AE and Miadlikowska, J and Higgins, KL and Sarvate, SD and Gugger, P and Way, A and Hofstetter, V and Kauff, F and Lutzoni, F}, Title = {A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?}, Journal = {Systematic biology}, Volume = {58}, Number = {3}, Pages = {283-297}, Year = {2009}, Month = {June}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Fungi associated with photosynthetic organisms are major determinants of terrestrial biomass, nutrient cycling, and ecosystem productivity from the poles to the equator. Whereas most fungi are known because of their fruit bodies (e.g., saprotrophs), symptoms (e.g., pathogens), or emergent properties as symbionts (e.g., lichens), the majority of fungal diversity is thought to occur among species that rarely manifest their presence with visual cues on their substrate (e.g., the apparently hyperdiverse fungal endophytes associated with foliage of plants). Fungal endophytes are ubiquitous among all lineages of land plants and live within overtly healthy tissues without causing disease, but the evolutionary origins of these highly diverse symbionts have not been explored. Here, we show that a key to understanding both the evolution of endophytism and the diversification of the most species-rich phylum of Fungi (Ascomycota) lies in endophyte-like fungi that can be isolated from the interior of apparently healthy lichens. These "endolichenic" fungi are distinct from lichen mycobionts or any other previously recognized fungal associates of lichens, represent the same major lineages of Ascomycota as do endophytes, largely parallel the high diversity of endophytes from the arctic to the tropics, and preferentially associate with green algal photobionts in lichen thalli. Using phylogenetic analyses that incorporate these newly recovered fungi and ancestral state reconstructions that take into account phylogenetic uncertainty, we show that endolichenism is an incubator for the evolution of endophytism. In turn, endophytism is evolutionarily transient, with endophytic lineages frequently transitioning to and from pathogenicity. Although symbiotrophic lineages frequently give rise to free-living saprotrophs, reversions to symbiosis are rare. Together, these results provide the basis for estimating trophic transition networks in the Ascomycota and provide a first set of hypotheses regarding the evolution of symbiotrophy and saprotrophy in the most species-rich fungal phylum. [Ancestral state reconstruction; Ascomycota; Bayesian analysis; endolichenic fungi; fungal endophytes; lichens; pathogens; phylogeny; saprotrophy; symbiotrophy; trophic transition network.].}, Doi = {10.1093/sysbio/syp001}, Key = {fds329441} } @article{fds329443, Author = {Schoch, CL and Sung, G-H and López-Giráldez, F and Townsend, JP and Miadlikowska, J and Hofstetter, V and Robbertse, B and Matheny, PB and Kauff, F and Wang, Z and Gueidan, C and Andrie, RM and Trippe, K and Ciufetti, LM and Wynns, A and Fraker, E and Hodkinson, BP and Bonito, G and Groenewald, JZ and Arzanlou, M and de Hoog, GS and Crous, PW and Hewitt, D and Pfister, DH and Peterson, K and Gryzenhout, M and Wingfield, MJ and Aptroot, A and Suh, S-O and Blackwell, M and Hillis, DM and Griffith, GW and Castlebury, LA and Rossman, AY and Lumbsch, HT and Lücking, R and Büdel, B and Rauhut, A and Diederich, P and Ertz, D and Geiser, DM and Hosaka, K and Inderbitzin, P and Kohlmeyer, J and Volkmann-Kohlmeyer, B and Mostert, L and O'Donnell, K and Sipman, H and Rogers, JD and Shoemaker, RA and Sugiyama, J and Summerbell, RC and Untereiner, W and Johnston, PR and Stenroos, S and Zuccaro, A and Dyer, PS and Crittenden, PD and Cole, MS and Hansen, K and Trappe, JM and Yahr, R and Lutzoni, F and Spatafora, JW}, Title = {The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.}, Journal = {Systematic biology}, Volume = {58}, Number = {2}, Pages = {224-239}, Year = {2009}, Month = {April}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.}, Doi = {10.1093/sysbio/syp020}, Key = {fds329443} } @article{fds329442, Author = {Ertz, D and Miadlikowska, J and Lutzoni, F and Dessein, S and Raspé, O and Vigneron, N and Hofstetter, V and Diederich, P}, Title = {Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha.}, Journal = {Mycological research.