Dense sampling of bird diversity increases power of comparative genomics.

Authors:
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 da Fonseca, Edward L Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B Frandsen, Henriette van der Zwan, Rencia van der 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, Guojie Zhang
Year of publication:
2020
Volume:
587
Issue:
7833
Issn:
0028-0836
Journal title abbreviated:
NATURE
Journal title long:
Nature : a weekly illustrated journal of science
Impact factor:
42.778
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.