Dense sampling of bird diversity increases power of comparative genomics

Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sánchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George Pacheco, Mikkel-Holger S. Sinding, Lara Puetz, Emily Cavill, Ângela M. Ribeiro, Leopold Eckhart, Jon Fjeldså, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jérôme Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud Andreas Jønsson, Ian G. Jamieson, Rute R. Fonseca, Edward L. Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B. Frandsen, Henriette Zwan, Rencia Sluis, Carina Visser, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Scott V. Edwards, Dustin J. Foote, Subir B. Shakya, Frederick H. Sheldon, Alain Vignal, André E. R. Soares, Beth Shapiro, Jacob González-Solís, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalén, Araxi O. Urrutia, Tamás Székely, Yang Liu, Michael G. Campana, André Corvelo, Robert C. Fleischer, Kim M. Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Milá, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Ángela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Haw Chuan Lim, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, T. Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M. Thomas P. Gilbert, Gary R. Graves, Erich D. Jarvis, Benedict Paten () and Guojie Zhang ()
Additional contact information
Shaohong Feng: China National GeneBank, BGI-Shenzhen
Josefin Stiller: University of Copenhagen
Yuan Deng: China National GeneBank, BGI-Shenzhen
Joel Armstrong: UC Santa Cruz Genomics Institute, UC Santa Cruz
Qi Fang: China National GeneBank, BGI-Shenzhen
Andrew Hart Reeve: University of Copenhagen
Duo Xie: China National GeneBank, BGI-Shenzhen
Guangji Chen: China National GeneBank, BGI-Shenzhen
Chunxue Guo: China National GeneBank, BGI-Shenzhen
Brant C. Faircloth: Louisiana State University
Bent Petersen: AIMST University
Zongji Wang: China National GeneBank, BGI-Shenzhen
Qi Zhou: Zhejiang University
Mark Diekhans: UC Santa Cruz Genomics Institute, UC Santa Cruz
Wanjun Chen: China National GeneBank, BGI-Shenzhen
Sergio Andreu-Sánchez: University of Copenhagen
Ashot Margaryan: University of Copenhagen
Jason Travis Howard: Novogene
Carole Parent: Duke University Medical Center
George Pacheco: University of Copenhagen
Mikkel-Holger S. Sinding: University of Copenhagen
Lara Puetz: University of Copenhagen
Emily Cavill: University of Copenhagen
Ângela M. Ribeiro: University of Copenhagen
Leopold Eckhart: Medical University of Vienna
Jon Fjeldså: University of Copenhagen
Peter A. Hosner: University of Copenhagen
Robb T. Brumfield: Louisiana State University
Les Christidis: Southern Cross University
Mads F. Bertelsen: Centre for Zoo and Wild Animal Health, Copenhagen Zoo
Thomas Sicheritz-Ponten: AIMST University
Dieter Thomas Tietze: Universität Hamburg
Bruce C. Robertson: University of Otago
Gang Song: Institute of Zoology, Chinese Academy of Sciences
Gerald Borgia: University of Maryland
Santiago Claramunt: Royal Ontario Museum
Irby J. Lovette: Cornell University
Saul J. Cowen: Biodiversity and Conservation Science, Department of Biodiversity Conservation and Attractions
Peter Njoroge: National Museums of Kenya
John Philip Dumbacher: California Academy of Sciences
Oliver A. Ryder: San Diego Zoo Institute for Conservation Research
Jérôme Fuchs: Université des Antilles
Michael Bunce: Curtin University
David W. Burt: University of Queensland
Joel Cracraft: American Museum of Natural History
Guanliang Meng: China National GeneBank, BGI-Shenzhen
Shannon J. Hackett: Integrative Research Center, Field Museum of Natural History
Peter G. Ryan: University of Cape Town
Knud Andreas Jønsson: University of Copenhagen
Ian G. Jamieson: University of Otago
Rute R. Fonseca: University of Copenhagen
Edward L. Braun: University of Florida
Peter Houde: New Mexico State University
Siavash Mirarab: University of California San Diego
Alexander Suh: Uppsala University
Bengt Hansson: Lund University
Suvi Ponnikas: Lund University
Hanna Sigeman: Lund University
Martin Stervander: Lund University
Paul B. Frandsen: Brigham Young University
Henriette Zwan: North-West University
Rencia Sluis: North-West University
Carina Visser: University of Pretoria
Christopher N. Balakrishnan: East Carolina University
Andrew G. Clark: Cornell University
