Dataset Information

Dense sampling of bird diversity increases power of comparative genomics.

ABSTRACT: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity^1-4. 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.

SUBMITTER: Feng S

PROVIDER: S-EPMC7759463 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Dense sampling of bird diversity increases power of comparative genomics.

Feng Shaohong S Stiller Josefin J Deng Yuan Y Armstrong Joel J Fang Qi Q Reeve Andrew Hart AH Xie Duo D Chen Guangji G Guo Chunxue C Faircloth Brant C BC Petersen Bent B Wang Zongji Z Zhou Qi Q Diekhans Mark M Chen Wanjun W Andreu-Sánchez Sergio S Margaryan Ashot A Howard Jason Travis JT Parent Carole C Pacheco George G Sinding Mikkel-Holger S MS Puetz Lara L Cavill Emily E Ribeiro Ângela M ÂM Eckhart Leopold L Fjeldså Jon J Hosner Peter A PA Brumfield Robb T RT Christidis Les L Bertelsen Mads F MF Sicheritz-Ponten Thomas T Tietze Dieter Thomas DT Robertson Bruce C BC Song Gang G Borgia Gerald G Claramunt Santiago S Lovette Irby J IJ Cowen Saul J SJ Njoroge Peter P Dumbacher John Philip JP Ryder Oliver A OA Fuchs Jérôme J Bunce Michael M Burt David W DW Cracraft Joel J Meng Guanliang G Hackett Shannon J SJ Ryan Peter G PG Jønsson Knud Andreas KA Jamieson Ian G IG da Fonseca Rute R RR Braun Edward L EL Houde Peter P Mirarab Siavash S Suh Alexander A Hansson Bengt B Ponnikas Suvi S Sigeman Hanna H Stervander Martin M Frandsen Paul B PB van der Zwan Henriette H van der Sluis Rencia R Visser Carina C Balakrishnan Christopher N CN Clark Andrew G AG Fitzpatrick John W JW Bowman Reed R Chen Nancy N Cloutier Alison A Sackton Timothy B TB Edwards Scott V SV Foote Dustin J DJ Shakya Subir B SB Sheldon Frederick H FH Vignal Alain A Soares André E R AER Shapiro Beth B González-Solís Jacob J Ferrer-Obiol Joan J Rozas Julio J Riutort Marta M Tigano Anna A Friesen Vicki V Dalén Love L Urrutia Araxi O AO Székely Tamás T Liu Yang Y Campana Michael G MG Corvelo André A Fleischer Robert C RC Rutherford Kim M KM Gemmell Neil J NJ Dussex Nicolas N Mouritsen Henrik H Thiele Nadine N Delmore Kira K Liedvogel Miriam M Franke Andre A Hoeppner Marc P MP Krone Oliver O Fudickar Adam M AM Milá Borja B Ketterson Ellen D ED Fidler Andrew Eric AE Friis Guillermo G Parody-Merino Ángela M ÁM Battley Phil F PF Cox Murray P MP Lima Nicholas Costa Barroso NCB Prosdocimi Francisco F Parchman Thomas Lee TL Schlinger Barney A BA Loiselle Bette A BA Blake John G JG Lim Haw Chuan HC Day Lainy B LB Fuxjager Matthew J MJ Baldwin Maude W MW Braun Michael J MJ Wirthlin Morgan M Dikow Rebecca B RB Ryder T Brandt TB Camenisch Glauco G Keller Lukas F LF DaCosta Jeffrey M JM Hauber Mark E ME Louder Matthew I M MIM Witt Christopher C CC McGuire Jimmy A JA Mudge Joann J Megna Libby C LC Carling Matthew D MD Wang Biao B Taylor Scott A SA Del-Rio Glaucia G Aleixo Alexandre A Vasconcelos Ana Tereza Ribeiro ATR Mello Claudio V CV Weir Jason T JT Haussler David D Li Qiye Q Yang Huanming H Wang Jian J Lei Fumin F Rahbek Carsten C Gilbert M Thomas P MTP Graves Gary R GR Jarvis Erich D ED Paten Benedict B Zhang Guojie G

Nature 20201111 7833

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity<sup>1-4</sup>. Sparse taxon sampling has previously been proposed to confound phylogenetic inference<sup>5</sup>, 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 pha ...[more]

PMID: 33177665

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Dense sampling of bird diversity increases power of comparative genomics.

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Dense sampling of bird diversity increases power of comparative genomics.

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