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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 252-257 |
| Number of pages | 6 |
| Journal | Nature |
| Volume | 587 |
| Issue number | 7833 |
| DOIs | |
| State | Published - Nov 12 2020 |
ASJC Scopus subject areas
- General
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Dense sampling of bird diversity increases power of comparative genomics. / 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-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel Holger S.; Puetz, Lara; Cavill, Emily; Ribeiro, Ângela M.; Eckhart, Leopold; Fjeldså, 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.; Shapiro, Beth; González-Solís, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, 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.; Gemmell, Neil J.; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Milá, Borja; Ketterson, Ellen D.; Fidler, Andrew Eric; Friis, Guillermo; Parody-Merino, Ángela 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.
In: Nature, Vol. 587, No. 7833, 12.11.2020, p. 252-257.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Dense sampling of bird diversity increases power of comparative genomics
AU - Feng, Shaohong
AU - Stiller, Josefin
AU - Deng, Yuan
AU - Armstrong, Joel
AU - Fang, Qi
AU - Reeve, Andrew Hart
AU - Xie, Duo
AU - Chen, Guangji
AU - Guo, Chunxue
AU - Faircloth, Brant C.
AU - Petersen, Bent
AU - Wang, Zongji
AU - Zhou, Qi
AU - Diekhans, Mark
AU - Chen, Wanjun
AU - Andreu-Sánchez, Sergio
AU - Margaryan, Ashot
AU - Howard, Jason Travis
AU - Parent, Carole
AU - Pacheco, George
AU - Sinding, Mikkel Holger S.
AU - Puetz, Lara
AU - Cavill, Emily
AU - Ribeiro, Ângela M.
AU - Eckhart, Leopold
AU - Fjeldså, Jon
AU - Hosner, Peter A.
AU - Brumfield, Robb T.
AU - Christidis, Les
AU - Bertelsen, Mads F.
AU - Sicheritz-Ponten, Thomas
AU - Tietze, Dieter Thomas
AU - Robertson, Bruce C.
AU - Song, Gang
AU - Borgia, Gerald
AU - Claramunt, Santiago
AU - Lovette, Irby J.
AU - Cowen, Saul J.
AU - Njoroge, Peter
AU - Dumbacher, John Philip
AU - Ryder, Oliver A.
AU - Fuchs, Jérôme
AU - Bunce, Michael
AU - Burt, David W.
AU - Cracraft, Joel
AU - Meng, Guanliang
AU - Hackett, Shannon J.
AU - Ryan, Peter G.
AU - Jønsson, Knud Andreas
AU - Jamieson, Ian G.
AU - da Fonseca, Rute R.
AU - Braun, Edward L.
AU - Houde, Peter
AU - Mirarab, Siavash
AU - Suh, Alexander
AU - Hansson, Bengt
AU - Ponnikas, Suvi
AU - Sigeman, Hanna
AU - Stervander, Martin
AU - Frandsen, Paul B.
AU - van der Zwan, Henriette
AU - van der Sluis, Rencia
AU - Visser, Carina
AU - Balakrishnan, Christopher N.
AU - Clark, Andrew G.
AU - Fitzpatrick, John W.
AU - Bowman, Reed
AU - Chen, Nancy
AU - Cloutier, Alison
AU - Sackton, Timothy B.
AU - Edwards, Scott V.
AU - Foote, Dustin J.
AU - Shakya, Subir B.
AU - Sheldon, Frederick H.
AU - Vignal, Alain
AU - Soares, André E.R.
AU - Shapiro, Beth
AU - González-Solís, Jacob
AU - Ferrer-Obiol, Joan
AU - Rozas, Julio
AU - Riutort, Marta
AU - Tigano, Anna
AU - Friesen, Vicki
AU - Dalén, Love
AU - Urrutia, Araxi O.
AU - Székely, Tamás
AU - Liu, Yang
AU - Campana, Michael G.
AU - Corvelo, André
AU - Fleischer, Robert C.
AU - Rutherford, Kim M.
AU - Gemmell, Neil J.