}, Volume = {113}, Number = {Pt 1}, Pages = {141-152}, Year = {2009}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha. With the inclusion of sequences from GenBank, ten genera and 35 species are included in this study, representing about 18% of the genera and ca 3% of the species of this order. Our study revealed the homoplastic nature of morphological characters traditionally used to circumscribe genera within the Arthoniales, such as exciple carbonization and ascomatal structure. The genus Opegrapha appears polyphyletic, species of that genus being nested in all the major clades identified within Arthoniales. The transfer of O. atra and O. calcarea to the genus Arthonia will allow this genus and family Arthoniaceae to be recognized as monophyletic. The genus Enterographa was also found to be polyphyletic. Therefore, the following new combinations are needed: Arthonia calcarea (basionym: O. calcarea), and O. anguinella (basionym: Stigmatidium anguinellum); and the use of the names A. atra and Enterographa zonata are proposed here. The simultaneous use of a mitochondrial gene and two nuclear genes led to the detection of what seems to be a case of introgression of a mitochondrion from one species to another (mitochondrion capture; cytoplasmic gene flow) resulting from hybridization.}, Doi = {10.1016/j.mycres.2008.09.002}, Key = {fds329442} } @article{fds328008, Author = {Sérusiaux, E. and Goffinet, B. and Miadlikowska, J. and Vitikainen, O.}, Title = {Taxonomy, phylogeny, and biogeography of the lichen genus Peltigera in Papua New Guinea}, Journal = {Fungal Diversity}, Volume = {38}, Pages = {185-224}, Year = {2009}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds328008} } @article{fds329444, Author = {Amtoft, A and Lutzoni, F and Miadlikowska, J}, Title = {Dermatocarpon (Verrucariaceae) in the Ozark Highlands, North America}, Journal = {Bryologist}, Volume = {111}, Number = {1}, Pages = {1-40}, Publisher = {American Bryological and Lichenological Society}, Year = {2008}, Month = {March}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Dermatocarpon, a saxicolous lichen, is common throughout the Ozarks Highlands of North America where exposed rock is abundant. Dermatocarpon is an understudied genus. Species delimitation is difficult because of a paucity of morphological characters and a large degree of variation within this genus. The taxonomy of Dermatocarpon in North America was recently thrown into flux because of a molecular study which limited the use of a once widely applied name, D. miniatum. The Melzer's reagent test, currently used for identifying members of the miniatum-complex in North America, is not useful for identifying Ozark specimens. A revision of Dermatocarpon for the Ozark Highlands of North America is presented based on morphological, molecular and ecological studies. The results of these studies indicate that eight taxa are present in the Ozarks. Four taxa are described new to science: D. arenosaxi, D. dolomiticum, D. luridum var. xerophilum and D. multifolium. Copyright ©2008 by The American Bryological and Lichenological Society, Inc.}, Doi = {10.1639/0007-2745(2008)111[1:DVITOH]2.0.CO;2}, Key = {fds329444} } @article{fds329445, Author = {Hofstetter, V and Miadlikowska, J and Kauff, F and Lutzoni, F}, Title = {Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).}, Journal = {Molecular phylogenetics and evolution}, Volume = {44}, Number = {1}, Pages = {412-426}, Year = {2007}, Month = {July}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.}, Doi = {10.1016/j.ympev.2006.10.016}, Key = {fds329445} } @article{fds329446, Author = {Higgins, KL and Arnold, AE and Miadlikowska, J and Sarvate, SD and Lutzoni, F}, Title = {Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages.}, Journal = {Molecular phylogenetics and evolution}, Volume = {42}, Number = {2}, Pages = {543-555}, Year = {2007}, Month = {February}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Although associated with all plants, fungal endophytes (microfungi that live within healthy plant tissues) represent an unknown proportion of fungal diversity. While there is a growing appreciation of their ecological importance and human uses, little is known about their host specificity, geographic structure, or phylogenetic relationships. We surveyed endophytic Ascomycota from healthy photosynthetic tissues of three plant species (Huperzia selago, Picea mariana, and Dryas integrifolia, representing lycophytes, conifers, and angiosperms, respectively) in northern and southern boreal forest (Québec, Canada) and arctic tundra (Nunavut, Canada). Endophytes were recovered from all plant species surveyed, and were present in <1-41% of 2 mm2 tissue segments examined per host species. Sequence data from the nuclear ribosomal internal transcribed spacer region (ITS) were obtained for 280 of 558 isolates. Species-accumulation curves based on ITS genotypes remained non-asymptotic, and bootstrap analyses indicated that a large number of genotypes remain to be found. The majority of genotypes were recovered from only a single host species, and only 6% of