Dense sampling of bird diversity increases power of comparative genomics

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.

2020 Nov;587(7833):252-257. doi: 10.1038/s41586-020-2873-9. Epub 2020 Nov 11

PMID: 33177665 DOI: 10.1038/s41586-020-2873-9


Other Contributors

Shaohong Feng 1 2 3Josefin Stiller 4Yuan Deng 1 3 4Joel Armstrong 5Qi Fang 1 3 4Andrew Hart Reeve 6Duo Xie 1 3 7Guangji Chen 1 3 7Chunxue Guo 1 3Brant C Faircloth 8 9Bent Petersen 10 11Zongji Wang 1 3 12 13Qi Zhou 12 13 14Mark Diekhans 5Wanjun Chen 1 3Sergio Andreu-Sánchez 4Ashot Margaryan 11 15Jason Travis Howard 16Carole Parent 17George Pacheco 11Mikkel-Holger S Sinding 11Lara Puetz 11Emily Cavill 11Ângela M Ribeiro 6Leopold Eckhart 18Jon Fjeldså 6 19Peter A Hosner 6 19Robb T Brumfield 8 9Les Christidis 20Mads F Bertelsen 21Thomas Sicheritz-Ponten 10 11Dieter Thomas Tietze 22Bruce C Robertson 23Gang Song 24 25Gerald Borgia 26Santiago Claramunt 27 28Irby J Lovette 29Saul J Cowen 30Peter Njoroge 31John Philip Dumbacher 32Oliver A Ryder 33 34Jérôme Fuchs 35Michael Bunce 36David W Burt 37Joel Cracraft 38Guanliang Meng 1Shannon J Hackett 39Peter G Ryan 40Knud Andreas Jønsson 6Ian G Jamieson 23Rute R da Fonseca 19Edward L Braun 41Peter Houde 42Siavash Mirarab 43Alexander Suh 44 45 46Bengt Hansson 47Suvi Ponnikas 47Hanna Sigeman 47Martin Stervander 47 48Paul B Frandsen 49 50Henriette van der Zwan 51Rencia van der Sluis 51Carina Visser 52Christopher N Balakrishnan 53Andrew G Clark 54John W Fitzpatrick 29Reed Bowman 55Nancy Chen 56Alison Cloutier 57 58Timothy B Sackton 59Scott V Edwards 57 58Dustin J Foote 53 60Subir B Shakya 8 9Frederick H Sheldon 8 9Alain Vignal 61André E R Soares 62 63Beth Shapiro 63 64Jacob González-Solís 65 66Joan Ferrer-Obiol 65 67Julio Rozas 65 67Marta Riutort 65 67Anna Tigano 68 69Vicki Friesen 69Love Dalén 70 71Araxi O Urrutia 72 73Tamás Székely 72Yang Liu 74Michael G Campana 75André Corvelo 76Robert C Fleischer 75Kim M Rutherford 77Neil J Gemmell 77Nicolas Dussex 70 71 77Henrik Mouritsen 78Nadine Thiele 78Kira Delmore 79 80Miriam Liedvogel 80Andre Franke 81Marc P Hoeppner 81Oliver Krone 82Adam M Fudickar 83Borja Milá 84Ellen D Ketterson 85Andrew Eric Fidler 86Guillermo Friis 87Ángela M Parody-Merino 88Phil F Battley 88Murray P Cox 89Nicholas Costa Barroso Lima 62 90Francisco Prosdocimi 91Thomas Lee Parchman 92Barney A Schlinger 93 94Bette A Loiselle 95 96John G Blake 95Haw Chuan Lim 75 97Lainy B Day 98Matthew J Fuxjager 99Maude W Baldwin 100Michael J Braun 101 102Morgan Wirthlin 103Rebecca B Dikow 50T Brandt Ryder 104Glauco Camenisch 105Lukas F Keller 105Jeffrey M DaCosta 106Mark E Hauber 107Matthew I M Louder 53 107 108Christopher C Witt 109Jimmy A McGuire 110Joann Mudge 111Libby C Megna 112Matthew D Carling 112Biao Wang 113Scott A Taylor 114Glaucia Del-Rio 9Alexandre Aleixo 115Ana Tereza Ribeiro Vasconcelos 62Claudio V Mello 116Jason T Weir 27 28 117David Haussler 5Qiye Li 1 3Huanming Yang 3 118Jian Wang 3Fumin Lei 24 119Carsten Rahbek 19 120 121 122M Thomas P Gilbert 11 123Gary R Graves 19 101Erich D Jarvis 17 124 125Benedict Paten 126Guojie Zhang 127 128 129 130