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Dense sampling of bird diversity increases power of comparative genomics

机译：鸟类多样性的密集采样增加了比较基因组学的力量

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摘要

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
机译：全基因组测序项目越来越多地填充生命之树并表征生物多样性（1-4）。先前已经提出了稀疏的分类水抽样来混淆系统发育推理（5），并且仅捕获基因组多样性的一小部分。在这里，我们通过分析来自92.4％的鸟类家庭的363个基因组 - 包括为鸟类10,000个基因组（B10K）项目的II期产生的267个新序列的基因组来报告禽流地发育和分子多样性的致密阶段。我们将该比较基因组数据集与利用的渠道组合使用，该管道利用了可参考的全基因组对准，以识别比先前更大的正交区域，并识别特定鸟类谱系中的基因组Novelties。密集采样的对准提供单键对选择的图谱图，该碱基的分数增加了一倍以上，这些碱基被自信地预测为守恒，并且揭示了主要是非编码DNA的广泛选择的弱选择模式。我们的结果表明，增加比较研究中使用的基因组的多样性可以揭示更多的共同和谱系特异性的变异，并改善基因组特征的调查。我们预期，这种基因组资源将对跨物种的进化过程提供新的观点，并协助努力保护物种。从鸟类10,000个基因组项目的363种基因组的数据集显示出来的力量，以检测共享和血统的增加具体变异，展示了在全基因组测序中的系统源性多样性分类的重要性。

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  • 来源
    《Nature》 |2020年第7833期|252-257|共6页
  • 作者

    Feng Shaohong; Stiller Josefin; Deng Yuan; Armstrong Joel; Fang Qi; Reeve Andrew Hart; Xie Duo; Chen Guangji; Guo Chunxue; Faircloth Brant C.; Petersen Bent; Wang Zongji; Zhou Qi; Diekhans Mark; Chen Wanjun; Andreu-Sanchez Sergio; Margaryan Ashot; Howard Jason Travis; Parent Carole; Pacheco George; Sinding Mikkel-Holger S.; Puetz Lara; Cavill Emily; Ribeiro Angela M.; Eckhart Leopold; Fjeldsa Jon; Hosner Peter A.; Brumfield Robb T.; Christidis Les; Bertelsen Mads F.; Sicheritz-Ponten Thomas; Tietze Dieter Thomas; Robertson Bruce C.; Song Gang; Borgia Gerald; Claramunt Santiago; Lovette Irby J.; Cowen Saul J.; Njoroge Peter; Dumbacher John Philip; Ryder Oliver A.; Fuchs Jerome; Bunce Michael; Burt David W.; Cracraft Joel; Meng Guanliang; Hackett Shannon J.; Ryan Peter G.; Jonsson Knud Andreas; Jamieson Ian G.; da Fonseca Rute R.; Braun Edward L.; Houde Peter; Mirarab Siavash; Suh Alexander; Hansson Bengt; Ponnikas Suvi; Sigeman Hanna; Stervander Martin; Frandsen Paul B.; van der Zwan Henriette; van der Sluis Rencia; Visser Carina; Balakrishnan Christopher N.; Clark Andrew G.; Fitzpatrick John W.; Bowman Reed; Chen Nancy; Cloutier Alison; Sackton Timothy B.; Edwards Scott V.; Foote Dustin J.; Shakya Subir B.; Sheldon Frederick H.; Vignal Alain; Soares Andre E. R.; Shapiro Beth; Gonzalez-Solis Jacob; Ferrer-Obiol Joan; Rozas Julio; Riutort Marta; Tigano Anna; Friesen Vicki; Dalen Love; Urrutia Araxi O.; Szekely Tamas; Liu Yang; Campana Michael G.; Corvelo Andre; Fleischer Robert C.; Rutherford Kim M.; Gemmell Neil J.; Dussex Nicolas; Mouritsen Henrik; Thiele Nadine; Delmore Kira; Liedvogel Miriam; Franke Andre; Hoeppner Marc P.; Krone Oliver; Fudickar Adam M.; Mila Borja; Ketterson Ellen D.; Fidler Andrew Eric; Friis Guillermo; Parody-Merino Angela M.; Battley Phil F.; Cox Murray P.; Lima Nicholas Costa Barroso; Prosdocimi Francisco; Parchman Thomas Lee; Schlinger Barney A.; Loiselle Bette A.; Blake John G.; Lim Haw Chuan; Day Lainy B.; Fuxjager Matthew J.; Baldwin Maude W.; Braun Michael J.; Wirthlin Morgan; Dikow Rebecca B.; Ryder T. Brandt; Camenisch Glauco; Keller Lukas F.; DaCosta Jeffrey M.; Hauber Mark E.; Louder Matthew I. M.; Witt Christopher C.; McGuire Jimmy A.; Mudge Joann; Megna Libby C.; Carling Matthew D.; Wang Biao; Taylor Scott A.; Del-Rio Glaucia; Aleixo Alexandre; Vasconcelos Ana Tereza Ribeiro; Mello Claudio V.; Weir Jason T.; Haussler David; Li Qiye; Yang Huanming; Wang Jian; Lei Fumin; Rahbek Carsten; Gilbert M. Thomas P.; Graves Gary R.; Jarvis Erich D.; Paten Benedict; Zhang Guojie;