genotypes were shared between boreal and arctic communities. Two independent Bayesian analyses and a neighbor-joining bootstrapping analysis of combined data from the nuclear large and small ribosomal subunits (LSUrDNA, SSUrDNA; 2.4 kb) showed that boreal and arctic endophytes represent Dothideomycetes, Sordariomycetes, Chaetothyriomycetidae, Leotiomycetes, and Pezizomycetes. Many well-supported phylotypes contained only endophytes despite exhaustive sampling of available sequences of Ascomycota. Together, these data demonstrate greater than expected diversity of endophytes at high-latitude sites and provide a framework for assessing the evolution of these poorly known but ubiquitous symbionts of living plants.}, Doi = {10.1016/j.ympev.2006.07.012}, Key = {fds329446} } @article{fds329447, Author = {Hibbett, DS and Binder, M and Bischoff, JF and Blackwell, M and Cannon, PF and Eriksson, O and Huhndorf, S and James, T and Kirk, PM and Lücking, R and Lumbsch, T and Lutzoni, F and Matheny, PB and McLaughlin, DJ and Powell, MJ and Redhead, S and Schoch, CL and Spatafora, JW and Stalpers, JA and Vilgalys, R and Aime, MC and Aptroot, A and Bauer, R and Begerow, D and Benny, GL and Castlebury, LA and Crous, PW and Dai, YC and Gams, W and Geiser, DM and Griffith, GW and Gueidan, C and Hawksworth, DL and Hestmark, G and Hosaka, K and Humber, RA and Hyde, K and Koljalg, U and Kurtzman, CP and Larsson, KH and Lichtward, R and Longcore, J and Miadlikowska, J and Miller, A and Monclavo, JM and Mozley Standridge, S and Oberwinkler, F and Parmasto, E and Reeb, V and Rogers, JD and Roux, C and Ryvarden, L and Sampaio, JP and Schuessler, A and Sugiyama, J and Thorn, RG and Tibell, L and Untereiner, WA and Walker, C and Wang, Z and Weir, A and Weiss, M and White, M and Winka, K and Yao, YJ and Zhang, N}, Title = {A higher-level phylogenetic classification of the Fungi}, Journal = {Mycological Research}, Volume = {111}, Number = {Pt 5}, Pages = {509-547}, Year = {2007}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.}, Doi = {10.1016/j.mycres.2007.03.004}, Key = {fds329447} } @article{fds329449, Author = {Geiser, DM and Gueidan, C and Miadlikowska, J and Lutzoni, F and Kauff, F and Hofstetter, V and Fraker, E and Schoch, CL and Tibell, L and Untereiner, WA and Aptroot, A}, Title = {Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1053-1064}, Year = {2006}, Month = {November}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales.}, Doi = {10.3852/mycologia.98.6.1053}, Key = {fds329449} } @article{fds329450, Author = {Spatafora, JW and Sung, G-H and Johnson, D and Hesse, C and O'Rourke, B and Serdani, M and Spotts, R and Lutzoni, F and Hofstetter, V and Miadlikowska, J and Reeb, V and Gueidan, C and Fraker, E and Lumbsch, T and Lücking, R and Schmitt, I and Hosaka, K and Aptroot, A and Roux, C and Miller, AN and Geiser, DM and Hafellner, J and Hestmark, G and Arnold, AE and Büdel, B and Rauhut, A and Hewitt, D and Untereiner, WA and Cole, MS and Scheidegger, C and Schultz, M and Sipman, H and Schoch, CL}, Title = {A five-gene phylogeny of Pezizomycotina.}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1018-1028}, Year = {2006}, Month = {November}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.}, Doi = {10.3852/mycologia.98.6.1018}, Key = {fds329450} } @article{fds324069, Author = {Miadlikowska, J and Kauff, F and Hofstetter, V and Fraker, E and Grube, M and Hafellner, J and Reeb, V and Hodkinson, BP and Kukwa, M and Lücking, R and Hestmark, G and Otalora, MG and Rauhut, A and Büdel, B and Scheidegger, C and Timdal, E and Stenroos, S and Brodo, I and Perlmutter, GB and Ertz, D and Diederich, P and Lendemer, JC and May, P and Schoch, CL and Arnold, AE and Gueidan, C and Tripp, E and Yahr, R and Robertson, C and Lutzoni, F}, Title = {New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.}, Journal = {Mycologia}, Volume = {98}, Number = {6}, Pages = {1088-1103}, Year = {2006}, Month = {November}, url = {http://dx.doi.org/10.1080/15572536.2006.11832636}, Abstract = {The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.