Duke Herbarium : Publications since January 2023

%% Aguero, Blanka   
@article{fds372350,
   Author = {Piatkowski, B and Weston, DJ and Aguero, B and Duffy, A and Imwattana,
             K and Healey, AL and Schmutz, J and Shaw, AJ},
   Title = {Divergent selection and climate adaptation fuel genomic
             differentiation between sister species of Sphagnum (peat
             moss).},
   Journal = {Annals of botany},
   Volume = {132},
   Number = {3},
   Pages = {499-512},
   Year = {2023},
   Month = {November},
   url = {http://dx.doi.org/10.1093/aob/mcad104},
   Abstract = {<h4>Background and aims</h4>New plant species can evolve
             through the reinforcement of reproductive isolation via
             local adaptation along habitat gradients. Peat mosses
             (Sphagnaceae) are an emerging model system for the study of
             evolutionary genomics and have well-documented niche
             differentiation among species. Recent molecular studies have
             demonstrated that the globally distributed species Sphagnum
             magellanicum is a complex of morphologically cryptic
             lineages that are phylogenetically and ecologically
             distinct. Here, we describe the architecture of genomic
             differentiation between two sister species in this complex
             known from eastern North America: the northern S. diabolicum
             and the largely southern S. magniae.<h4>Methods</h4>We
             sampled plant populations from across a latitudinal gradient
             in eastern North America and performed whole genome and
             restriction-site associated DNA sequencing. These sequencing
             data were then analyzed computationally.<h4>Key
             results</h4>Using sliding-window population genetic analyses
             we find that differentiation is concentrated within
             'islands' of the genome spanning up to 400 kb that are
             characterized by elevated genetic divergence, suppressed
             recombination, reduced nucleotide diversity and increased
             rates of non-synonymous substitution. Sequence variants that
             are significantly associated with genetic structure and
             bioclimatic variables occur within genes that have
             functional enrichment for biological processes including
             abiotic stress response, photoperiodism and hormone-mediated
             signalling. Demographic modelling demonstrates that these
             two species diverged no more than 225 000 generations ago
             with secondary contact occurring where their ranges
             overlap.<h4>Conclusions</h4>We suggest that this
             heterogeneity of genomic differentiation is a result of
             linked selection and reflects the role of local adaptation
             to contrasting climatic zones in driving speciation. This
             research provides insight into the process of speciation in
             a group of ecologically important plants and strengthens our
             predictive understanding of how plant populations will
             respond as Earth's climate rapidly changes.},
   Doi = {10.1093/aob/mcad104},
   Key = {fds372350}
}


%% 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}
}


%% 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}
}


%% Pryer, Kathleen M.   
@article{fds373350,
   Author = {Hay, NM and Windham, MD and Mandáková, T and Lysak, MA and Hendriks,
             KP and Mummenhoff, K and Lens, F and Pryer, KM and Bailey,
             CD},
   Title = {A Hyb-Seq phylogeny of Boechera and related genera using a
             combination of Angiosperms353 and Brassicaceae-specific bait
             sets.},
   Journal = {American journal of botany},
   Volume = {110},
   Number = {10},
   Pages = {e16226},
   Year = {2023},
   Month = {October},
   url = {http://dx.doi.org/10.1002/ajb2.16226},
   Abstract = {<h4>Premise</h4>Although Boechera (Boechereae, Brassicaceae)
             has become a plant model system for both ecological genomics
             and evolutionary biology, all previous phylogenetic studies
             have had limited success in resolving species relationships
             within the genus. The recent effective application of
             sequence data from target enrichment approaches to resolve
             the evolutionary relationships of several other challenging
             plant groups prompted us to investigate their usefulness in
             Boechera and Boechereae.<h4>Methods</h4>To resolve the
             phylogeny of Boechera and closely related genera, we
             utilized the Hybpiper pipeline to analyze two combined bait
             sets: Angiosperms353, with broad applicability across
             flowering plants; and a Brassicaceae-specific bait set
             designed for use in the mustard family. Relationships for
             101 samples representing 81 currently recognized species
             were inferred from a total of 1114 low-copy nuclear genes
             using both supermatrix and species coalescence
             methods.<h4>Results</h4>Our analyses resulted in a
             well-resolved and highly supported phylogeny of the tribe
             Boechereae. Boechereae is divided into two major clades, one
             comprising all western North American species of Boechera,
             the other encompassing the eight other genera of the tribe.
             Our understanding of relationships within Boechera is
             enhanced by the recognition of three core clades that are
             further subdivided into robust regional species
             complexes.<h4>Conclusions</h4>This study presents the first
             broadly sampled, well-resolved phylogeny for most known
             sexual diploid Boechera. This effort provides the foundation
             for a new phylogenetically informed taxonomy of Boechera
             that is crucial for its continued use as a model
             system.},
   Doi = {10.1002/ajb2.16226},
   Key = {fds373350}
}

