Dense sampling of bird diversity increases power of comparative genomics

Shaohong Feng; Josefin Stiller; Yuan Deng; Joel Armstrong; Qi Fang; Andrew Hart Reeve; Duo Xie; Guangji Chen; Chunxue Guo; Brant C Faircloth; Bent Petersen; Zongji Wang; Qi Zhou; Mark Diekhans; Wanjun Chen; Sergio Andreu-Sánchez; Ashot Margaryan; Jason Travis Howard; Carole Parent; George Pacheco; Mikkel-Holger S Sinding; Lara Puetz; Emily Cavill; Ângela M Ribeiro; Leopold Eckhart; Jon Fjeldså; Peter A Hosner; Robb T Brumfield; Les Christidis; Mads F Bertelsen; Thomas Sicheritz-Ponten; Dieter Thomas Tietze; Bruce C Robertson; Gang Song; Gerald Borgia; Santiago Claramunt; Irby J Lovette; Saul J Cowen; Peter Njoroge; John Philip Dumbacher; Oliver A Ryder; Jérôme Fuchs; Michael Bunce; David W Burt; Joel Cracraft; Guanliang Meng; Shannon J Hackett; Peter G Ryan; Knud Andreas Jønsson; Ian G Jamieson; Rute R da Fonseca; Edward L Braun; Peter Houde; Siavash Mirarab; Alexander Suh; Bengt Hansson; Suvi Ponnikas; Hanna Sigeman; Martin Stervander; Paul B Frandsen; Henriette van der Zwan; Rencia van der Sluis; Carina Visser; Christopher N Balakrishnan; Andrew G Clark; John W Fitzpatrick; Reed Bowman; Nancy Chen; Alison Cloutier; Timothy B Sackton; Scott V Edwards; Dustin J Foote; Subir B Shakya; Frederick H Sheldon; Alain Vignal; André E R Soares; Beth Shapiro; Jacob González-Solís; Joan Ferrer-Obiol; Julio Rozas; Marta Riutort; Anna Tigano; Vicki Friesen; Love Dalén; Araxi O Urrutia; Tamás Székely; Yang Liu; Michael G Campana; André Corvelo; Robert C Fleischer; Kim M Rutherford; Neil J Gemmell; Nicolas Dussex; Henrik Mouritsen; Nadine Thiele; Kira Delmore; Miriam Liedvogel; Andre Franke; Marc P Hoeppner; Oliver Krone; Adam M Fudickar; Borja Milá; Ellen D Ketterson; Andrew Eric Fidler; Guillermo Friis; Ángela M Parody-Merino; Phil F Battley; Murray P Cox; Nicholas Costa Barroso Lima; Francisco Prosdocimi; Thomas Lee Parchman; Barney A Schlinger; Bette A Loiselle; John G Blake; Haw Chuan Lim; Lainy B Day; Matthew J Fuxjager; Maude W Baldwin; Michael J Braun; Morgan Wirthlin; Rebecca B Dikow; T Brandt Ryder; Glauco Camenisch; Lukas F Keller; Jeffrey M DaCosta; Mark E Hauber; Matthew I M Louder; Christopher C Witt; Jimmy A McGuire; Joann Mudge; Libby C Megna; Matthew D Carling; Biao Wang; Scott A Taylor; Glaucia Del-Rio; Alexandre Aleixo; Ana Tereza Ribeiro Vasconcelos; Claudio V Mello; Jason T Weir; David Haussler; Qiye Li; Huanming Yang; Jian Wang; Fumin Lei; Carsten Rahbek; M Thomas P Gilbert; Gary R Graves; Erich D Jarvis; Benedict Paten; Guojie Zhang