}, Doi = {10.1080/15572536.2006.11832636}, Key = {fds324069} } @article{fds329448, Author = {James, TY and Kauff, F and Schoch, C and Matheny, PB and Hofstetter, V and Cox, CJ and Celio, G and Gueidan, C and Fraker, E and Miadlikowska, J and Lumbsch, T and Rauhut, A and Reeb, V and Arnold, AE and Amtoft, A and Stajich, JE and Hosaka, K and Sung, GH and Johnson, D and O’Rourke, B and Binder, M and Curtis, JM and Slot, JC and Wang, Z and Wilson, AW and Schüßler, A and Longcore, JE and O’Donnell, K and Mozley Standridge, S and Porter, D and Letcher, PM and Powell, MJ and Taylor, JW and White, MM and Griffith, GW and Davies, DR and Sugiyama, J and Rossman, AY and Rogers, JD and Pfister, DH and Hewitt, D and Hansen, K and Hambleton, S and Shoemaker, RA and Kohlmeyer, J and Volkmann Kohlmeyer, B and Spotts, RA and Serdani, M and Crous, PW and Hughes, KW and Matsuura, K and Langer, E and Langer, G and Untereiner, WA and Lücking, R and Büdel, B and Geiser, DM and Aptroot, A and Buck, WR and Cole, MS and Diederich, P and Printzen, C and Schmitt, I and Schultz, M and Yahr, R and Zavarzin, A and Hibbett, DH and Lutzoni, F and McLaughlin, DJ and Spatafora, JW and Vilgalys, R}, Title = {Reconstructing the early evolution of the Fungi using a six-gene phylogeny}, Journal = {Nature}, Volume = {443}, Number = {7113}, Pages = {818-822}, Year = {2006}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.}, Doi = {10.1038/nature05110}, Key = {fds329448} } @article{fds329451, Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F}, Title = {Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungus Peltigera}, Journal = {European Journal of Phycology}, Volume = {40}, Number = {4}, Pages = {363-378}, Publisher = {Informa UK Limited}, Year = {2005}, Month = {November}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Heterocystous cyanobacteria form symbiotic associations with a wide range of plant and fungal hosts. We used a molecular phylogenetic approach to investigate the degree of host specialization of cyanobacteria associated with four closely related species of the lichenized fungus Peltigera, and to compare these strains with other symbiotic cyanobacteria. We conducted phylogenetic analyses on 16S, rbcLX, and trnL sequences from cyanobacteria associated with multiple specimens of each lichen species and from symbionts of other fungi and plants, as well as from free-living strains of Nostoc and related genera of cyanobacteria. The genus Nostoc comprises two divergent lineages, but symbiotic strains occur primarily within a single monophyletic lineage that also includes free-living representatives. Cyanobacteria from the same lichen species were often more closely related to strains from other species or to plant symbionts or free-living strains than to each other. These results indicate that host specialization is low for the genus Nostoc, and suggest that opportunities for coevolution with its partners may be rare. © 2005 British Phycological Society.}, Doi = {10.1080/09670260500342647}, Key = {fds329451} } @article{fds329452, Author = {Lutzoni, F and Kauff, F and Cox, CJ and McLaughlin, D and Celio, G and Dentinger, B and Padamsee, M and Hibbett, D and James, TY and Baloch, E and Grube, M and Reeb, V and Hofstetter, V and Schoch, C and Arnold, AE and Miadlikowska, J and Spatafora, J and Johnson, D and Hambleton, S and Crockett, M and Shoemaker, R and Sung, G-H and Lücking, R and Lumbsch, T and O'Donnell, K and Binder, M and Diederich, P and Ertz, D and Gueidan, C and Hansen, K and Harris, RC and Hosaka, K and Lim, Y-W and Matheny, B and Nishida, H and Pfister, D and Rogers, J and Rossman, A and Schmitt, I and Sipman, H and Stone, J and Sugiyama, J and Yahr, R and Vilgalys, R}, Title = {Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.}, Journal = {American journal of botany}, Volume = {91}, Number = {10}, Pages = {1446-1480}, Year = {2004}, Month = {October}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.}, Doi = {10.3732/ajb.91.10.1446}, Key = {fds329452} } @article{fds329453, Author = {Miadlikowska, J and Lutzoni, F}, Title = {Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits.}, Journal = {American journal of botany}, Volume = {91}, Number = {3}, Pages = {449-464}, Year = {2004}, Month = {March}, url = {http://dx.doi.org/10.3732/ajb.91.3.449}, Abstract = {To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup consisted of 59 individuals representing six families, 12 genera, and 54 species potentially part of the Peltigerineae/Peltigerales. Our study revealed that all six families together formed a strongly supported monophyletic group within the Lecanoromycetidae. We propose here a new classification for these lichens consisting of the order Peltigerales and two suborders-Collematineae subordo nov. (Collemataceae, Placynthiaceae, and Pannariaceae) and Peltigerineae (Lobariaceae, Nephromataceae, and Peltigeraceae). To accommodate these new monophyletic groups, we redefined the Lecanorineae, Pertusariales, and Lecanorales sensu Eriksson et al. (Outline of Ascomycota-2003, Myconet 9: 1-103, 2003). Our study confirms the monophyly of the Collemataceae, Lobariaceae, Nephromataceae, and Peltigeraceae, and the genera Nephroma, Sticta, and Peltigera. However, Leptogium, Lobaria, Pseudocyphellaria, and Solorina were found to be nonmonophyletic genera. Reconstruction of ancestral symbiotic states within the Peltigerales, using maximum likelihood (ML) and a Bayesian approach to account for phylogenetic uncertainty, revealed an evolutionary scenario in which bimembered associations with cyanobacteria were ancestral, followed by multiple independent acquisitions of green algae to form tripartite symbioses and rare subsequent losses of the cyanobiont to form bimembered symbioses with green algae.