@article{fds372242,
   Author = {Hay, NM and Akinwuntan, JV and Cai, V and Windham, MD and Pryer,
             KM},
   Title = {Exploring Past and Future Distributions of the Rare
             Appalachian Oak Fern Using MaxEnt Modeling},
   Journal = {American Fern Journal},
   Volume = {113},
   Number = {2},
   Pages = {109-125},
   Year = {2023},
   Month = {June},
   url = {http://dx.doi.org/10.1640/0002-8444-113.2.109},
   Abstract = {Abstract . Anthropogenic climate change is projected to have
             an especially negative impact on the survival of plants that
             are dependent on limited microclimatic refugia or that
             already reside at their climatic extreme. Gymnocarpium
             appalachianum is a narrowly endemic fern restricted to cold
             mountaintops and algific vents in the central and southern
             Appalachian region of eastern North America. It is the much
             rarer of the two documented diploid parents of the
             circumboreal allotetraploid G. dryopteris - one of the most
             widespread fern species on the planet. Gymnocarpium
             appalachianum is a good case study for forecasting how
             evolutionarily significant, but rare, species might survive
             on a warming planet. We utilize an ecological niche modeling
             approach (MaxEnt) to explore the projected distribution of
             G. appalachianum under past (Last Glacial Maximum) and
             future climate models. All known verified herbarium records
             of G. appalachianum were georeferenced, for a total of 70
             occurrence points. Nineteen standard bioclimatic variables
             extracted from WorldClim were used to model near-current
             climate projections; representative concentration pathways
             (RCPs 2.6 and 8.5) were used for future climate projections
             (2070). The temperature annual range, mean temperature of
             warmest quarter, precipitation of driest month,
             precipitation of coldest quarter, and mean diurnal range
             were identified as the key variables for shaping the
             distribution of G. appalachianum. An unanticipated result
             from our analyses is that G. appalachianum has past and
             current projected habitat suitability in Alaska. Because
             this overlaps with the current range of G. disjunctum, the
             other diploid parent of G. dryopteris, it suggests a
             possible region of origin for this circumboreal tetraploid
             descendent of G. appalachianum - a research avenue to be
             pursued in the future. Our study envisions a dire fate for
             G. appalachianum; its survival will likely require an urgent
             contingency plan that includes human-mediated population
             relocation to cooler, northern locations. Understanding the
             long-term sustainability of narrowly endemic plants such as
             G. appalachianum is critical in decisions about their
             management and conservation.},
   Doi = {10.1640/0002-8444-113.2.109},
   Key = {fds372242}
}

@article{fds369759,
   Author = {Windham, MD and Picard, KT and Pryer, KM},
   Title = {An in-depth investigation of cryptic taxonomic diversity in
             the rare endemic mustard Draba maguirei.},
   Journal = {American journal of botany},
   Volume = {110},
   Number = {3},
   Pages = {1-22},
   Year = {2023},
   Month = {March},
   url = {http://dx.doi.org/10.1002/ajb2.16138},
   Abstract = {<h4>Premise</h4>Previously published evidence suggests that
             Draba maguirei, a mustard endemic to a few localities in the
             Bear River, Wellsville, and Wasatch Mountains of northern
             Utah, may represent a cryptic species complex rather than a
             single species. Conservation concerns prompted an in-depth
             systematic study of this taxon and its putative
             relatives.<h4>Methods</h4>Sampling most known populations of
             D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei
             var. burkei), we integrate data from geography, ecology,
             morphology, cytogenetics and pollen, enzyme electrophoresis,
             and the phylogenetic analysis of nuclear internal
             transcribed spacer sequences to explore potential taxonomic
             diversity in the species complex.<h4>Results</h4>Draba
             maguirei var. burkei is shown here to be a distinct species
             (D. burkei) most closely related to D. globosa, rather than
             to D. maguirei. Within D. maguirei s.s., the northern (high
             elevation) and southern (low elevation) population clusters
             are genetically isolated and morphologically
             distinguishable, leading to the recognition here of the
             southern taxon as D. maguirei subsp. stonei.<h4>Conclusions</h4>Our
             study reveals that plants traditionally assigned to D.
             maguirei comprise three genetically divergent lineages (D.
             burkei and two newly recognized subspecies of D. maguirei),
             each exhibiting a different chromosome number and occupying
             a discrete portion of the geographic range. Although
             previously overlooked and underappreciated taxonomically,
             the three taxa are morphologically recognizable based on the
             distribution and types of trichomes present on the leaves,
             stems, and fruit. Our clarification of the diversity and
             distribution of these taxa provides an improved framework
             for conservation efforts.},
   Doi = {10.1002/ajb2.16138},
   Key = {fds369759}
}


