The comparative genomics and complex population history of Papio baboons

Jeffrey Rogers; Muthuswamy Raveendran; R. Alan Harris; Thomas Mailund; Kalle Leppälä; Georgios Athanasiadis; Mikkel Heide Schierup; Jade Cheng; Kasper Munch; Jerilyn A. Walker; Miriam K. Konkel; Vallmer E. Jordan; Cody J. Steely; Thomas O. Beckstrom; Christina Bergey; Andrew Burrell; Dominik Schrempf; Angela Noll; Maximillian Kothe; Gisela H. Kopp; Yue Liu; Shwetha Murali; Konstantinos Billis; Fergal J. Martin; Matthieu Muffato; Laura A. Cox; James Else; Todd Disotell; Donna M. Muzny; Jane Phillips-Conroy; Bronwen Aken; Evan E. Eichler; Tomas Marques-Bonet; Carolin Kosiol; Mark A. Batzer; Matthew W. Hahn; Jenny Tung; Dietmar Zinner; Christian Roos; Clifford J. Jolly; Richard A. Gibbs; Kim C. Worley; Nicoletta Archidiacono; Oronzo Capozzi; Claudia R. Catacchio; Huyen H. Dinh; Harsha Vardhan Doddapaneni; Yi Han; John Huddleston; Shalini N. Jhangiani; Anis Karimpour-Fard; Viktoriya Korchina; Christie L. Kovar; Lukas Kuderna; Sandra L. Lee; Xiaoming Liu; Alessia Marra-Campanale; Christopher E. Mason; Marc de Manuel Montero; Kymberleigh A. Pagel; Antonio Palazzo; Jera Pecotte; Vikas Pejaver; Lenore Pipes; Veronica Searles Quick; Predrag Radivojac; Archana Raja; Brian J. Raney; Karen Rice; Mariano Rocchi; James M. Sikela; Roscoe Stanyon; Gregg W.C. Thomas; Mario Ventura; Tauras P. Vilgalys; Tomas Vinar; Lutz Walter

doi:10.1126/sciadv.aau6947

The comparative genomics and complex population history of Papio baboons

Jeffrey Rogers, Muthuswamy Raveendran, R. Alan Harris, Thomas Mailund, Kalle Leppälä, Georgios Athanasiadis, Mikkel Heide Schierup, Jade Cheng, Kasper Munch, Jerilyn A. Walker, Miriam K. Konkel, Vallmer E. Jordan, Cody J. Steely, Thomas O. Beckstrom, Christina Bergey, Andrew Burrell, Dominik Schrempf, Angela Noll, Maximillian Kothe, Gisela H. KoppYue Liu, Shwetha Murali, Konstantinos Billis, Fergal J. Martin, Matthieu Muffato, Laura A. Cox, James Else, Todd Disotell, Donna M. Muzny, Jane Phillips-Conroy, Bronwen Aken, Evan E. Eichler, Tomas Marques-Bonet, Carolin Kosiol, Mark A. Batzer, Matthew W. Hahn, Jenny Tung, Dietmar Zinner, Christian Roos, Clifford J. Jolly, Richard A. Gibbs, Kim C. Worley, Nicoletta Archidiacono, Oronzo Capozzi, Claudia R. Catacchio, Huyen H. Dinh, Harsha Vardhan Doddapaneni, Yi Han, John Huddleston, Shalini N. Jhangiani, Anis Karimpour-Fard, Viktoriya Korchina, Christie L. Kovar, Lukas Kuderna, Sandra L. Lee, Xiaoming Liu, Alessia Marra-Campanale, Christopher E. Mason, Marc de Manuel Montero, Kymberleigh A. Pagel, Antonio Palazzo, Jera Pecotte, Vikas Pejaver, Lenore Pipes, Veronica Searles Quick, Predrag Radivojac, Archana Raja, Brian J. Raney, Karen Rice, Mariano Rocchi, James M. Sikela, Roscoe Stanyon, Gregg W.C. Thomas, Mario Ventura, Tauras P. Vilgalys, Tomas Vinar, Lutz Walter

