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Phylogenomic reconstruction addressing the Peltigeralean backbone(Lecanoromycetes,Ascomycota)

Fungal Diversity 2021年第5期110卷 59-73页

作者： Todd J.Widhelm felix grewe Bernard Goffinet Mats Wedin Trevor Goward Luis F.Coca Isabel Distefano Alica Košuthová· H.Thorsten Lumbsch Science&Education The Grainger Bioinformatics CenterNegaunee Integrative Research CenterGantz Family Collections Centerand Pritzker Laboratory for Molecular SystematicsThe Field Museum1400 S.Lake Shore DriveChicagoIL 60605USA Department of Ecology and Evolutionary Biology University of Connecticut75 North Eagleville RoadStorrsCT 06269-3043USA Department of Botany Swedish Museum of Natural HistoryP.O.Box 5000710405 StockholmSweden Herbarium Beaty MuseumUniversity of British ColumbiaVancouverBC V6T 1Z4Canada Herbario Univ Caldas FAUC Edificio BicentenarioCalle 6526-10275 ManizalesColombia

Rapid radiations in Fungi are only beginning to be studied with phylogenomic *** evolutionary history of the lichenized fungal order Peltigerales has not been well resolved,particularly for the ***,we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples,representing 58 *** uneven,lineage-specific missing data and significant topological incongruence of individual exon trees,the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the *** in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree,due in part to conflicting signal in exon trees,suggesting rapid diversification events in the early evolution of the *** tree distance measures,we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon *** between the minimum and complete datasets in species tree inferences,bipartition analyses,and divergence time estimations displayed similar results,although the minimum dataset was characterized by higher levels of error in estimations of divergence *** our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers,but the target capture datasets had much higher support *** demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.

关键词： Lichenized fungi Phylogenomics Rapid radiations High-throughput sequencing

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Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi

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Fungal Diversity 2018年第5期92卷 31-41页

作者： David Pizarro Pradeep K.Divakar felix grewe Steven D.Leavitt Jen-Pan Huang Francesco Dal Grande Imke Schmitt Mats Wedin Ana Crespo H.Thorsten Lumbsch Departamento de Farmacologı́a Farmacognosia y BotánicaFacultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain Science&Education The Field Museum1400 S.Lake Shore DriveChicagoILUSA Department of Biology and M.L.Bean Life Science Museum Brigham Young UniversityLife Science Building 4102ProvoUT 84602USA Senckenberg Biodiversity and Climate Research Centre(SBiK-F) Senckenberganlage 2560325 Frankfurt am MainGermany Institute of Ecology Evolution and DiversityGoethe UniversityFrankfurt am MainMax-von-Laue-Str.960438 Frankfurt am MainGermany Department of Botany Swedish Museum of Natural HistoryPO Box 5000710405 StockholmSweden

Phylogenomic datasets continue to enhance our understanding of evolutionary relationships in many lineages of ***,genome-scale data have not been widely implemented in reconstructing relationships in lichenized *** we generate a data set comprised of 2556 single-copy protein-coding genes to reconstruct previously unresolved rela-tionships in the most diverse family of lichen-forming fungi,*** sampling included 51 taxa,mainly from the subfamily Parmelioideae,and represented six of the seven previously identified major clades within the *** results provided strong support for the monophyly of each of these major clades and most backbone relationships in the topology were recovered with high nodal support based on concatenated dataset and species tree *** alectorioid clade was strongly supported as sister-group to all remaining clades,which were divided into two major *** the first major clade the anzioid and usneoid clades formed a strongly supported sister-group relationship with the cetrarioid?hypogymnioid *** sister-group relationship of Evernia with the cetrarioid clade was also strongly supported,whereas that between the anzioid and usneoid clades needs further *** the second major clade Oropogon and Platismatia were sister to the parmelioid group,while the position of Omphalora was not fully *** study demonstrates the power of genome-scale data sets to resolve long-standing,ambiguous phylogenetic rela-tionships of lichen-forming ***,the topology inferred in this study will provide a valuable framework for better understanding diversification in the most diverse lineage of lichen-forming fungi,Parmeliaceae.

关键词： Fungi Lecanorales Lichenized fungi Parmeliaceae Parmelioideae Phylogeny Systematics

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