%% Shaw, A. Jonathan   
@article{fds369316,
   Author = {Healey, AL and Piatkowski, B and Lovell, JT and Sreedasyam, A and Carey,
             SB and Mamidi, S and Shu, S and Plott, C and Jenkins, J and Lawrence, T and Aguero, B and Carrell, AA and Nieto-Lugilde, M and Talag, J and Duffy,
             A and Jawdy, S and Carter, KR and Boston, L-B and Jones, T and Jaramillo-Chico, J and Harkess, A and Barry, K and Keymanesh, K and Bauer, D and Grimwood, J and Gunter, L and Schmutz, J and Weston, DJ and Shaw, AJ},
   Title = {Newly identified sex chromosomes in the Sphagnum (peat moss)
             genome alter carbon sequestration and ecosystem
             dynamics.},
   Journal = {Nature plants},
   Volume = {9},
   Number = {2},
   Pages = {238-254},
   Year = {2023},
   Month = {February},
   url = {http://dx.doi.org/10.1038/s41477-022-01333-5},
   Abstract = {Peatlands are crucial sinks for atmospheric carbon but are
             critically threatened due to warming climates. Sphagnum
             (peat moss) species are keystone members of peatland
             communities where they actively engineer hyperacidic
             conditions, which improves their competitive advantage and
             accelerates ecosystem-level carbon sequestration. To dissect
             the molecular and physiological sources of this unique
             biology, we generated chromosome-scale genomes of two
             Sphagnum species: S. divinum and S. angustifolium. Sphagnum
             genomes show no gene colinearity with any other reference
             genome to date, demonstrating that Sphagnum represents an
             unsampled lineage of land plant evolution. The genomes also
             revealed an average recombination rate an order of magnitude
             higher than vascular land plants and short putative U/V sex
             chromosomes. These newly described sex chromosomes interact
             with autosomal loci that significantly impact growth across
             diverse pH conditions. This discovery demonstrates that the
             ability of Sphagnum to sequester carbon in acidic peat bogs
             is mediated by interactions between sex, autosomes and
             environment.},
   Doi = {10.1038/s41477-022-01333-5},
   Key = {fds369316}
}

@article{fds374506,
   Author = {Robinson, S. C. and M. Nieto-Lugilde and A. M. Duffy and K. M. Munoz and B. Aguero and A. Merced and K. Hassel and K. I. Flatberg and A. J.
             Shaw. 2023},
   Title = {The Sphagnum cuspidatum complex: phylogeny, specie
             delimitation, and morphology},
   Journal = {Biological Journal of the Linnean Society},
   Volume = {https://doi.org/10.1093/biolinnean/blad1},
   Year = {2023},
   Key = {fds374506}
}

@article{fds374505,
   Author = {Piatkowski, B. and D. J. Weston and B. Aguero and A. Duffy and K.
             Imwattana, A. L. Healey and J. Schmutz and A. Jonathan
             Shaw},
   Title = {Divergent selection fuels genomic differentiation between
             incipient species of Sphagnum (peat moss)},
   Journal = {Annals of Botany},
   Volume = {132},
   Pages = {499–512},
   Year = {2023},
   Key = {fds374505}
}

@article{fds374502,
   Author = {Shaw, A. J. and M. Nieto-Lugilde and B. Aguero and A. Duffy and B. T.
             Piatkowski and J. Jaramillo-Chico and S. Robinson and K. Hassel and K.
             I. Flatberg and D. J. Weston and S. Schuette and K. A.
             Hicks},
   Title = {Sphagnum diabolicum sp. nov. and S. magniae sp. nov.;
             morphological variation and taxonomy of the “S.
             magellanicum complex”},
   Journal = {The Bryologist},
   Volume = {126},
   Pages = {69-89},
   Year = {2023},
   Key = {fds374502}
}