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

Abstract

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

Original language	English (US)
Article number	eaau6947
Journal	Science Advances
Volume	5
Issue number	1
DOIs	https://doi.org/10.1126/sciadv.aau6947
State	Published - Jan 30 2019

ASJC Scopus subject areas

General

Access to Document

10.1126/sciadv.aau6947

Cite this

Rogers, J., Raveendran, M., Harris, R. A., Mailund, T., Leppälä, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V. E., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., Kothe, M., ... Walter, L. (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1), Article eaau6947. https://doi.org/10.1126/sciadv.aau6947

Rogers, J, Raveendran, M, Harris, RA, Mailund, T, Leppälä, K, Athanasiadis, G, Schierup, MH, Cheng, J, Munch, K, Walker, JA, Konkel, MK, Jordan, VE, Steely, CJ, Beckstrom, TO, Bergey, C, Burrell, A, Schrempf, D, Noll, A, Kothe, M, Kopp, GH, Liu, Y, Murali, S, Billis, K, Martin, FJ, Muffato, M, Cox, LA, Else, J, Disotell, T, Muzny, DM, Phillips-Conroy, J, Aken, B, Eichler, EE, Marques-Bonet, T, Kosiol, C, Batzer, MA, Hahn, MW, Tung, J, Zinner, D, Roos, C, Jolly, CJ, Gibbs, RA, Worley, KC, Archidiacono, N, Capozzi, O, Catacchio, CR, Dinh, HH, Doddapaneni, HV, Han, Y, Huddleston, J, Jhangiani, SN, Karimpour-Fard, A, Korchina, V, Kovar, CL, Kuderna, L, Lee, SL, Liu, X, Marra-Campanale, A, Mason, CE, Montero, MDM, Pagel, KA, Palazzo, A, Pecotte, J, Pejaver, V, Pipes, L, Quick, VS, Radivojac, P, Raja, A, Raney, BJ, Rice, K, Rocchi, M, Sikela, JM, Stanyon, R, Thomas, GWC, Ventura, M, Vilgalys, TP, Vinar, T & Walter, L 2019, 'The comparative genomics and complex population history of Papio baboons', Science Advances, vol. 5, no. 1, eaau6947. https://doi.org/10.1126/sciadv.aau6947

@article{98531d8af8b34f0b995e401107cfe7f4,

title = "The comparative genomics and complex population history of Papio baboons",

abstract = "Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.",

author = "Jeffrey Rogers and Muthuswamy Raveendran and Harris, {R. Alan} and Thomas Mailund and Kalle Lepp{\"a}l{\"a} and Georgios Athanasiadis and Schierup, {Mikkel Heide} and Jade Cheng and Kasper Munch and Walker, {Jerilyn A.} and Konkel, {Miriam K.} and Jordan, {Vallmer E.} and Steely, {Cody J.} and Beckstrom, {Thomas O.} and Christina Bergey and Andrew Burrell and Dominik Schrempf and Angela Noll and Maximillian Kothe and Kopp, {Gisela H.} and Yue Liu and Shwetha Murali and Konstantinos Billis and Martin, {Fergal J.} and Matthieu Muffato and Cox, {Laura A.} and James Else and Todd Disotell and Muzny, {Donna M.} and Jane Phillips-Conroy and Bronwen Aken and Eichler, {Evan E.} and Tomas Marques-Bonet and Carolin Kosiol and Batzer, {Mark A.} and Hahn, {Matthew W.} and Jenny Tung and Dietmar Zinner and Christian Roos and Jolly, {Clifford J.} and Gibbs, {Richard A.} and Worley, {Kim C.} and Nicoletta Archidiacono and Oronzo Capozzi and Catacchio, {Claudia R.} and Dinh, {Huyen H.} and Doddapaneni, {Harsha Vardhan} and Yi Han and John Huddleston and Jhangiani, {Shalini N.} and Anis Karimpour-Fard and Viktoriya Korchina and Kovar, {Christie L.} and Lukas Kuderna and Lee, {Sandra L.} and Xiaoming Liu and Alessia Marra-Campanale and Mason, {Christopher E.} and Montero, {Marc de Manuel} and Pagel, {Kymberleigh A.} and Antonio Palazzo and Jera Pecotte and Vikas Pejaver and Lenore Pipes and Quick, {Veronica Searles} and Predrag Radivojac and Archana Raja and Raney, {Brian J.} and Karen Rice and Mariano Rocchi and Sikela, {James M.} and Roscoe Stanyon and Thomas, {Gregg W.C.} and Mario Ventura and Vilgalys, {Tauras P.} and Tomas Vinar and Lutz Walter",