doi:10.1038/s41586-020-2873-9

Dense sampling of bird diversity increases power of comparative genomics

Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sánchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George PachecoMikkel-Holger S Sinding, Lara Puetz, Emily Cavill, Ângela M Ribeiro, Leopold Eckhart, Jon Fjeldså, Peter A Hosner, Robb T Brumfield, Les Christidis, Mads F Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J Lovette, Saul J Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A Ryder, Jérôme Fuchs, Michael Bunce, David W Burt, Joel Cracraft, Guanliang Meng, Shannon J Hackett, Peter G Ryan, Knud Andreas Jønsson, Ian G Jamieson, Rute R da Fonseca, Edward L Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B Frandsen, Henriette van der Zwan, Rencia van der Sluis, Carina Visser, Christopher N Balakrishnan, Andrew G Clark, John W Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B Sackton, Scott V Edwards, Dustin J Foote, Subir B Shakya, Frederick H Sheldon, Alain Vignal, André E R Soares, Beth Shapiro, Jacob González-Solís, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalén, Araxi O Urrutia, Tamás Székely, Yang Liu, Michael G Campana, André Corvelo, Robert C Fleischer, Kim M Rutherford, Neil J Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P Hoeppner, Oliver Krone, Adam M Fudickar, Borja Milá, Ellen D Ketterson, Andrew Eric Fidler, Guillermo Friis, Ángela M Parody-Merino, Phil F Battley, Murray P Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A Schlinger, Bette A Loiselle, John G Blake, Haw Chuan Lim, Lainy B Day, Matthew J Fuxjager, Maude W Baldwin, Michael J Braun, Morgan Wirthlin, Rebecca B Dikow, T Brandt Ryder, Glauco Camenisch, Lukas F Keller, Jeffrey M DaCosta, Mark E Hauber, Matthew I M Louder, Christopher C Witt, Jimmy A McGuire, Joann Mudge, Libby C Megna, Matthew D Carling, Biao Wang, Scott A Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V Mello, Jason T Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M Thomas P Gilbert, Gary R Graves, Erich D Jarvis, Benedict Paten, Guojie Zhang

Research output: Contribution to journal › Article › peer-review

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	https://doi.org/10.1038/s41586-020-2873-9
State	Published - Nov 12 2020

Keywords

Animals
Birds/classification
Chickens/genetics
Conservation of Natural Resources
Datasets as Topic
Finches/genetics
Genome/genetics
Genomics/methods
Humans
Phylogeny
Selection, Genetic/genetics
Synteny/genetics

ASJC Scopus subject areas

General

Online availability

10.1038/s41586-020-2873-9

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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-Sánchez, S., Margaryan, A., Howard, J. T., Parent, C., ... Zhang, G. (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature, 587(7833), 252-257. https://doi.org/10.1038/s41586-020-2873-9

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sánchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, ÂM, Eckhart, L, Fjeldså, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jønsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, González-Solís, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalén, L, Urrutia, AO, Székely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Milá, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, ÁM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B & Zhang, G 2020, 'Dense sampling of bird diversity increases power of comparative genomics', Nature, vol. 587, no. 7833, pp. 252-257. https://doi.org/10.1038/s41586-020-2873-9

@article{ceef08daccea44248a1c4cfaa286f27c,

title = "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.",

keywords = "Animals, Birds/classification, Chickens/genetics, Conservation of Natural Resources, Datasets as Topic, Finches/genetics, Genome/genetics, Genomics/methods, Humans, Phylogeny, Selection, Genetic/genetics, Synteny/genetics",

