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Dense sampling of bird diversity increases power of comparative genomics

Shaohong Feng 1, 2, 3 Josefin Stiller 4 Yuan Deng 1, 3, 4 Joel Armstrong 5 Qi Fang 1, 3, 4 Andrew Hart Reeve 6 Duo Xie 1, 3, 7 Guangji Chen 1, 3, 7 Chunxue Guo 1, 3 Brant Faircloth 8, 9, 10 Bent Petersen 11, 4 Zongji Wang 1, 3, 12, 13 Qi Zhou 12, 13, 14 Mark Diekhans 5 Wanjun Chen 1, 3 Sergio Andreu-Sánchez 4 Ashot Margaryan 4, 15 Jason Travis Howard 16 Carole Parent 17 George Pacheco 4 Mikkel-Holger Sinding 4 Lara Puetz 4 Emily Cavill 4 Ângela Ribeiro Leopold Eckhart Jon Fjeldså Peter Hosner Robb Brumfield Les Christidis Mads Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce Robertson Gang Song Gerald Borgia Santiago Claramunt Irby Lovette Saul Cowen Peter Njoroge John Philip Dumbacher Oliver Ryder Jérôme Fuchs Michael Bunce David Burt Joel Cracraft Guanliang Meng Shannon Hackett Peter Ryan Knud Andreas Jønsson Ian Jamieson Rute da Fonseca Edward Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher Balakrishnan Andrew Clark John Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy Sackton Scott Edwards Dustin Foote Subir Shakya Frederick Sheldon Alain Vignal 18 André Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi Urrutia Tamás Székely Yang Liu Michael Campana André Corvelo Robert Fleischer Kim Rutherford Neil Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc Hoeppner Oliver Krone Adam Fudickar Borja Milá Ellen Ketterson Andrew Eric Fidler Guillermo Friis Ángela Parody-Merino Phil Battley Murray Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney Schlinger Bette Loiselle John Blake Haw Chuan Lim Lainy Day Matthew Fuxjager Maude Baldwin Michael Braun Morgan Wirthlin Rebecca Dikow T. Brandt Ryder Glauco Camenisch Lukas Keller Jeffrey Dacosta Mark Hauber Matthew Louder Christopher Witt Jimmy Mcguire Joann Mudge Libby Megna Matthew Carling Biao Wang Scott Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio Mello Jason Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M. Thomas P. Gilbert Gary Graves Erich Jarvis Benedict Paten Guojie Zhang
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 confdently 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-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species.
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Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, et al.. Dense sampling of bird diversity increases power of comparative genomics. Nature, Nature Publishing Group, 2020, 587 (7833), pp.252-257. ⟨10.1038/s41586-020-2873-9⟩. ⟨hal-03155898⟩

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