@article{fds374504,
   Author = {Shaw, A. J. and A. Duffy and M. Nieto-Lugilde and B. Aguero and S.
             Schuette, S. Robinson and J. Loveland and K. A. Hicks and D. Weston and B. Piatkowski and M. Kolton and J. Koska and A.
             Healey},
   Title = {Clonality, local population structure, and gametophyte sex
             ratios in cryptic species of the Sphagnum magellanicum
             complex},
   Journal = {Annals of Botany},
   Volume = {132},
   Pages = {77–94},
   Year = {2023},
   Key = {fds374504}
}

@article{fds374503,
   Author = {Wieczynski, D. and Yoshimura, K. and Denison, E. and Geisen, S. and DeBruyn, J. and Shaw, A. J. and Weston, D. and Pelletier, D. and Wilhelm, S. and J-P., Gibert},
   Title = {Viral infections likely mediate microbial controls on
             ecosystem responses to global warming},
   Journal = {FEMS Microbiology Ecology},
   Year = {2023},
   Key = {fds374503}
}


%% Vilgalys, Rytas J.   
@article{fds376011,
   Author = {Marqués-Gálvez, JE and Pandharikar, G and Basso, V and Kohler, A and Lackus, ND and Barry, K and Keymanesh, K and Johnson, J and Singan, V and Grigoriev, IV and Vilgalys, R and Martin, F and Veneault-Fourrey,
             C},
   Title = {Populus MYC2 orchestrates root transcriptional reprogramming
             of defence pathway to impair Laccaria bicolor
             ectomycorrhizal development.},
   Journal = {The New phytologist},
   Volume = {242},
   Number = {2},
   Pages = {658-674},
   Year = {2024},
   Month = {April},
   url = {http://dx.doi.org/10.1111/nph.19609},
   Abstract = {The jasmonic acid (JA) signalling pathway plays an important
             role in the establishment of the ectomycorrhizal symbiosis.
             The Laccaria bicolor effector MiSSP7 stabilizes JA
             corepressor JAZ6, thereby inhibiting the activity of Populus
             MYC2 transcription factors. Although the role of MYC2 in
             orchestrating plant defences against pathogens is well
             established, its exact contribution to ECM symbiosis remains
             unclear. This information is crucial for understanding the
             balance between plant immunity and symbiotic relationships.
             Transgenic poplars overexpressing or silencing for the two
             paralogues of MYC2 transcription factor (MYC2s) were
             produced, and their ability to establish ectomycorrhiza was
             assessed. Transcriptomics and DNA affinity purification
             sequencing were performed. MYC2s overexpression led to a
             decrease in fungal colonization, whereas its silencing
             increased it. The enrichment of terpene synthase genes in
             the MYC2-regulated gene set suggests a complex interplay
             between the host monoterpenes and fungal growth.
             Several root monoterpenes have been identified as
             inhibitors of fungal growth and ECM symbiosis. Our results
             highlight the significance of poplar MYC2s and terpenes in
             mutualistic symbiosis by controlling root fungal
             colonization. We identified poplar genes which direct or
             indirect control by MYC2 is required for ECM establishment.
             These findings deepen our understanding of the molecular
             mechanisms underlying ECM symbiosis.},
   Doi = {10.1111/nph.19609},
   Key = {fds376011}
}

@article{fds376823,
   Author = {Lofgren, L and Nguyen, NH and Kennedy, P and Pérez-Pazos, E and Fletcher, J and Liao, H-L and Wang, H and Zhang, K and Ruytinx, J and Smith, AH and Ke, Y-H and Cotter, HVT and Engwall, E and Hameed, KM and Vilgalys, R and Branco, S},
   Title = {Suillus: an emerging model for the study of ectomycorrhizal
             ecology and evolution.},
   Journal = {The New phytologist},
   Year = {2024},
   Month = {April},
   url = {http://dx.doi.org/10.1111/nph.19700},
   Abstract = {Research on mycorrhizal symbiosis has been slowed by a lack
             of established study systems. To address this challenge, we
             have been developing Suillus, a widespread ecologically and
             economically relevant fungal genus primarily associated with
             the plant family Pinaceae, into a model system for studying
             ectomycorrhizal (ECM) associations. Over the last decade, we
             have compiled extensive genomic resources, culture
             libraries, a phenotype database, and protocols for
             manipulating Suillus fungi with and without their tree
             partners. Our efforts have already resulted in a large
             number of publicly available genomes, transcriptomes, and
             respective annotations, as well as advances in our
             understanding of mycorrhizal partner specificity and host
             communication, fungal and plant nutrition, environmental
             adaptation, soil nutrient cycling, interspecific
             competition, and biological invasions. Here, we highlight
             the most significant recent findings enabled by Suillus,
             present a suite of protocols for working with the genus, and
             discuss how Suillus is emerging as an important model to
             elucidate the ecology and evolution of ECM
             interactions.},
   Doi = {10.1111/nph.19700},
   Key = {fds376823}
}