}, Doi = {10.3732/ajb.91.3.449}, Key = {fds329453} } @article{fds329504, Author = {Ertz, D and Diederich, P and Miadlikowska, J}, Title = {The lichenicolous Opegrapha species (Roccellaceae, Ascomycota) with 3-septate ascospores on Pertusaria and Ochrolechia}, Journal = {Botanical Journal of the Linnean Society}, Volume = {144}, Number = {2}, Pages = {235-241}, Publisher = {Oxford University Press (OUP)}, Year = {2004}, Month = {February}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The Opegrapha species with 3-septate ascospores growing on Pertusaria and Ochrolechia are revised. Two species are recognized: Opegrapha anomea (of which O. pertusariae, O. quaternella, O. wetmorei and possibly Leciographa weissii are considered to be synonyms), and O. blakii Ertz & Diederich sp. nov. described from a sterile lichen with an Ochrolechia-like thallus, known from Ecuador and Venezuela. Opegrapha anomea and several related lichenicolous species with roundish or irregular, often multilocular ascomata are morphologically intermediate between Opegrapha and Plectocarpon, and might represent a distinct genus. © 2004 The Linnean Society of London.}, Doi = {10.1111/j.1095-8339.2003.00239.x}, Key = {fds329504} } @article{fds329454, Author = {Miadlikowska, J and Lutzoni, F and Goward, T and Zoller, S and Posada, D}, Title = {New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex.}, Journal = {Mycologia}, Volume = {95}, Number = {6}, Pages = {1181-1203}, Year = {2003}, Month = {November}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The Peltigera canina species complex consists of foliose lichenized bitunicate ascohymenial discomycetes forming section Peltigera within the genus Peltigera (Lecanoromycetes, lichen-forming Ascomycetes). To test the circumscription of highly polymorphic species and to resolve relationships among putative members of the P. canina complex, part of the nuclear ribosomal DNA large subunit (LSU rDNA) and the entire internal-transcribed spacer (ITS rDNA) were sequenced for 84 individuals representing 33 putative Peltigera taxa. Seventeen of the 25 taxa from the P. canina complex are well established and widely accepted. The remaining eight taxa have been proposed recently but are undescribed. A hypervariable region in ITS1 (ITS1-HR, sites 111-237 in our alignment) showed remarkable variation in length, especially in the P. canina complex, ranging from 8 to 126 bp, and contained several microsatellites. We describe here an alignment-free method to code such large gap-rich hypervariable regions for phylogenetic analyses. Variation among ITS1-HR sequences greatly contributed to species delimitation and species identification and can be a major asset to future population studies for specific species within section Peltigera. Sequences of ITS1-HR alone were sufficient to identify all existing species of Peltigera from the P. canina species complex and related sections Retifoveatae and Horizontales included in this study. However, only when INAASE (for short ambiguously aligned regions) and ITS1-HR coded characters were added to the combined analysis of nonambiguous LSU and ITS sites was it possible to reach the level of phylogenetic resolution and support necessary to disentangle the P. canina complex. We report here complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. canina complex (P. canina, P. cinnamomea, P. degenii, P. evansiana, P. frigida, P. kristinssonii, P. laciniata, P. lambinonii, P. lepidophora, P. membranacea, P. monticola, P. ponojensis, P. praetextata, P. rufescens and P. ulcerata). Four of the eight newly proposed but undescribed taxa most likely represent new species (P. "fuscopraetextata", P. "neocanina", P. "neorufescens" and P. "scotteri") within the P. canina complex. We found that morphologically and chemically distinct P. didactyla s. str. and P. didactyla var. extenuata form two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level (P. extenuata). The North American and European populations of the morphologically uniform P. degenii might represent two sibling species because they were found to be genetically distinct and monophyletic. Two major monophyletic groups within the P. canina complex (CICADE = CInnamomea + CAnina + DEgenii group and PORUDI = POnojensis + RUfescens + DIdactyla group) seem to be correlated with different humidity preferences. Although some authors previously have suggested interspecies recombination within the P. canina complex, we did not find statistically significant evidence for this phenomenon based on LSU and ITS sequences.