Dense sampling of bird diversity increases power of comparative genomics

Show simple item record

dc.contributor.author Feng, Shaohong
dc.contributor.author Stiller, Josefin
dc.contributor.author Deng, Yuan
dc.contributor.author Armstrong, Joel
dc.contributor.author Fang, Qi
dc.contributor.author Reeve, Andrew Hart
dc.contributor.author Xie, Duo
dc.contributor.author Chen, Guangji
dc.contributor.author Guo, Chunxue
dc.contributor.author Faircloth, Brant C.
dc.contributor.author Petersen, Bent
dc.contributor.author Wang, Zongji
dc.contributor.author Zhou, Qi
dc.contributor.author Diekhans, Mark
dc.contributor.author Chen, Wanjun
dc.contributor.author Andreu-Sanchez, Sergio
dc.contributor.author Margaryan, Ashot
dc.contributor.author Howard, Jason Travis
dc.contributor.author Parent, Carole
dc.contributor.author Pacheco, George
dc.contributor.author Sinding, Mikkel-Holger S.
dc.contributor.author Puetz, Lara
dc.contributor.author Cavill, Emily
dc.contributor.author Ribeiro, Angela M.
dc.contributor.author Eckhart, Leopold
dc.contributor.author Fjeldsa, Jon
dc.contributor.author Hosner, Peter A.
dc.contributor.author Brumfield, Robb T.
dc.contributor.author Christidis, Les
dc.contributor.author Bertelsen, Mads F.
dc.contributor.author Sicheritz-Ponten, Thomas
dc.contributor.author Tietze, Dieter Thomas
dc.contributor.author Robertson, Bruce C.
dc.contributor.author Song, Gang
dc.contributor.author Borgia, Gerald
dc.contributor.author Claramunt, Santiago
dc.contributor.author Lovette, Irby J.
dc.contributor.author Cowen, Saul J.
dc.contributor.author Njoroge, Peter
dc.contributor.author Dumbacher, John Philip
dc.contributor.author Ryder, Oliver A.
dc.contributor.author Fuchs, Jerome
dc.contributor.author Bunce, Michael
dc.contributor.author Burt, David W.
dc.contributor.author Cracraft, Joel
dc.contributor.author Meng, Guanliang
dc.contributor.author Hackett, Shannon J.
dc.contributor.author Ryan, Peter G.
dc.contributor.author Jønsson, Knud Andreas
dc.contributor.author Jamieson, Ian G.
dc.contributor.author da Fonseca, Rute R.
dc.contributor.author Braun, Edward L.
dc.contributor.author Houde, Peter
dc.contributor.author Mirarab, Siavash
dc.contributor.author Suh, Alexander
dc.contributor.author Hansson, Bengt
dc.contributor.author Ponnikas, Suvi
dc.contributor.author Sigeman, Hanna
dc.contributor.author Stervander, Martin
dc.contributor.author Frandsen, Paul B.
dc.contributor.author van der Zwan, Henriette
dc.contributor.author van der Sluis, Rencia
dc.contributor.author Visser, Carina
dc.contributor.author Balakrishnan, Christopher N.
dc.contributor.author Clark, Andrew G.
dc.contributor.author Fitzpatrick, John W.
dc.contributor.author Bowman, Reed
dc.contributor.author Chen, Nancy
dc.contributor.author Cloutier, Alison
dc.contributor.author Sackton, Timothy B.
dc.contributor.author Edwards, Scott V.
dc.contributor.author Foote, Dustin J.
dc.contributor.author Shakya, Subir B.
dc.contributor.author Sheldon, Frederick H.
dc.contributor.author Vignal, Alain
dc.contributor.author Soares, Andre E. R.
dc.contributor.author Shapiro, Beth
dc.contributor.author Gonzalez-Solis, Jacob
dc.contributor.author Ferrer-Obiol, Joan
dc.contributor.author Rozas, Julio
dc.contributor.author Riutort, Marta