@article{fds373944,
   Author = {Swenie, RA and Looney, BP and Ke, Y-H and Alejandro Rojas and J and Cubeta,
             MA and Langer, GJ and Vilgalys, R and Brandon Matheny,
             P},
   Title = {PacBio high-throughput multi-locus sequencing reveals high
             genetic diversity in mushroom-forming fungi.},
   Journal = {Molecular ecology resources},
   Volume = {24},
   Number = {1},
   Pages = {e13885},
   Year = {2024},
   Month = {January},
   url = {http://dx.doi.org/10.1111/1755-0998.13885},
   Abstract = {Multi-locus sequence data are widely used in fungal
             systematic and taxonomic studies to delimit species and
             infer evolutionary relationships. We developed and assessed
             the efficacy of a multi-locus pooled sequencing method using
             PacBio long-read high-throughput sequencing. Samples
             included fresh and dried voucher specimens, cultures and
             archival DNA extracts of Agaricomycetes with an emphasis on
             the order Cantharellales. Of the 283 specimens sequenced,
             93.6% successfully amplified at one or more loci with a mean
             of 3.3 loci amplified. Our method recovered multiple
             sequence variants representing alleles of rDNA loci and
             single copy protein-coding genes rpb1, rpb2 and tef1.
             Within-sample genetic variation differed by locus and
             taxonomic group, with the greatest genetic divergence
             observed among sequence variants of rpb2 and tef1 from
             corticioid Cantharellales. Our method is a cost-effective
             approach for generating accurate multi-locus sequence data
             coupled with recovery of alleles from polymorphic samples
             and multi-organism specimens. These results have important
             implications for understanding intra-individual genomic
             variation among genetic loci commonly used in species
             delimitation of fungi.},
   Doi = {10.1111/1755-0998.13885},
   Key = {fds373944}
}

@article{fds374383,
   Author = {Zhang, K and Wang, H and Tappero, R and Bhatnagar, JM and Vilgalys, R and Barry, K and Keymanesh, K and Tejomurthula, S and Grigoriev, IV and Kew,
             WR and Eder, EK and Nicora, CD and Liao, H-L},
   Title = {Ectomycorrhizal fungi enhance pine growth by stimulating
             iron-dependent mechanisms with trade-offs in symbiotic
             performance.},
   Journal = {The New phytologist},
   Year = {2023},
   Month = {December},
   url = {http://dx.doi.org/10.1111/nph.19449},
   Abstract = {Iron (Fe) is crucial for metabolic functions of living
             organisms. Plants access occluded Fe through interactions
             with rhizosphere microorganisms and symbionts. Yet, the
             interplay between Fe addition and plant-mycorrhizal
             interactions, especially the molecular mechanisms underlying
             mycorrhiza-assisted Fe processing in plants, remains largely
             unexplored. We conducted mesocosms in Pinus plants
             inoculated with different ectomycorrhizal fungi (EMF)
             Suillus species under conditions with and without Fe
             coatings. Meta-transcriptomic, biogeochemical, and X-ray
             fluorescence imaging analyses were applied to investigate
             early-stage mycorrhizal roots. While Fe addition promoted
             Pinus growth, it concurrently reduced mycorrhiza formation
             rate, symbiosis-related metabolites in plant roots, and
             aboveground plant carbon and macronutrient content. This
             suggested potential trade-offs between Fe-enhanced plant
             growth and symbiotic performance. However, the extent of
             this trade-off may depend on interactions between host
             plants and EMF species. Interestingly, dual EMF species were
             more effective at facilitating plant Fe uptake by inducing
             diverse Fe-related functions than single-EMF species. This
             subsequently triggered various Fe-dependent physiological
             and biochemical processes in Pinus roots, significantly
             contributing to Pinus growth. However, this resulted in a
             greater carbon allocation to roots, relatively reducing the
             aboveground plant carbon content. Our study offers critical
             insights into how EMF communities rebalance benefits of
             Fe-induced effects on symbiotic partners.},
   Doi = {10.1111/nph.19449},
   Key = {fds374383}
}