}, Doi = {10.1080/15572536.2004.11833027}, Key = {fds329454} } @article{fds329505, Author = {Goffinet, B and Miadlikowska, J and Goward, T}, Title = {Phylogenetic inferences based on nrDNA sequences support five morphospecies within the Peltigera didactyla complex (Lichenized Ascomycota)}, Journal = {Bryologist}, Volume = {106}, Number = {3}, Pages = {349-364}, Publisher = {American Bryological and Lichenological Society}, Year = {2003}, Month = {January}, url = {http://dx.doi.org/10.1639/01}, Abstract = {The Peltigera didactyla complex comprises species of section Peltigera with laminal and submarginal soredia. Three species (P. didactyla, P. lambinonii, and P. ulcerata) and one atypical variety (P. didactyla var. extenuata) are currently recognized within this complex. Phylogenetic inferences of the entire Internal Transcribed Spacer region (ITS) and the 5′ half of the gene encoding the large subunit of the rRNA reveal a robust structure within the complex. Under both the maximum parsimony and the maximum likelihood criterion, P. didactyla is resolved as a polyphyletic entity, whereas P. ulcerata, P. lambinonii, and P. didactyla var. extenuata are delimited as monophyletic entities. Peltigera didactyla var. extenuata appears basal within the group, whereas var. didactyla is nested within a clade that also comprises P. lambinonii and P. ulcerata. The polyphyly of P. didactyla is further characterized by the existence of populations that resemble var. extenuata, but differ by their brownish upper cortex. These populations, all from the boreal zone of Canada, compose a monophyletic group sister to the P. didactyla-P. lambinonii clade. For P. didactyla to satisfy a phylogenetic species concept, the var. extenuata is reinstated at the species level, and a new species, P. castanea, is described. Three populations sampled are characterized by unique sequences that may indicate the presence of additional cryptic taxa within the complex. A key to the accepted species is provided. The presence of P. lambinonii in Australia is confirmed and P. ulcerata is reported as new for Chile.}, Doi = {10.1639/01}, Key = {fds329505} } @article{fds329506, Author = {Ertz, D and Zhurbenko, M and Diederich, P and Miadlikowska, J}, Title = {A new species of Plectocarpon (Lichenicolous Roccellaceae, Ascomycota) on Peltigera}, Journal = {Bryologist}, Volume = {106}, Number = {3}, Pages = {465-467}, Publisher = {American Bryological and Lichenological Society}, Year = {2003}, Month = {January}, url = {http://dx.doi.org/10.1639/15}, Abstract = {A new lichenicolous species, Plectocarpon peltigerae, growing on Peltigera leucophlebia thalli, is described from Canada and Russia.}, Doi = {10.1639/15}, Key = {fds329506} } @article{fds329455, Author = {McDonald, T and Miadlikowska, J and Lutzoni, F}, Title = {The lichen genus Sticta in the Great Smoky Mountains: A phylogenetic study of morphological, chemical, and molecular data}, Journal = {Bryologist}, Volume = {106}, Number = {1}, Pages = {61-79}, Publisher = {American Bryological and Lichenological Society}, Year = {2003}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {In this paper we segregate specimens from the genus Sticta in the Great Smoky Mountains National Park into phenotypic groups corresponding to putative species using traditional taxonomic methods, paying particular attention to specimens from the S. weigelii s. 1. group, then employ phylogenetic analyses and rigorous statistics to test the robustness of these species groups. In order to circumscribe putative species and to resolve the S. weigelii complex, morphological, chemical, and molecular characters from the nuclear ribosomal DNA sequences of the entire Internal Transcribed Spacer region are analyzed separately and simultaneously using maximum parsimony or maximum likelihood. In addition to the bootstrap method, Bayesian statistics with the Markov Chain Monte Carlo algorithm are used to estimate branch robustness on the resulting reconstructed trees. Five out of six analyses recover the same five monophyletic putative species from the genus Sticta, indicating the concordance of DNA-based and morphology-based species delimitation. The phylogenies show that lichens identified as S. weigelii represented S. beauvoisii and the two new species described here - S. carolinensis and S. fragilinata. Sticta weigelii s. s. does not occur in the park. Specimens from Oregon identified as S. weigelii belong to another unnamed Sticta taxon. The remaining two monophyletic groups represent two species well known from the park-S. fuliginosa and S. limbata. Characteristics of secondary compounds detected by Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography (HPLC) in S. fragilinata thalli are provided. Detailed descriptions, including morphology and chemistry, are provided for four Sticta species found in the Smoky Mountains: S. beauvoisii, S. carolinensis, S. fragilinata and S. fuliginosa.