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    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|Chinese Acad Sci Kunming Inst Zool State Key Lab Genet Resources & Evolut Kunming Yunnan Peoples R China|BGI Shenzhen Shenzhen Peoples R China;

    Univ Copenhagen Sect Ecol & Evolut Dept Biol Villum Ctr Biodivers Genom Copenhagen Denmark;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China|Univ Copenhagen Sect Ecol & Evolut Dept Biol Villum Ctr Biodivers Genom Copenhagen Denmark;

    UC Santa Cruz Genom Inst Santa Cruz CA 95064 USA;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China|Univ Copenhagen Sect Ecol & Evolut Dept Biol Villum Ctr Biodivers Genom Copenhagen Denmark;

    Univ Copenhagen Nat Hist Museum Denmark Copenhagen Denmark;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China|Univ Chinese Acad Sci BGI Educ Ctr Shenzhen Peoples R China;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China|Univ Chinese Acad Sci BGI Educ Ctr Shenzhen Peoples R China;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China;

    Louisiana State Univ Dept Biol Sci Baton Rouge LA 70803 USA|Louisiana State Univ Museum Nat Sci Baton Rouge LA 70803 USA;

    Fac Sci Appl Ctr Excellence Om Driven Computat Biodiscovery CO AIMST Univ Bedong Kedah Malaysia|Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China|Zhejiang Univ Life Sci Inst MOE Lab Biosyst Homeostasis & Protect Hangzhou Peoples R China|Univ Vienna Dept Neurosci & Dev Biol Vienna Austria;

    Zhejiang Univ Life Sci Inst MOE Lab Biosyst Homeostasis & Protect Hangzhou Peoples R China|Univ Vienna Dept Neurosci & Dev Biol Vienna Austria|Zhejiang Univ Sch Med Affiliated Hosp 2 Ctr Reprod Med Hangzhou Peoples R China;

    UC Santa Cruz Genom Inst Santa Cruz CA 95064 USA;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China;

    Univ Copenhagen Sect Ecol & Evolut Dept Biol Villum Ctr Biodivers Genom Copenhagen Denmark;

    Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark|Natl Acad Sci Inst Mol Biol Yerevan Armenia;

    Novogene Durham NC USA;

    Duke Univ Med Ctr Durham NC USA;

    Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark;

    Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark;

    Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark;

    Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark;

    Univ Copenhagen Nat Hist Museum Denmark Copenhagen Denmark;

    Med Univ Vienna Dept Dermatol Vienna Austria;

    Univ Copenhagen Nat Hist Museum Denmark Copenhagen Denmark|Univ Copenhagen GLOBE Inst Ctr Macroecol Evolut & Climate Copenhagen Denmark;

    Univ Copenhagen Nat Hist Museum Denmark Copenhagen Denmark|Univ Copenhagen GLOBE Inst Ctr Macroecol Evolut & Climate Copenhagen Denmark;

    Louisiana State Univ Dept Biol Sci Baton Rouge LA 70803 USA|Louisiana State Univ Museum Nat Sci Baton Rouge LA 70803 USA;

    Southern Cross Univ Coffs Harbour NSW Australia;