@article{fds372202,
   Author = {Gryganskyi, AP and Golan, J and Muszewska, A and Idnurm, A and Dolatabadi, S and Mondo, SJ and Kutovenko, VB and Kutovenko, VO and Gajdeczka, MT and Anishchenko, IM and Pawlowska, J and Tran, NV and Ebersberger, I and Voigt, K and Wang, Y and Chang, Y and Pawlowska, TE and Heitman, J and Vilgalys, R and Bonito, G and Benny, GL and Smith, ME and Reynolds, N and James, TY and Grigoriev, IV and Spatafora, JW and Stajich, JE},
   Title = {Sequencing the Genomes of the First Terrestrial Fungal
             Lineages: What Have We Learned?},
   Journal = {Microorganisms},
   Volume = {11},
   Number = {7},
   Pages = {1830},
   Year = {2023},
   Month = {July},
   url = {http://dx.doi.org/10.3390/microorganisms11071830},
   Abstract = {The first genome sequenced of a eukaryotic organism was for
             Saccharomyces cerevisiae, as reported in 1996, but it was
             more than 10 years before any of the zygomycete fungi, which
             are the early-diverging terrestrial fungi currently placed
             in the phyla Mucoromycota and Zoopagomycota, were sequenced.
             The genome for Rhizopus delemar was completed in 2008;
             currently, more than 1000 zygomycete genomes have been
             sequenced. Genomic data from these early-diverging
             terrestrial fungi revealed deep phylogenetic separation of
             the two major clades-primarily plant-associated saprotrophic
             and mycorrhizal Mucoromycota versus the primarily
             mycoparasitic or animal-associated parasites and commensals
             in the Zoopagomycota. Genomic studies provide many valuable
             insights into how these fungi evolved in response to the
             challenges of living on land, including adaptations to
             sensing light and gravity, development of hyphal growth, and
             co-existence with the first terrestrial plants. Genome
             sequence data have facilitated studies of genome
             architecture, including a history of genome duplications and
             horizontal gene transfer events, distribution and
             organization of mating type loci, rDNA genes and
             transposable elements, methylation processes, and genes
             useful for various industrial applications. Pathogenicity
             genes and specialized secondary metabolites have also been
             detected in soil saprobes and pathogenic fungi. Novel
             endosymbiotic bacteria and viruses have been discovered
             during several zygomycete genome projects. Overall, genomic
             information has helped to resolve a plethora of research
             questions, from the placement of zygomycetes on the
             evolutionary tree of life and in natural ecosystems, to the
             applied biotechnological and medical questions.},
   Doi = {10.3390/microorganisms11071830},
   Key = {fds372202}
}

@article{fds370537,
   Author = {Ke, Y-H and Branco, S and Bazzicalupo, AL and Nguyen, NH and Liao, H-L and Kennedy, P and Bruns, TD and Kuo, A and LaButti, K and Barry, K and Grigoriev, I and Vilgalys, R},
   Title = {Genomic determination of breeding systems and trans-specific
             evolution of HD MAT genes in suilloid fungi.},
   Journal = {Genetics},
   Volume = {224},
   Number = {2},
   Pages = {iyad069},
   Year = {2023},
   Month = {May},
   url = {http://dx.doi.org/10.1093/genetics/iyad069},
   Abstract = {Studying the signatures of evolution can help to understand
             genetic processes. Here, we demonstrate how the existence of
             balancing selection can be used to identify the breeding
             systems of fungi from genomic data. The breeding systems of
             fungi are controlled by self-incompatibility loci that
             determine mating types between potential mating partners,
             resulting in strong balancing selection at the loci. Within
             the fungal phylum Basidiomycota, two such
             self-incompatibility loci, namely HD MAT locus and P/R MAT
             locus, control mating types of gametes. Loss of function at
             one or both MAT loci results in different breeding systems
             and relaxes the MAT locus from balancing selection. By
             investigating the signatures of balancing selection at MAT
             loci, one can infer a species' breeding system without
             culture-based studies. Nevertheless, the extreme sequence
             divergence among MAT alleles imposes challenges for
             retrieving full variants from both alleles when using the
             conventional read-mapping method. Therefore, we employed a
             combination of read-mapping and local de novo assembly to
             construct haplotypes of HD MAT alleles from genomes in
             suilloid fungi (genera Suillus and Rhizopogon). Genealogy
             and pairwise divergence of HD MAT alleles showed that the
             origins of mating types predate the split between these two
             closely related genera. High sequence divergence,
             trans-specific polymorphism, and the deeply diverging
             genealogy confirm the long-term functionality and
             multiallelic status of HD MAT locus in suilloid fungi. This
             work highlights a genomics approach to studying breeding
             systems regardless of the culturability of organisms based
             on the interplay between evolution and genetics.},
   Doi = {10.1093/genetics/iyad069},
   Key = {fds370537}
}