}, Doi = {10.1639/0007-2745(2003)106[0061:TLGSIT]2.0.CO;2}, Key = {fds329455} } @article{fds328024, Author = {Goffinet, B. and Miadlikowska, J. and Goward, T.}, Title = {Phylogenetic inferences support five morphospecies within the morphologically, chemically, and ecologically diverse Peltigera didactyla species complex (lichenized Ascomycota).}, Journal = {The Bryologist}, Volume = {106}, Pages = {349-364}, Year = {2003}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds328024} } @article{fds328026, Author = {Ertz, D. and Zhurbenko, M. and Diederich, P. and Miadlikowska, J.}, Title = {A new species of Plectocarpon on Peltigera (lichenicolous Roccellaceae, Ascomycota).}, Journal = {The Lichenologist}, Volume = {106}, Pages = {465-467}, Year = {2003}, url = {http://lutzonilab.org/publications-datasets/}, Key = {fds328026} } @article{fds329456, Author = {Miadlikowska, J and McCune, B and Lutzoni, F}, Title = {Pseudocyphellaria perpetua, a new lichen from western North America}, Journal = {Bryologist}, Volume = {105}, Number = {1}, Pages = {1-10}, Publisher = {American Bryological and Lichenological Society}, Year = {2002}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Pseudocyphellaria perpetua McCune & Miadlikowska is described as a new species of lichenized fungus from Oregon, U.S.A. Morphologically similar to some forms of P. crocata, P. perpetua is separated from that species by a yellow medulla and predominantly marginal soralia. Comparison of ITS and LSU nrDNA sequences support taxonomic distinctness of these two species. Phylogenetic analyses were conducted on LSU and ITS nrDNA data sets separately and simultaneously using maximum parsimony and maximum likelihood as optimization criteria. All analyses except one (maximum parsimony on LSU nrDNA data alone) confirmed the monophyly of P. perpetua. There are two distinct groups within the P. perpetua clade represented by specimens sampled from near the type locality in Oregon, and specimens outside of Oregon (eastern Canada, eastern Russia and eastern U.S.A.). The genus Pseudocyphellaria is very likely polyphyletic, consisting of at least two highly divergent groups.}, Doi = {10.1639/0007-2745(2002)105[0001:PPANLF]2.0.CO;2}, Key = {fds329456} } @article{fds329457, Author = {Miadlikowska, J and Lutzoni, F}, Title = {Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA data}, Journal = {International Journal of Plant Sciences}, Volume = {161}, Number = {6}, Pages = {925-958}, Publisher = {University of Chicago Press}, Year = {2000}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi- and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra- and inter-specific levels is present in this genus. Compared to many other genera of macrolichens: its taxonomy, including chemotaxonomy, still remains poorly understood. Existing infrageneric classifications of Peltigera are almost exclusively based on photobiont composition of the thallus. These classifications assumed that bi- and trimembered taxa were distinct monophyletic entities. The genus Peltigera has never been the focus of a comprehensive phylogenetic study. The most recent and widely accepted subdivision of the genus into seven groups is based mainly on morphological and chemical characters. Relationships among species of Peltigera are investigated here using chemical, morphological, and large subunit nuclear ribosomal DNA (LSU nrDNA) data. We test the monophyly of these seven morpho-chemical Peltigera groups and propose a classification based on a phylogenetic approach. Data sets of 42 chemical characters (terpenoids), 31 morphological characters, and 1135 LSU nrDNA characters for 96 samples representing 38 Peltigera species, eight undescribed putative Peltigera species, and nine species from seven potentially closely related genera from Peltigerineae were subjected to maximum parsimony analyses. Morphological, chemical, and molecular analyses were carried out independently and on a combined data set. Monophyly of Peltigera, including Hydrothyria, was confirmed. The genus Hydrothyria is transferred to Peltigera