Unknown

Dataset Information

0

Dense sampling of bird diversity increases power of comparative genomics.


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.

SUBMITTER: Feng S 

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

REPOSITORIES: biostudies-literature

altmetric image

Publications

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]

Similar Datasets

| S-EPMC8081657 | biostudies-literature
| S-EPMC1142384 | biostudies-literature
| S-EPMC1174907 | biostudies-literature
| PRJNA1192322 | ENA
| S-EPMC6972490 | biostudies-literature
| S-EPMC3063683 | biostudies-literature
| S-EPMC4103989 | biostudies-literature
| S-EPMC7029076 | biostudies-literature
| S-EPMC4110425 | biostudies-literature
| S-EPMC7779000 | biostudies-literature