@article{fds367835,
   Author = {Policelli, N and Hoeksema, JD and Moyano, J and Vilgalys, R and Vivelo,
             S and Bhatnagar, JM},
   Title = {Global pine tree invasions are linked to invasive root
             symbionts.},
   Journal = {The New phytologist},
   Volume = {237},
   Number = {1},
   Pages = {16-21},
   Year = {2023},
   Month = {January},
   url = {http://dx.doi.org/10.1111/nph.18527},
   Doi = {10.1111/nph.18527},
   Key = {fds367835}
}

@article{fds141088,
   Author = {PB Matheny and JM Curtis and V Hofstetter and MC Aime and JM Moncalvo and ZW Ge and JC Slot and JF Ammirati and TJ Baroni and NL Bougher and KW
             Hughes, DJ Lodge and RW Kerrigan and MT Seidl and DK Aanen and M
             DeNitis, GM Daniele and DE Desjardin and BR Kropp and LL Norvell and A
             Parker, EC Vellinga and R Vilgalys and DS Hibbett},
   Title = {Major clades of Agaricales: a multilocus phylogenetic
             overview.},
   Journal = {Mycologia, United States},
   Volume = {98},
   Number = {6},
   Pages = {982-95},
   Year = {2007},
   Month = {October},
   ISSN = {0027-5514},
   Keywords = {Agaricales Cluster Analysis DNA, Fungal DNA, Ribosomal
             Ecology Introns Mitochondrial Proton-Translocating ATPases
             Molecular Sequence Data Mycorrhizae Phylogeny* RNA,
             Ribosomal RNA, Ribosomal, 18S RNA, Ribosomal, 5.8S Sequence
             Analysis, DNA Sequence Homology chemistry classification*
             genetics genetics* physiology},
   Abstract = {An overview of the phylogeny of the Agaricales is presented
             based on a multilocus analysis of a six-gene region
             supermatrix. Bayesian analyses of 5611 nucleotide characters
             of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S
             ribosomal RNA genes recovered six major clades, which are
             recognized informally and labeled the Agaricoid,
             Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and
             Plicaturopsidoid clades. Each clade is discussed in terms of
             key morphological and ecological traits. At least 11 origins
             of the ectomycorrhizal habit appear to have evolved in the
             Agaricales, with possibly as many as nine origins in the
             Agaricoid plus Tricholomatoid clade alone. A family-based
             phylogenetic classification is sketched for the Agaricales,
             in which 30 families, four unplaced tribes and two
             informally named clades are recognized.},
   Language = {eng},
   Key = {fds141088}
}

@article{fds141089,
   Author = {JM Moncalvo and RH Nilsson and B Koster and SM Dunham and T Bernauer and PB
             Matheny, TM Porter and S Margaritescu and M Weiss and S Garnica and E
             Danell, G Langer and E Langer and E Larsson and KH Larsson and R
             Vilgalys},
   Title = {The cantharelloid clade: dealing with incongruent gene trees
             and phylogenetic reconstruction methods.},
   Journal = {Mycologia, United States},
   Volume = {98},
   Number = {6},
   Pages = {937-48},
   Year = {2007},
   Month = {October},
   ISSN = {0027-5514},
   Keywords = {Basidiomycota Computational Biology DNA, Fungal DNA,
             Mitochondrial DNA, Ribosomal Evolution, Molecular Molecular
             Sequence Data Phylogeny* RNA Polymerase II RNA, Ribosomal,
             18S RNA, Ribosomal, 28S Sequence Analysis, DNA
             classification* genetics genetics* methods*
             physiology},
   Abstract = {We reassessed the circumscription of the cantharelloid clade
             and identified monophyletic groups by using nLSU, nSSU,
             mtSSU and RPB2 sequence data. Results agreed with earlier
             studies that placed the genera Cantharellus, Craterellus,
             Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema,
             Botryobasidium and the family Ceratobasidiaceae in that
             clade. Phylogenetic analyses support monophyly of all genera
             except Sistotrema, which was highly polyphyletic. Strongly
             supported monophyletic groups were: (i) Cantharellus-Craterellus,
             Hydnum, and the Sistotrema confluens group; (ii)
             Clavulina-Membranomyces and the S. brinkmannii-oblongisporum
             group, with Multiclavula being possibly sister of that
             clade; (iii) the Sistotrema eximum-octosporum group; (iv)
             Sistotrema adnatum and S. coronilla. Positions of Sistotrema
             raduloides and S. athelioides were unresolved, as were basal
             relationships. Botryobasidium was well supported as the
             sister taxon of all the above taxa, while Ceratobasidiaceae
             was the most basal lineage. The relationship between
             Tulasnella and members of the cantharelloid clade will
             require further scrutiny, although there is cumulative
             evidence that they are probably sister groups. The rates of
             molecular evolution of both the large and small nuclear
             ribosomal RNA genes (nuc-rDNA) are much higher in
             Cantharellus, Craterellus and Tulasnella than in the other
             cantharelloid taxa, and analyses of nuc-rDNA sequences
             strongly placed Tulasnella close to Cantharellus-Craterellus.
             In contrast analyses with RPB2 and mtSSU sequences placed
             Tulasnella at the base of the cantharelloid clade. Our
             attempt to reconstruct a "supertree" from tree topologies
             resulting from separate analyses that avoided phylogenetic
             reconstruction problems associated with missing data and/or
             unalignable sequences proved unsuccessful.},
   Language = {eng},
   Key = {fds141089}
}

