The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Au...The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic genera.Here,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic genera.We propose a new subfamily classification,and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae.Our study supports recently proposed species splits as well as some recent lumps,while also questioning some of the latter.This comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.展开更多
Trapelioid fungi constitute a widespread group of mostly crust-forming lichen mycobionts that are key to understanding the early evolutionary splits in the Ostropomycetidae,the second-most species-rich subclass of lic...Trapelioid fungi constitute a widespread group of mostly crust-forming lichen mycobionts that are key to understanding the early evolutionary splits in the Ostropomycetidae,the second-most species-rich subclass of lichenized Ascomycota.The uncertain phylogenetic resolution of the approximately 170 species referred to this group contributes to a poorly resolved backbone for the entire subclass.Based on a data set including 657 newly generated sequences from four ribosomal and four protein-coding gene loci,we tested a series of a priori and new evolutionary hypotheses regarding the relationships of trapelioid clades within Ostropomycetidae.We found strong support for a monophyletic group of nine core trapelioid genera but no statistical support to reject the long-standing hypothesis that trapelioid genera are sister to Baeomycetaceae or Hymeneliaceae.However,we can reject a sister group relationship to Ostropales with high confidence.Our data also shed light on several longstanding questions,recovering Anamylopsoraceae nested within Baeomycetaceae,elucidating two major monophyletic groups within trapelioids(recognized here as Trapeliaceae and Xylographaceae),and rejecting the monophyly of the genus Rimularia.We transfer eleven species of the latter genus to Lambiella and describe the genus Parainoa to accommodate a previously misunderstood species of Trapeliopsis.Past phylogenetic studies in Ostropomycetidae have invoked Bdivergence order^for drawing taxonomic conclusions on higher level taxa.Our data show that if backbone support is lacking,contrasting solutions may be recovered with different or added data.We accordingly urge caution in concluding evolutionary relationships from unresolved phylogenies.展开更多
基金the National Swedish Research Council(grants No.2015-04402,2019-04486)the Carl Trygger Foundation(CTS 20:6)+3 种基金the Jornvall FoundationJulian Francis for financial supportthe National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory,the Knut and Alice Wallenberg Foundationthe Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the"UK's Crop Diversity Bioinformatics HPC"(BBSRC grant BB/S019669/1)。
文摘The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic genera.Here,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic genera.We propose a new subfamily classification,and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae.Our study supports recently proposed species splits as well as some recent lumps,while also questioning some of the latter.This comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.
基金We would like to thank the numerous individuals who provided specimens for DNA sequencing for this study,including A.Acton,A.Aptroot,C.Björk,B.Coppins,G.Kantvilas,J.McCarthy,B.McCune,L.Muggia,O.Peksa,S.Pérez-Ortega,T.Tønsberg,P.van den Boom and the curators of F,GZU,O and UPS.Thanks go to Walter Obermayer,Graz,for performing thin layer chromatography on several specimens.Fernando Fernández-Mendoza and Martin Grube provided helpful comments at earlier stages of this project.We also thank Joseph Ryan for help with troubleshooting the SOWHAT analyses.DNA sequencing of Alaskan specimens was funded in part by a materials contribution from the Tongass National Forest,U.S.Department of Agriculture,courtesy of K.Dillman,for which we are grateful.The project was funded by the Austrian Science Foundation(FWF grant P25237,BEvolution of Substrate Specificity in Lichens^).The work by MW was financed by the Swedish Taxonomy Initiative(Svenska Artprojektet,administered by the Swedish Species Information Centre/ArtDatabanken).CP gratefully acknowledges financial support through the program BLOEWE-LandesOffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz^of the Hessen Ministry of Higher Education,Research,and the Arts.ZP thanks for the support by the Czech Academy of Science(AV0Z60050516,RVO 67985939)and the Minsitry of Education,Youth and Sports of the Czech Republic.
文摘Trapelioid fungi constitute a widespread group of mostly crust-forming lichen mycobionts that are key to understanding the early evolutionary splits in the Ostropomycetidae,the second-most species-rich subclass of lichenized Ascomycota.The uncertain phylogenetic resolution of the approximately 170 species referred to this group contributes to a poorly resolved backbone for the entire subclass.Based on a data set including 657 newly generated sequences from four ribosomal and four protein-coding gene loci,we tested a series of a priori and new evolutionary hypotheses regarding the relationships of trapelioid clades within Ostropomycetidae.We found strong support for a monophyletic group of nine core trapelioid genera but no statistical support to reject the long-standing hypothesis that trapelioid genera are sister to Baeomycetaceae or Hymeneliaceae.However,we can reject a sister group relationship to Ostropales with high confidence.Our data also shed light on several longstanding questions,recovering Anamylopsoraceae nested within Baeomycetaceae,elucidating two major monophyletic groups within trapelioids(recognized here as Trapeliaceae and Xylographaceae),and rejecting the monophyly of the genus Rimularia.We transfer eleven species of the latter genus to Lambiella and describe the genus Parainoa to accommodate a previously misunderstood species of Trapeliopsis.Past phylogenetic studies in Ostropomycetidae have invoked Bdivergence order^for drawing taxonomic conclusions on higher level taxa.Our data show that if backbone support is lacking,contrasting solutions may be recovered with different or added data.We accordingly urge caution in concluding evolutionary relationships from unresolved phylogenies.