    Copenhagen Zoo Ctr Zoo & Wild Anim Hlth Frederiksberg Denmark;

    Fac Sci Appl Ctr Excellence Om Driven Computat Biodiscovery CO AIMST Univ Bedong Kedah Malaysia|Univ Copenhagen GLOBE Inst Fac Hlth & Med Sci Sect Evolutionary Genom Copenhagen Denmark;

    Univ Hamburg Ctr Nat Hist Hamburg Germany;

    Univ Otago Dept Zool Dunedin New Zealand;

    Chinese Acad Sci Inst Zool Key Lab Zool Systemat & Evolut Beijing Peoples R China|Griffith Univ Environm Futures Res Inst Nathan Qld Australia;

    Univ Maryland Dept Biol College Pk MD 20742 USA;

    Royal Ontario Museum Dept Nat Hist Toronto ON Canada|Cornell Univ Cornell Lab Ornithol Ithaca NY USA;

    Cornell Univ Cornell Lab Ornithol Ithaca NY USA;

    Dept Biodivers Conservat & Attract Biodivers & Conservat Sci Perth WA Australia;

    Natl Museums Kenya Ornithol Sect Zool Dept Nairobi Kenya;

    Calif Acad Sci Ornithol & Mammal San Francisco CA 94118 USA;

    San Diego Zoo Inst Conservat Res Escondido CA USA|Univ Calif San Diego Div Biol Evolut Behav & Ecol La Jolla CA 92093 USA;

    Univ Antilles Sorbonne Univ Natl Hist Nat Inst Systemat Evolut Biodivers ISYEB CNRS EPHE Paris France;

    Curtin Univ Trace & Environm DNA TrEnD Lab Sch Mol & Life Sci Perth WA Australia;

    Univ Queensland UQ Genom Brisbane Qld Australia;

    Amer Museum Nat Hist Dept Ornithol New York NY 10024 USA;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China;

    Field Museum Nat Hist Integrat Res Ctr Chicago IL 60605 USA;

    Univ Cape Town FitzPatrick Inst African Ornithol Cape Town South Africa;

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    Univ Otago Dept Zool Dunedin New Zealand;

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    Univ Florida Dept Biol Gainesville FL USA;

    New Mexico State Univ Dept Biol Las Cruces NM 88003 USA;

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    Lund Univ Dept Biol Lund Sweden;

    Lund Univ Dept Biol Lund Sweden;

    Lund Univ Dept Biol Lund Sweden;

    Lund Univ Dept Biol Lund Sweden|Univ Oregon Inst Ecol & Evolut Eugene OR 97403 USA;

    Brigham Young Univ Dept Plant & Wildlife Sci Provo UT 84602 USA|Smithsonian Inst Data Sci Lab Off Chief Informat Officer Washington DC 20560 USA;

    North West Univ Focus Area Human Metabol Potchefstroom South Africa;

    North West Univ Focus Area Human Metabol Potchefstroom South Africa;

    Univ Pretoria Dept Anim Sci Pretoria South Africa;

    East Carolina Univ Dept Biol Greenville NC 27858 USA;

    Cornell Univ Dept Mol Biol & Genet Ithaca NY USA;

    Cornell Univ Cornell Lab Ornithol Ithaca NY USA;

    Archbold Biol Stn Avian Ecol Program Venus FL USA;

    Univ Rochester Dept Biol Rochester NY 14627 USA;

    Harvard Univ Dept Organism & Evolutionary Biol Cambridge MA 02138 USA|Harvard Univ Museum Comparat Zool Cambridge MA 02138 USA;

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    Harvard Univ Dept Organism & Evolutionary Biol Cambridge MA 02138 USA|Harvard Univ Museum Comparat Zool Cambridge MA 02138 USA;

    East Carolina Univ Dept Biol Greenville NC 27858 USA|Sylvan Hts Bird Pk Scotland Neck NC USA;

    Louisiana State Univ Dept Biol Sci Baton Rouge LA 70803 USA|Louisiana State Univ Museum Nat Sci Baton Rouge LA 70803 USA;

    Louisiana State Univ Dept Biol Sci Baton Rouge LA 70803 USA|Louisiana State Univ Museum Nat Sci Baton Rouge LA 70803 USA;