@article{fds141090,
   Author = {TY James and PM Letcher and JE Longcore and SE Mozley-Standridge and D
             Porter, MJ Powell and GW Griffith and R Vilgalys},
   Title = {A molecular phylogeny of the flagellated fungi
             (Chytridiomycota) and description of a new phylum
             (Blastocladiomycota).},
   Journal = {Mycologia, United States},
   Volume = {98},
   Number = {6},
   Pages = {860-71},
   Year = {2007},
   Month = {October},
   ISSN = {0027-5514},
   Keywords = {Chytridiomycota DNA, Fungal DNA, Ribosomal Fungi Microscopy,
             Electron, Transmission Phylogeny* RNA, Ribosomal, 18S RNA,
             Ribosomal, 28S RNA, Ribosomal, 5.8S Sequence Analysis, DNA
             chemistry classification* genetics genetics*
             ultrastructure},
   Abstract = {Chytridiomycota (chytrids) is the only phylum of true Fungi
             that reproduces with motile spores (zoospores). Chytrids
             currently are classified into five orders based on habitat,
             zoospore characters and life cycles. In this paper we
             estimate the phylogeny of the chytrids with DNA sequences
             from the ribosomal RNA operon (18S+5.8S+28S subunits). To
             our surprise the morphologically reduced parasites Olpidium
             and Rozella comprise two entirely new, and separate,
             lineages on the fungal tree. Olpidium brassicae groups among
             the Zygomycota, and Rozella spp. are the earliest branch to
             diverge in the fungal kingdom. The phylogeny also suggests
             that Chytridiomycota is not monophyletic and there are four
             major lineages of chytrids: Rozella spp., Olpidium
             brassicae, the Blastocladiales and a "core chytrid clade"
             containing the remaining orders and families and the
             majority of flagellated fungi. Within the core chytrid group
             11 subclades can be identified, each of which correlates
             well with zoospore ultrastructure or morphology. We provide
             a synopsis of each clade and its morphological
             circumscription. The Blastocladiales appears to be the
             sister taxon of most nonflagellated fungi. Based on
             molecular phylogenetic and ultrastructural characters this
             order is elevated to a phylum, the Blastocladiomycota.},
   Language = {eng},
   Key = {fds141090}
}

@article{fds141086,
   Author = {AE Arnold and DA Henk and RL Eells and F Lutzoni and R
             Vilgalys},
   Title = {Diversity and phylogenetic affinities of foliar fungal
             endophytes in loblolly pine inferred by culturing and
             environmental PCR.},
   Journal = {Mycologia, United States},
   Volume = {99},
   Number = {2},
   Pages = {185-206},
   Year = {2007},
   Month = {September},
   ISSN = {0027-5514},
   Keywords = {Biodiversity* DNA, Fungal DNA, Ribosomal DNA, Ribosomal
             Spacer Fungi North Carolina Phylogeny Pinus taeda Plant
             Leaves Polymerase Chain Reaction Sequence Analysis, DNA
             Symbiosis* chemistry classification* genetics growth &
             development isolation & purification* microbiology*},
   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.},
   Language = {eng},
   Key = {fds141086}
}