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Title: Dense sampling of bird diversity increases power of comparative genomics
Author: Feng, Shaohong
Stiller, Josefin
Deng, Yuan
Armstrong, Joel
Fang, Qi
Reeve, Andrew Hart
Xie, Duo
Chen, Guangji
Guo, Chunxue
Faircloth, Brant C.
Petersen, Bent
Gemmell, Neil J.
Dussex, Nicolas
Mouritsen, Henrik
Thiele, Nadine
Delmore, Kira
Liedvogel, Miriam
Franke, Andre
Hoeppner, Marc P.
Fidler, Ellen
Krone, Oliver
Milá, Borja
Fudickar, Adam M.
Wang, Zongji
Zhou, Qi
Diekhans, Mark
Chen, Wanjun
Andreu Sanchez, Sergio
Margaryan, Ashot
Howard, Jason Travis
Parent, Carole
Pacheco, George
Sinding, Mikkel-Holger S.
Puetz, Lara
Cavill, Emily
Ribeiro, Angela M.
Eckhart, Leopold
Fjeldsa, Jon
Hosner, Peter A.
Brumfield, Robb T.
Christidis, Les
Bertelsen, Mads F.
Sicheritz Ponten, Thomas
Tietze, Dieter Thomas
Robertson, Bruce C.
Song, Gang
Borgia, Gerald
Claramunt, Santiago
Lovette, Irby J.
Cowen, Saul J.
Njoroge, Peter
Dumbacher, John Philip
Ryder, Oliver A.
Fuchs, Jérôme
Bunce, Michael
Burt, David W.
Cracraft, Joel
Meng, Guanliang
Hackett, Shannon J.
Ryan, Peter G.
Jønsson, Knud Andreas
Jamieson, Ian G.
da Fonseca, Rute R.
Braun, Edward L.
Houde, Peter
Mirarab, Siavash
Suh, Alexander
Hansson, Bengt
Ponnikas, Suvi
Sigeman, Hanna
Stervander, Martin
Frandsen, Paul B.
van der Zwan, Henriette
van der Sluis, Rencia
Visser, Carina
Balakrishnan, Christopher N.
Clark, Andrew G.
Fitzpatrick, John W.
Bowman, Reed
Chen, Nancy
Cloutier, Alison
Sackton, Timothy B.
Edwards, Scott V.
Foote, Dustin J.
Shakya, Subir B.
Sheldon, Frederick H.
Vignal, Alain
Soares, André E. R.
Shaphiro, Beth
González-Solís, Jacob
Ferrer-Obiol, Joan
Rozas Liras, Julio A.
Riutort León, Marta
Tigano, Anna
Friesen, Vicki
Dalén, Love
Urrutia, Araxi O.
Székely, Tamás
Liu, Yang
Campana, Michael G.
Corvelo, André
Fleischer, Robert C.
Rutherford, Kim M.
Keywords: Genomes
Cladistic analysis
Issue Date: 11-Nov-2020
Publisher: Nature Publishing Group
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.
Note: Reproducció del document publicat a:
It is part of: Nature, 2020, vol. 587, num. 7833, p. 252-257
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ISSN: 0028-0836
Appears in Collections:Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)
Articles publicats en revistes (Institut de Recerca de la Biodiversitat (IRBio))
Publicacions de projectes de recerca finançats per la UE
Articles publicats en revistes (Genètica, Microbiologia i Estadística)

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