    Univ Toulouse GenPhySE INRA INP ENVT INPT Castanet Tolosan France;

    Lab Nacl Computac Cientif Petropolis RJ Brazil|Univ Calif Santa Cruz Dept Ecol & Evolutionary Biol Santa Cruz CA 95064 USA;

    Univ Calif Santa Cruz Dept Ecol & Evolutionary Biol Santa Cruz CA 95064 USA|Univ Calif Santa Cruz Howard Hughes Med Inst Santa Cruz CA 95064 USA;

    Univ Barcelona Inst Recerca Biodivers IRBio Barcelona Spain|Univ Barcelona Dept Biol Evolut Ecol & Ciencies Ambientals BEECA Barcelona Spain;

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    Univ Barcelona Dept Biol Evolut Ecol & Ciencies Ambientals BEECA Barcelona Spain|Univ Barcelona Dept Genet Microbiol & Estadist Barcelona Spain;

    Univ Barcelona Dept Biol Evolut Ecol & Ciencies Ambientals BEECA Barcelona Spain|Univ Barcelona Dept Genet Microbiol & Estadist Barcelona Spain;

    Univ New Hampshire Dept Mol Cellular & Biomed Sci Durham NH 03824 USA|Queens Univ Dept Biol Kingston ON Canada;

    Queens Univ Dept Biol Kingston ON Canada;

    Swedish Museum Nat Hist Dept Bioinformat & Genet Stockholm Sweden|Ctr Palaeogenet Stockholm Sweden;

    Univ Bath Milner Ctr Evolut Bath Avon England|Univ Nacl Autonoma Mexico Inst Ecol Mexico City DF Mexico;

    Univ Bath Milner Ctr Evolut Bath Avon England;

    Sun Yat Sen Univ Sch Ecol State Key Lab Biocontrol Guangzhou Peoples R China;

    Smithsonian Inst Smithsonian Conservat Biol Inst Ctr Conservat Genom Washington DC 20560 USA;

    New York Genome Ctr New York NY USA;

    Smithsonian Inst Smithsonian Conservat Biol Inst Ctr Conservat Genom Washington DC 20560 USA;

    Univ Otago Dept Anat Dunedin New Zealand;

    Univ Otago Dept Anat Dunedin New Zealand;

    Swedish Museum Nat Hist Dept Bioinformat & Genet Stockholm Sweden|Ctr Palaeogenet Stockholm Sweden|Univ Otago Dept Anat Dunedin New Zealand;

    Carl von Ossietzky Univ Oldenburg Inst Biol & Umweltwissensch AG Neurosensory Sci Oldenburg Germany;

    Carl von Ossietzky Univ Oldenburg Inst Biol & Umweltwissensch AG Neurosensory Sci Oldenburg Germany;

    Texas A&M Univ Dept Biol College Stn TX 77843 USA|Max Planck Inst Evolutionary Biol MPRG Behav Genom Plon Germany;

    Max Planck Inst Evolutionary Biol MPRG Behav Genom Plon Germany;

    Christian Albrechts Univ Kiel Inst Clin Mol Biol Kiel Germany;

    Christian Albrechts Univ Kiel Inst Clin Mol Biol Kiel Germany;

    Leibniz Inst Zoo & Wildlife Res Dept Wildlife Dis Berlin Germany;

    Indiana Univ Environm Resilience Inst Bloomington IN USA;

    CSIC Natl Museum Nat Sci Madrid Spain;

    Indiana Univ Dept Biol Bloomington IN USA;

    Univ Auckland Inst Marine Sci Auckland New Zealand;

    New York Univ Abu Dhabi Dept Biol Ctr Genom & Syst Biol Abu Dhabi U Arab Emirates;

    Massey Univ Wildlife & Ecol Grp Palmerston North New Zealand;

    Massey Univ Sch Fundamental Sci Palmerston North New Zealand;

    Massey Univ Sch Fundamental Sci Palmerston North New Zealand;

    Lab Nacl Computac Cientif Petropolis RJ Brazil|Univ Fed Ceara Ctr Ciencias Dept Bioquim & Biol Mol Fortaleza Ceara Brazil;

    Inst Bioquim Med Leopoldo Meis Lab Genom & Biodivers Rio De Janeiro Brazil;