John W. Fitzpatrick: Cornell University
Reed Bowman: Archbold Biological Station
Nancy Chen: University of Rochester
Alison Cloutier: Harvard University
Timothy B. Sackton: Harvard University
Scott V. Edwards: Harvard University
Dustin J. Foote: East Carolina University
Subir B. Shakya: Louisiana State University
Frederick H. Sheldon: Louisiana State University
Alain Vignal: Université de Toulouse
André E. R. Soares: Laboratório Nacional de Computação Científica
Beth Shapiro: University of California Santa Cruz
Jacob González-Solís: Universitat de Barcelona
Joan Ferrer-Obiol: Universitat de Barcelona
Julio Rozas: Universitat de Barcelona
Marta Riutort: Universitat de Barcelona
Anna Tigano: University of New Hampshire
Vicki Friesen: Queen’s University
Love Dalén: Swedish Museum of Natural History
Araxi O. Urrutia: University of Bath
Tamás Székely: University of Bath
Yang Liu: Sun Yat-sen University
Michael G. Campana: Smithsonian Conservation Biology Institute, Smithsonian Institution
André Corvelo: New York Genome Center
Robert C. Fleischer: Smithsonian Conservation Biology Institute, Smithsonian Institution
Kim M. Rutherford: University of Otago
Neil J. Gemmell: University of Otago
Nicolas Dussex: Swedish Museum of Natural History
Henrik Mouritsen: University of Oldenburg
Nadine Thiele: University of Oldenburg
Kira Delmore: Texas A&M University
Miriam Liedvogel: Max Planck Institute for Evolutionary Biology
Andre Franke: Christian-Albrechts-University of Kiel
Marc P. Hoeppner: Christian-Albrechts-University of Kiel
Oliver Krone: Leibniz Institute for Zoo and Wildlife Research
Adam M. Fudickar: Indiana University
Borja Milá: Spanish National Research Council (CSIC)
Ellen D. Ketterson: Indiana University
Andrew Eric Fidler: University of Auckland
Guillermo Friis: New York University – Abu Dhabi
Ángela M. Parody-Merino: Massey University
Phil F. Battley: Massey University
Murray P. Cox: Massey University
Nicholas Costa Barroso Lima: Laboratório Nacional de Computação Científica
Francisco Prosdocimi: Instituto de Bioquímica Médica Leopoldo de Meis
Thomas Lee Parchman: University of Nevada Reno
Barney A. Schlinger: UCLA
Bette A. Loiselle: University of Florida
John G. Blake: University of Florida
Haw Chuan Lim: Smithsonian Conservation Biology Institute, Smithsonian Institution
Lainy B. Day: University of Mississippi
Matthew J. Fuxjager: Brown University
Maude W. Baldwin: Max Planck Institute for Ornithology
Michael J. Braun: Smithsonian Institution
Morgan Wirthlin: Carnegie Mellon University
Rebecca B. Dikow: Smithsonian Institution
T. Brandt Ryder: Smithsonian National Zoological Park and Conservation Biology Institute
Glauco Camenisch: University of Zurich
Lukas F. Keller: University of Zurich
Jeffrey M. DaCosta: Boston College
Mark E. Hauber: University of Illinois at Urbana-Champaign
Matthew I. M. Louder: East Carolina University
Christopher C. Witt: University of New Mexico
Jimmy A. McGuire: University of California, Berkeley
Joann Mudge: National Center for Genome Resources
Libby C. Megna: University of Wyoming
Matthew D. Carling: University of Wyoming
Biao Wang: The University of Melbourne
Scott A. Taylor: University of Colorado Boulder
Glaucia Del-Rio: Louisiana State University
Alexandre Aleixo: University of Helsinki
Ana Tereza Ribeiro Vasconcelos: Laboratório Nacional de Computação Científica
Claudio V. Mello: Oregon Health and Science University
Jason T. Weir: Royal Ontario Museum
David Haussler: UC Santa Cruz Genomics Institute, UC Santa Cruz
Qiye Li: China National GeneBank, BGI-Shenzhen
Huanming Yang: BGI-Shenzhen
Jian Wang: BGI-Shenzhen
Fumin Lei: Institute of Zoology, Chinese Academy of Sciences
Carsten Rahbek: University of Copenhagen
M. Thomas P. Gilbert: University of Copenhagen
Gary R. Graves: University of Copenhagen
Erich D. Jarvis: Duke University Medical Center
Benedict Paten: UC Santa Cruz Genomics Institute, UC Santa Cruz
Guojie Zhang: China National GeneBank, BGI-Shenzhen

Nature, 2020, vol. 587, issue 7833, 252-257

Abstract: Abstract Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, 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.

Date: 2020
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DOI: 10.1038/s41586-020-2873-9

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