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 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 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

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 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 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

^*Corresponding author for this work

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
Article number	eaau6947
Number of pages	15
Journal	Science Advances
Volume	5
Issue number	1
DOIs	https://doi.org/10.1126/sciadv.aau6947
Publication status	Published - 30 Jan 2019

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Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
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Dr Carolin Kosiol: Genome-wide Molecular Dating
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1/07/17 → 31/12/20
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Carolin Kosiol
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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., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., Kothe, M., ... Worley, K. C. (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1), Article eaau6947. https://doi.org/10.1126/sciadv.aau6947

@article{ac9f0a8a6aaf4b3a8e0d85353f7ea977,

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 Vallmer Jordan 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 Laura Cox 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.}",

note = "The sequencing and analysis activities at the Human Genome Sequencing Center, Baylor College of Medicine, were supported by NIH (NHGRI) grants U54-HG003273 and U54-HG006484 to R.A.G. and GAC grant 1 S10 RR026605 to J. G. Reid. This research was also supported by NIH grant R01-GM59290 to M.A.B.; grants from the Austrian Science Fund (FWF-P24551 and FWF-W1225) and Vienna Science and Technology Fund (WWTF-MA16-061) to C.K.; grants from the Wellcome Trust (WT108749/Z/15/Z) and EMBL to B.A., F.J.M., and M.M.; grants VEGA 1/0719/14 and APVV-14-0253 to T. Vinar (Consortium Member); MINECO/FEDER grant, NIH U01-MH106874 grant, Howard Hughes International Early Career award, and Obra Social “La Caixa” award to T.M.-B.; NSF grants BNS83-03506 to J.P.-C.; NSF1029302 to J.P.-C., J.R., and C.J.J.; BNS96-15150 to J.P.-C., C.J.J., and T.D.; and National Geographic Society and Leakey Foundation grants to J.P.-C. and C.J.J. E.E.E. is an investigator of the Howard Hughes Medical Institute. This work was supported, in part, by U.S. NIH grant HG002385 to E.E.E.",

year = "2019",

month = jan,

day = "30",

doi = "10.1126/sciadv.aau6947",

language = "English",

volume = "5",

journal = "Science Advances",

issn = "2375-2548",

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

number = "1",

}

Rogers, J, Raveendran, M, Harris, RA, Mailund, T, Leppälä, K, Athanasiadis, G, Schierup, MH, Cheng, J, Munch, K, Walker, JA, Konkel, MK, Jordan, V, 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, L, 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 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

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

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

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.

N1 - The sequencing and analysis activities at the Human Genome Sequencing Center, Baylor College of Medicine, were supported by NIH (NHGRI) grants U54-HG003273 and U54-HG006484 to R.A.G. and GAC grant 1 S10 RR026605 to J. G. Reid. This research was also supported by NIH grant R01-GM59290 to M.A.B.; grants from the Austrian Science Fund (FWF-P24551 and FWF-W1225) and Vienna Science and Technology Fund (WWTF-MA16-061) to C.K.; grants from the Wellcome Trust (WT108749/Z/15/Z) and EMBL to B.A., F.J.M., and M.M.; grants VEGA 1/0719/14 and APVV-14-0253 to T. Vinar (Consortium Member); MINECO/FEDER grant, NIH U01-MH106874 grant, Howard Hughes International Early Career award, and Obra Social “La Caixa” award to T.M.-B.; NSF grants BNS83-03506 to J.P.-C.; NSF1029302 to J.P.-C., J.R., and C.J.J.; BNS96-15150 to J.P.-C., C.J.J., and T.D.; and National Geographic Society and Leakey Foundation grants to J.P.-C. and C.J.J. E.E.E. is an investigator of the Howard Hughes Medical Institute. This work was supported, in part, by U.S. NIH grant HG002385 to E.E.E.

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.

U2 - 10.1126/sciadv.aau6947

DO - 10.1126/sciadv.aau6947

M3 - Article

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

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