    Univ Nevada Dept Biol Reno NV 89557 USA;

    Univ Calif Los Angeles Dept Integrat Biol & Physiol Los Angeles CA USA|Smithsonian Trop Res Inst Panama City Panama;

    Univ Florida Dept Wildlife Ecol & Conservat Gainesville FL USA|Univ Florida Ctr Latin Amer Studies Gainesville FL USA;

    Univ Florida Dept Wildlife Ecol & Conservat Gainesville FL USA;

    Smithsonian Inst Smithsonian Conservat Biol Inst Ctr Conservat Genom Washington DC 20560 USA|George Mason Univ Dept Biol Fairfax VA 22030 USA;

    Univ Mississippi Dept Biol & Neurosci Minor University MS USA;

    Brown Univ Dept Ecol & Evolutionary Biol Providence RI 02912 USA;

    Max Planck Inst Ornithol Seewiesen Germany;

    Smithsonian Inst Natl Museum Nat Hist Dept Vertebrate Zool Washington DC 20560 USA|Univ Maryland Behav Ecol Evolut & Systemat Program College Pk MD 20742 USA;

    Carnegie Mellon Univ Computat Biol Dept Pittsburgh PA 15213 USA;

    Smithsonian Inst Data Sci Lab Off Chief Informat Officer Washington DC 20560 USA;

    Smithsonian Natl Zool Pk & Conservat Biol Inst Migratory Bird Ctr Washington DC USA;

    Univ Zurich Dept Evolutionary Biol & Environm Studies Zurich Switzerland;

    Univ Zurich Dept Evolutionary Biol & Environm Studies Zurich Switzerland;

    Boston Coll Dept Biol Chestnut Hill MA 02167 USA;

    Univ Illinois Sch Integrat Biol Dept Evolut Ecol & Behav Urbana IL USA;

    East Carolina Univ Dept Biol Greenville NC 27858 USA|Univ Illinois Sch Integrat Biol Dept Evolut Ecol & Behav Urbana IL USA|Univ Tokyo Int Res Ctr Neurointelligence Tokyo Japan;

    Univ New Mexico Dept Biol Museum SouthWestern Biol Albuquerque NM 87131 USA;

    Univ Calif Berkeley Dept Integrat Biol Museum Vertebrate Zool Berkeley CA 94720 USA;

    Natl Ctr Genome Resources Santa Fe NM USA;

    Univ Wyoming Dept Zool & Physiol Laramie WY 82071 USA;

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    Univ Melbourne Sch BioSci Melbourne Vic Australia;

    Univ Colorado Dept Ecol & Evolutionary Biol Boulder CO 80309 USA;

    Louisiana State Univ Museum Nat Sci Baton Rouge LA 70803 USA;

    Univ Helsinki Finnish Museum Nat Hist Helsinki Finland;

    Lab Nacl Computac Cientif Petropolis RJ Brazil;

    Oregon Hlth & Sci Univ Dept Behav Neurosci Portland OR 97201 USA;

    Royal Ontario Museum Dept Nat Hist Toronto ON Canada|Univ Toronto Dept Ecol & Evolutionary Biol Toronto ON Canada|Univ Toronto Scarborough Dept Biol Sci Toronto ON Canada;

    UC Santa Cruz Genom Inst Santa Cruz CA 95064 USA;

    BGI Shenzhen China Natl GeneBank Shenzhen Peoples R China|BGI Shenzhen Shenzhen Peoples R China;

    BGI Shenzhen Shenzhen Peoples R China|James D Watson Inst Genome Sci Hangzhou Peoples R China;

    BGI Shenzhen Shenzhen Peoples R China;

    Chinese Acad Sci Inst Zool Key Lab Zool Systemat & Evolut Beijing Peoples R China|Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China;

    Univ Copenhagen GLOBE Inst Ctr Macroecol Evolut & Climate Copenhagen Denmark|Univ Southern Denmark Danish Inst Adv Study Odense Denmark|Peking Univ Inst Ecol Beijing Peoples R China|Imperial Coll London Dept Life Sci Ascot Berks England;

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    Duke Univ Med Ctr Durham NC USA|Rockefeller Univ 1230 York Ave New York NY 10021 USA|Howard Hughes Med Inst Chevy Chase MD USA;

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