Dense sampling of bird diversity increases power of comparative genomics

Show full item record



Permalink

http://hdl.handle.net/10138/322047

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

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; 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, Jerome; 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, Andre E. R.; Shapiro, Beth; Gonzalez-Solis, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki; Dalen, Love; Urrutia, Araxi O.; Szekely, Tamas; Liu, Yang; Campana, Michael G.; Corvelo, Andre; Fleischer, Robert C.; Rutherford, Kim M.; Gemmell, Neil J.; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Mila, Borja; Ketterson, Ellen D.; Fidler, Andrew Eric; Friis, Guillermo; Parody-Merino, Angela M.; Battley, Phil F.; Cox, Murray P.; Lima, Nicholas Costa Barroso; Prosdocimi, Francisco; Parchman, Thomas Lee; Schlinger, Barney A.; Loiselle, Bette A.; Blake, John G.; Lim, Haw Chuan; Day, Lainy B.; Fuxjager, Matthew J.; Baldwin, Maude W.; Braun, Michael J.; Wirthlin, Morgan; Dikow, Rebecca B.; Ryder, T. Brandt; Camenisch, Glauco; Keller, Lukas F.; DaCosta, Jeffrey M.; Hauber, Mark E.; Louder, Matthew I. M.; Witt, Christopher C.; McGuire, Jimmy A.; Mudge, Joann; Megna, Libby C.; Carling, Matthew D.; Wang, Biao; Taylor, Scott A.; Del-Rio, Glaucia; Aleixo, Alexandre; Vasconcelos, Ana Tereza Ribeiro; Mello, Claudio V.; Weir, Jason T.; Haussler, David; Li, Qiye; Yang, Huanming; Wang, Jian; Lei, Fumin; Rahbek, Carsten; Gilbert, M. Thomas P.; Graves, Gary R.; Jarvis, Erich D.; Paten, Benedict; Zhang, Guojie
Contributor: University of Helsinki, Zoology
Date: 2020-11-12
Language: eng
Number of pages: 21
Belongs to series: Nature
ISSN: 0028-0836
URI: http://hdl.handle.net/10138/322047
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.
Subject: ACCELERATED EVOLUTION
DNA
DUPLICATION
DIVERGENCE
SEQUENCES
PROTEINS
REVEALS
PACKAGE
GENES
TREE
1181 Ecology, evolutionary biology
Rights:


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 full item record