dc.contributor.author Tigano, Anna
dc.contributor.author Friesen, Vicki
dc.contributor.author Dalen, Love
dc.contributor.author Urrutia, Araxi O.
dc.contributor.author Szekely, Tamas
dc.contributor.author Liu, Yang
dc.contributor.author Campana, Michael G.
dc.contributor.author Corvelo, Andre
dc.contributor.author Fleischer, Robert C.
dc.contributor.author Rutherford, Kim M.
dc.contributor.author Gemmell, Neil J.
dc.contributor.author Dussex, Nicolas
dc.contributor.author Mouritsen, Henrik
dc.contributor.author Thiele, Nadine
dc.contributor.author Delmore, Kira
dc.contributor.author Liedvogel, Miriam
dc.contributor.author Franke, Andre
dc.contributor.author Hoeppner, Marc P.
dc.contributor.author Krone, Oliver
dc.contributor.author Fudickar, Adam M.
dc.contributor.author Mila, Borja
dc.contributor.author Ketterson, Ellen D.
dc.contributor.author Fidler, Andrew Eric
dc.contributor.author Friis, Guillermo
dc.contributor.author Parody-Merino, Angela M.
dc.contributor.author Battley, Phil F.
dc.contributor.author Cox, Murray P.
dc.contributor.author Lima, Nicholas Costa Barroso
dc.contributor.author Prosdocimi, Francisco
dc.contributor.author Parchman, Thomas Lee
dc.contributor.author Schlinger, Barney A.
dc.contributor.author Loiselle, Bette A.
dc.contributor.author Blake, John G.
dc.contributor.author Lim, Haw Chuan
dc.contributor.author Day, Lainy B.
dc.contributor.author Fuxjager, Matthew J.
dc.contributor.author Baldwin, Maude W.
dc.contributor.author Braun, Michael J.
dc.contributor.author Wirthlin, Morgan
dc.contributor.author Dikow, Rebecca B.
dc.contributor.author Ryder, T. Brandt
dc.contributor.author Camenisch, Glauco
dc.contributor.author Keller, Lukas F.
dc.contributor.author DaCosta, Jeffrey M.
dc.contributor.author Hauber, Mark E.
dc.contributor.author Louder, Matthew I. M.
dc.contributor.author Witt, Christopher C.
dc.contributor.author McGuire, Jimmy A.
dc.contributor.author Mudge, Joann
dc.contributor.author Megna, Libby C.
dc.contributor.author Carling, Matthew D.
dc.contributor.author Wang, Biao
dc.contributor.author Taylor, Scott A.
dc.contributor.author Del-Rio, Glaucia
dc.contributor.author Aleixo, Alexandre
dc.contributor.author Vasconcelos, Ana Tereza Ribeiro
dc.contributor.author Mello, Claudio V.
dc.contributor.author Weir, Jason T.
dc.contributor.author Haussler, David
dc.contributor.author Li, Qiye
dc.contributor.author Yang, Huanming
dc.contributor.author Wang, Jian
dc.contributor.author Lei, Fumin
dc.contributor.author Rahbek, Carsten
dc.contributor.author Gilbert, M. Thomas P.
dc.contributor.author Graves, Gary R.
dc.contributor.author Jarvis, Erich D.
dc.contributor.author Paten, Benedict
dc.contributor.author Zhang, Guojie
dc.date.accessioned 2020-11-27T12:35:02Z
dc.date.available 2020-11-27T12:35:02Z
dc.date.issued 2020-11-12
