Duke Herbarium Lichens: Publications since January 2023

%% Lutzoni, Francois M.   
@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{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{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{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}
}


%% Miadlikowska, Jolanta M.   
@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{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{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{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}
}