Portal de Periódicos da CAPES

Artigo Acesso aberto Produção Nacional Revisado por pares

BIBTEX RIS

Dense sampling of bird diversity increases power of comparative genomics

2020; Nature Portfolio; Volume: 587; Issue: 7833 Linguagem: Inglês

10.1038/s41586-020-2873-9

1476-4687

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 T. Howard, Carole A. Parent, George Pacheco, Mikkel‐Holger S. Sinding, Lara Puetz, Emily Louisa Cavill, Ângela M. Ribeiro, Leopold Eckhart, Jon Fjeldså, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz‐Pontén, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul Cowen, Peter Njoroge, John P. Dumbacher, Oliver A. Ryder, Jérôme Fuchs, Michael Bunce, David W. Burt, Joël Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud A. 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, Henriëtte 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, Julio Rozas, Marta Riutort, Anna Tigano, Vicki L. Friesen, Love Dalén, Araxi O. Urrutia, Tamás Székely, Yang Liu, Michael G. Campana, André Corvelo, Robert C. Fleischer, Kim Rutherford, Neil J. Gemmell, Nicolás Dussex, Henrik Mouritsen, Nadine Thiele, Kira E. Delmore, Miriam Liedvogel, André Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Milá, Ellen D. Ketterson, Andrew E. Fidler, Guillermo Friis, Ángela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas L. 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, Thomas B. Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Márk 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 Luis Padovan Aleixo, Ana Tereza Ribeiro de 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,

Chromosomal and Genetic Variations

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. 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.