dc.identifier.citation Feng , S , Stiller , J , Deng , Y , Armstrong , J , Fang , Q , Reeve , A H , Xie , D , Chen , G , Guo , C , Faircloth , B C , Petersen , B , Wang , Z , Zhou , Q , Diekhans , M , Chen , W , Andreu-Sanchez , S , Margaryan , A , Howard , J T , Parent , C , Pacheco , G , Sinding , M-H S , Puetz , L , Cavill , E , Ribeiro , A M , Eckhart , L , Fjeldsa , J , Hosner , P A , Brumfield , R T , Christidis , L , Bertelsen , M F , Sicheritz-Ponten , T , Tietze , D T , Robertson , B C , Song , G , Borgia , G , Claramunt , S , Lovette , I J , Cowen , S J , Njoroge , P , Dumbacher , J P , Ryder , O A , Fuchs , J , Bunce , M , Burt , D W , Cracraft , J , Meng , G , Hackett , S J , Ryan , P G , Jønsson , K A , Jamieson , I G , da Fonseca , R R , Braun , E L , Houde , P , Mirarab , S , Suh , A , Hansson , B , Ponnikas , S , Sigeman , H , Stervander , M , Frandsen , P B , van der Zwan , H , van der Sluis , R , Visser , C , Balakrishnan , C N , Clark , A G , Fitzpatrick , J W , Bowman , R , Chen , N , Cloutier , A , Sackton , T B , Edwards , S V , Foote , D J , Shakya , S B , Sheldon , F H , Vignal , A , Soares , A E R , Shapiro , B , Gonzalez-Solis , J , Ferrer-Obiol , J , Rozas , J , Riutort , M , Tigano , A , Friesen , V , Dalen , L , Urrutia , A O , Szekely , T , Liu , Y , Campana , M G , Corvelo , A , Fleischer , R C , Rutherford , K M , Gemmell , N J , Dussex , N , Mouritsen , H , Thiele , N , Delmore , K , Liedvogel , M , Franke , A , Hoeppner , M P , Krone , O , Fudickar , A M , Mila , B , Ketterson , E D , Fidler , A E , Friis , G , Parody-Merino , A M , Battley , P F , Cox , M P , Lima , N C B , Prosdocimi , F , Parchman , T L , Schlinger , B A , Loiselle , B A , Blake , J G , Lim , H C , Day , L B , Fuxjager , M J , Baldwin , M W , Braun , M J , Wirthlin , M , Dikow , R B , Ryder , T B , Camenisch , G , Keller , L F , DaCosta , J M , Hauber , M E , Louder , M I M , Witt , C C , McGuire , J A , Mudge , J , Megna , L C , Carling , M D , Wang , B , Taylor , S A , Del-Rio , G , Aleixo , A , Vasconcelos , A T R , Mello , C V , Weir , J T , Haussler , D , Li , Q , Yang , H , Wang , J , Lei , F , Rahbek , C , Gilbert , M T P , Graves , G R , Jarvis , E D , Paten , B & Zhang , G 2020 , ' Dense sampling of bird diversity increases power of comparative genomics ' , Nature , vol. 587 , no. 7833 , pp. 252-+ . https://doi.org/10.1038/s41586-020-2873-9
dc.identifier.other PURE: 156355003
dc.identifier.other PURE UUID: 39af2301-1be3-45fe-a816-bbd12a84e708
dc.identifier.other WOS: 000588830300012
dc.identifier.other ORCID: /0000-0002-7816-9725/work/84258583
dc.identifier.uri http://hdl.handle.net/10138/322047
dc.description.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 inference(5), 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. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing. en
dc.format.extent 21
dc.language.iso eng
dc.relation.ispartof Nature
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject ACCELERATED EVOLUTION
dc.subject DNA
dc.subject DUPLICATION
dc.subject DIVERGENCE
dc.subject SEQUENCES
dc.subject PROTEINS
dc.subject REVEALS
dc.subject PACKAGE
dc.subject GENES
dc.subject TREE
dc.subject 1181 Ecology, evolutionary biology
dc.title Dense sampling of bird diversity increases power of comparative genomics en
dc.type Article
dc.contributor.organization Zoology
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1038/s41586-020-2873-9
dc.relation.issn 0028-0836
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

Files in this item

Total number of downloads: Loading...

Files Size Format View
s41586_020_2873_9_1_2.pdf 11.11Mb PDF View/Open

This item appears in the following Collection(s)

Show simple item record