and a new combination Peltigera hydrothyria Miadlikowska and Lutzoni is proposed. Eight monophyletic sections within the genus Peltigera, with high bootstrap support, are circumscribed: sections Peltigera, Polydactylon Miadlikowska and Lutzoni, Chloropeltigera Gyeln., Peltidea (Ach.) Vain., Horizontales Miadlikowska and Lutzoni, Retifoveatae Miadlikowska and Lutzoni, Phlebia Wallr., and Hydrothyriae Miadlikowska and Lutzoni. Unequivocal morphological and chemical synapomorphies for all sections except section Peltidea are recognized and presented. A key for identification of the sections is provided. In addition, a key based on four main terpenoids for determination of the chemotypes and species within section Polydactylon is included. Five terpenoids (50-54) identified on thin-layer chromatography plates for P. elisabethae and P. horizontalis chemotype I are added to the list of substances found in Peltigera. Five chemotypes, mainly from Poland and Norway, are reported from Peltigera thalli for the first time: P. malacea chemotype V, P. leucophlebia chemotype II, P. hymenina chemotypes II and III, and P. collina chemotype IV. Three main types of vein structure in Peltigera were recognized based on SEM studies.}, Doi = {10.1086/317568}, Key = {fds329457} } @article{fds329507, Author = {Goffinet, B and Miadlikowska, J}, Title = {Peltigera phyllidiosa (Peltigeraceae, ascomycotina), a new species from the Southern Appalachians corroborated by its sequences}, Journal = {Lichenologist}, Volume = {31}, Number = {3}, Pages = {247-256}, Publisher = {Cambridge University Press (CUP)}, Year = {1999}, Month = {January}, url = {http://lutzonilab.org/publications-datasets/}, Abstract = {The new species Peltigera phyllidiosa Goffinet and Miadlikowska from the Southern Appalachians, eastern U.S.A., is closely related to P. collina and P. neckeri. Like these species it has a glabrous upper cortex and black fingernail- or saddle-shaped apothecial discs, but differs in its laminal phyllidia. Variation in nucleotide sequences of the Internal Transcribed Spacer (ITS) of the nrDNA repeat region correlates with the presence or absence of phyllidia, supporting the distinction of P. phyllidiosa from P. collina and P. neckeri.}, Doi = {10.1006/lich.1998.0201}, Key = {fds329507} } @article{fds329508, Author = {Hawksworth, DL and Miadlikowska, J}, Title = {New species of lichenicolous fungi occurring on Peltigera in Ecuador and Europe}, Journal = {Mycological Research}, Volume = {101}, Number = {9}, Pages = {1127-1134}, Publisher = {Elsevier BV}, Year = {1997}, Month = {January}, url = {http://dx.doi.org/10.1017/S0953756297003778}, Abstract = {A study of the lichenicolous fungi occurring on species of the lichenized genus Peltigera has resulted in six new species: Libertiella curvispora, L. didymospora, L. fennica Alstrup, Polycoccum superficiale, Roselliniella peltigericola, and Zwackhiomyces Kiszkianus. A key to the five known species of Libertiella is included. This paper brings the number of fungi known on this host to 87, of which 61 are not known from any other host genus, providing additional evidence for the richness of Peltigera thalli as a host for novel fungi. The possible hypotheses to explain the richness of this host genus for lichenicolous fungi are enumerated; these are not mutually exclusive.}, Doi = {10.1017/S0953756297003778}, Key = {fds329508} } @article{fds329509, Author = {Hawksworth, DL and Mia̧dlikowska, J}, Title = {Vagnia, a remarkable coelomycete producing a black columnar cirrus on Peltigera in Poland}, Journal = {Lichenologist}, Volume = {29}, Number = {1}, Pages = {45-49}, Publisher = {Cambridge University Press (CUP)}, Year = {1997}, Month = {January}, url = {http://dx.doi.org/10.1006/lich.1996.0059}, Abstract = {The new genus Vagnia is introduced for the single species V. cirriformia discovered on thalli of Peltigera in Poland; it appears to be a pathogen as the cortex is destroyed in a rounded patch within which the conidiomata occur. The fungus is characterized by cupulate to doliiform conidiomata clothed in white hairs and from which a black columnar cirrus of conidia arises. The simple ellipsoid conidia are hyaline when viewed individually and are formed enteroblastically from elongate conidiogenous cells supported by branched conidiophores.}, Doi = {10.1006/lich.1996.0059}, Key = {fds329509} } @article{fds328030, Author = {Hawksworth, D. L. and Miadlikowska, J.}, Title = {Vagnia, a remarkable celeomycete producing black columnar cirrus on Peltigera in Poland.}, Journal = {The Lichenologist}, Volume = {29}, Pages = {45-49}, Year = {1997}, Key = {fds328030} } | |
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