note = "Publisher Copyright: Copyright {\textcopyright} 2019 The Authors,",

year = "2019",

month = jan,

day = "30",

doi = "10.1126/sciadv.aau6947",

language = "English (US)",

volume = "5",

journal = "Science Advances",

issn = "2375-2548",

publisher = "American Association for the Advancement of Science",

number = "1",

}

TY - JOUR

T1 - The comparative genomics and complex population history of Papio baboons

AU - Rogers, Jeffrey

AU - Raveendran, Muthuswamy

AU - Harris, R. Alan

AU - Mailund, Thomas

AU - Leppälä, Kalle

AU - Athanasiadis, Georgios

AU - Schierup, Mikkel Heide

AU - Cheng, Jade

AU - Munch, Kasper

AU - Walker, Jerilyn A.

AU - Konkel, Miriam K.

AU - Jordan, Vallmer E.

AU - Steely, Cody J.

AU - Beckstrom, Thomas O.

AU - Bergey, Christina

AU - Burrell, Andrew

AU - Schrempf, Dominik

AU - Noll, Angela

AU - Kothe, Maximillian

AU - Kopp, Gisela H.

AU - Liu, Yue

AU - Murali, Shwetha

AU - Billis, Konstantinos

AU - Martin, Fergal J.

AU - Muffato, Matthieu

AU - Cox, Laura A.

AU - Else, James

AU - Disotell, Todd

AU - Muzny, Donna M.

AU - Phillips-Conroy, Jane

AU - Aken, Bronwen

AU - Eichler, Evan E.

AU - Marques-Bonet, Tomas

AU - Kosiol, Carolin

AU - Batzer, Mark A.

AU - Hahn, Matthew W.

AU - Tung, Jenny

AU - Zinner, Dietmar

AU - Roos, Christian

AU - Jolly, Clifford J.

AU - Gibbs, Richard A.

AU - Worley, Kim C.

AU - Archidiacono, Nicoletta

AU - Capozzi, Oronzo

AU - Catacchio, Claudia R.

AU - Dinh, Huyen H.

AU - Doddapaneni, Harsha Vardhan

AU - Han, Yi

AU - Huddleston, John

AU - Jhangiani, Shalini N.

AU - Karimpour-Fard, Anis

AU - Korchina, Viktoriya

AU - Kovar, Christie L.

AU - Kuderna, Lukas

AU - Lee, Sandra L.

AU - Liu, Xiaoming

AU - Marra-Campanale, Alessia

AU - Mason, Christopher E.

AU - Montero, Marc de Manuel

AU - Pagel, Kymberleigh A.

AU - Palazzo, Antonio

AU - Pecotte, Jera

AU - Pejaver, Vikas

AU - Pipes, Lenore

AU - Quick, Veronica Searles

AU - Radivojac, Predrag

AU - Raja, Archana

AU - Raney, Brian J.

AU - Rice, Karen

AU - Rocchi, Mariano

AU - Sikela, James M.

AU - Stanyon, Roscoe

AU - Thomas, Gregg W.C.

AU - Ventura, Mario

AU - Vilgalys, Tauras P.

AU - Vinar, Tomas

AU - Walter, Lutz

PY - 2019/1/30

Y1 - 2019/1/30

N2 - Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

AB - Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

UR - http://www.scopus.com/inward/record.url?scp=85060670885&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060670885&partnerID=8YFLogxK

U2 - 10.1126/sciadv.aau6947

DO - 10.1126/sciadv.aau6947

M3 - Article

C2 - 30854422

AN - SCOPUS:85060670885

SN - 2375-2548

VL - 5

JO - Science Advances

JF - Science Advances

IS - 1

M1 - eaau6947

ER -

The comparative genomics and complex population history of Papio baboons

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this