Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow

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Zhang, DezhiChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China. (author)

Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow

Article/chapterEnglish2021

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2021-03-31
Oxford University Press,2021
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LIBRIS-ID:oai:DiVA.org:uu-459066
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-459066URI
https://doi.org/10.1093/sysbio/syab024DOI

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Language:English
Summary in:English

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Subject category:art swepub-publicationtype

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Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leafwarblers) using one de novo genome assembly and 78 resequenced genomes. Onthe basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the "winner-takes-all democratic majority tree" is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.

Subject headings and genre

NATURVETENSKAP Biologi Evolutionsbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Evolutionary Biology hsv//eng
Bifurcation
introgression
recombination
reticulation
Phylloscopus

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Rheindt, Frank E.Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore. (author)
She, HuishangChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.;Univ Chinese Acad Sci, Coll Life Sci, Beijing 101408, Peoples R China. (author)
Cheng, YalinChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China. (author)
Song, GangChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China. (author)
Jia, ChenxiChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China. (author)
Qu, YanhuaChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China. (author)
Alström, Per,ProfessorUppsala universitet,Zooekologi,Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.;Uppsala Univ, Evolutionary Biol Ctr, Dept Ecol & Genet, Anim Ecol, Norbyvagen 18, SE-75236 Uppsala, Sweden.(Swepub:uu)peralstr (author)
Lei, FuminChinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.;Univ Chinese Acad Sci, Coll Life Sci, Beijing 101408, Peoples R China.;Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650201, Yunnan, Peoples R China. (author)
Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore. (creator_code:org_t)

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In:Systematic Biology: Oxford University Press70:5, s. 961-9751063-51571076-836X

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By the author/editor: Zhang, Dezhi; Rheindt, Frank E ...; She, Huishang; Cheng, Yalin; Song, Gang; Jia, Chenxi; show more...; Qu, Yanhua; Alström, Per, Pr ...; Lei, Fumin; show less...

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