AU - Dussex, Nicolas
AU - Mouritsen, Henrik
AU - Thiele, Nadine
AU - Delmore, Kira
AU - Liedvogel, Miriam
AU - Franke, Andre
AU - Hoeppner, Marc P.
AU - Krone, Oliver
AU - Fudickar, Adam M.
AU - Milá, Borja
AU - Ketterson, Ellen D.
AU - Fidler, Andrew Eric
AU - Friis, Guillermo
AU - Parody-Merino, Ángela M.
AU - Battley, Phil F.
AU - Cox, Murray P.
AU - Lima, Nicholas Costa Barroso
AU - Prosdocimi, Francisco
AU - Parchman, Thomas Lee
AU - Schlinger, Barney A.
AU - Loiselle, Bette A.
AU - Blake, John G.
AU - Lim, Haw Chuan
AU - Day, Lainy B.
AU - Fuxjager, Matthew J.
AU - Baldwin, Maude W.
AU - Braun, Michael J.
AU - Wirthlin, Morgan
AU - Dikow, Rebecca B.
AU - Ryder, T. Brandt
AU - Camenisch, Glauco
AU - Keller, Lukas F.
AU - DaCosta, Jeffrey M.
AU - Hauber, Mark E.
AU - Louder, Matthew I.M.
AU - Witt, Christopher C.
AU - McGuire, Jimmy A.
AU - Mudge, Joann
AU - Megna, Libby C.
AU - Carling, Matthew D.
AU - Wang, Biao
AU - Taylor, Scott A.
AU - Del-Rio, Glaucia
AU - Aleixo, Alexandre
AU - Vasconcelos, Ana Tereza Ribeiro
AU - Mello, Claudio V.
AU - Weir, Jason T.
AU - Haussler, David
AU - Li, Qiye
AU - Yang, Huanming
AU - Wang, Jian
AU - Lei, Fumin
AU - Rahbek, Carsten
AU - Gilbert, M. Thomas P.
AU - Graves, Gary R.
AU - Jarvis, Erich D.
AU - Paten, Benedict
AU - Zhang, Guojie
N1 - Funding Information: Rowe (Museums Victoria), K. Winker (University of Alaska Museum) and the late A. Baker (Royal Ontario Museum) for providing tissue samples; B. J. Novak for sample coordination; Dovetail Genomics for the assembly of Caloenas nicobarica; T. Riede for helpful discussions of the mechanism and evolution of the vocal tract filter in songbirds; and China National Genebank at BGI for contributing to the sequencing for the B10K Project. The final version of the manuscript was approved by H. G. Spencer (University of Otago), in place of the late I.G.J. This work was supported by Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000), International Partnership Program of Chinese Academy of Sciences (no. 152453KYSB20170002), Carlsberg Foundation (CF16-0663) and Villum Foundation (no. 25900) to G.Z. This work was also supported in part by National Natural Science Foundation of China no. 31901214 to S.F., ERC Consolidator Grant 681396 to M.T.P.G. and Howard Hughes Medical Institute funds to E.D.J., the National Institutes of Health (award numbers 5U54HG007990, 5T32HG008345-04, 1U01HL137183, R01HG010053, U01HL137183 and U54HG007990) to B. Paten. Supercomputing was partially performed using the DeiC National Life Science Supercomputer, Computerome, at the Technical University of Denmark. Portions of this research were also conducted with high-performance computing resources provided by Louisiana State University (http://www.hpc.lsu.edu). Parts of this work and its text were included in J.A.’s PhD thesis18. Publisher Copyright: © 2020, The Author(s).
PY - 2020/11/12
Y1 - 2020/11/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85095836366&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85095836366&partnerID=8YFLogxK
U2 - 10.1038/s41586-020-2873-9
DO - 10.1038/s41586-020-2873-9
M3 - Article
C2 - 33177665
AN - SCOPUS:85095836366
VL - 587
SP - 252
EP - 257
JO - Nature Cell Biology
JF - Nature Cell Biology
SN - 1465-7392
IS - 7833
ER -