author = "Shaohong Feng and Josefin Stiller and Yuan Deng and Joel Armstrong and Qi Fang and Reeve, {Andrew Hart} and Duo Xie and Guangji Chen and Chunxue Guo and Faircloth, {Brant C} and Bent Petersen and Zongji Wang and Qi Zhou and Mark Diekhans and Wanjun Chen and Sergio Andreu-S{\'a}nchez and Ashot Margaryan and Howard, {Jason Travis} and Carole Parent and George Pacheco and Sinding, {Mikkel-Holger S} and Lara Puetz and Emily Cavill and Ribeiro, {{\^A}ngela M} and Leopold Eckhart and Jon Fjelds{\aa} and Hosner, {Peter A} and Brumfield, {Robb T} and Les Christidis and Bertelsen, {Mads F} and Thomas Sicheritz-Ponten and Tietze, {Dieter Thomas} and Robertson, {Bruce C} and Gang Song and Gerald Borgia and Santiago Claramunt and Lovette, {Irby J} and Cowen, {Saul J} and Peter Njoroge and Dumbacher, {John Philip} and Ryder, {Oliver A} and J{\'e}r{\^o}me Fuchs and Michael Bunce and Burt, {David W} and Joel Cracraft and Guanliang Meng and Hackett, {Shannon J} and Ryan, {Peter G} and J{\o}nsson, {Knud Andreas} and Jamieson, {Ian G} and {da Fonseca}, {Rute R} and Braun, {Edward L} and Peter Houde and Siavash Mirarab and Alexander Suh and Bengt Hansson and Suvi Ponnikas and Hanna Sigeman and Martin Stervander and Frandsen, {Paul B} and {van der Zwan}, Henriette and {van der Sluis}, Rencia and Carina Visser and Balakrishnan, {Christopher N} and Clark, {Andrew G} and Fitzpatrick, {John W} and Reed Bowman and Nancy Chen and Alison Cloutier and Sackton, {Timothy B} and Edwards, {Scott V} and Foote, {Dustin J} and Shakya, {Subir B} and Sheldon, {Frederick H} and Alain Vignal and Soares, {Andr{\'e} E R} and Beth Shapiro and Jacob Gonz{\'a}lez-Sol{\'i}s and Joan Ferrer-Obiol and Julio Rozas and Marta Riutort and Anna Tigano and Vicki Friesen and Love Dal{\'e}n and Urrutia, {Araxi O} and Tam{\'a}s Sz{\'e}kely and Yang Liu and Campana, {Michael G} and Andr{\'e} Corvelo and Fleischer, {Robert C} and Rutherford, {Kim M} and Gemmell, {Neil J} and Nicolas Dussex and Henrik Mouritsen and Nadine Thiele and Kira Delmore and Miriam Liedvogel and Andre Franke and Hoeppner, {Marc P} and Oliver Krone and Fudickar, {Adam M} and Borja Mil{\'a} and Ketterson, {Ellen D} and Fidler, {Andrew Eric} and Guillermo Friis and Parody-Merino, {{\'A}ngela M} and Battley, {Phil F} and Cox, {Murray P} and Lima, {Nicholas Costa Barroso} and Francisco Prosdocimi and Parchman, {Thomas Lee} and Schlinger, {Barney A} and Loiselle, {Bette A} and Blake, {John G} and Lim, {Haw Chuan} and Day, {Lainy B} and Fuxjager, {Matthew J} and Baldwin, {Maude W} and Braun, {Michael J} and Morgan Wirthlin and Dikow, {Rebecca B} and Ryder, {T Brandt} and Glauco Camenisch and Keller, {Lukas F} and DaCosta, {Jeffrey M} and Hauber, {Mark E} and Louder, {Matthew I M} and Witt, {Christopher C} and McGuire, {Jimmy A} and Joann Mudge and Megna, {Libby C} and Carling, {Matthew D} and Biao Wang and Taylor, {Scott A} and Glaucia Del-Rio and Alexandre Aleixo and Vasconcelos, {Ana Tereza Ribeiro} and Mello, {Claudio V} and Weir, {Jason T} and David Haussler and Qiye Li and Huanming Yang and Jian Wang and Fumin Lei and Carsten Rahbek and Gilbert, {M Thomas P} and Graves, {Gary R} and Jarvis, {Erich D} and Benedict Paten and Guojie Zhang",

note = "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.{\textquoteright}s PhD thesis18.",

year = "2020",

month = nov,

day = "12",

doi = "10.1038/s41586-020-2873-9",

language = "English (US)",

volume = "587",

pages = "252--257",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7833",

}

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.

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.

KW - Animals

KW - Birds/classification

KW - Chickens/genetics

KW - Conservation of Natural Resources

KW - Datasets as Topic

KW - Finches/genetics

KW - Genome/genetics

KW - Genomics/methods

KW - Humans

KW - Phylogeny

KW - Selection, Genetic/genetics

KW - Synteny/genetics

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

SN - 0028-0836

VL - 587

SP - 252

EP - 257

JO - Nature

JF - Nature

IS - 7833

ER -

Dense sampling of bird diversity increases power of comparative genomics

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