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PMID: 30854422 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The comparative genomics and complex population history of Papio baboons.

Science advances ·Vol. 5 ·No. 1 ·2019-00-00 ·Pages eaau6947

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, Baboon Genome Analysis Consortium

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.

MeSH Terms
Animals Base Sequence Biological Evolution Female Gene Flow Genomics/methods Haplotypes/genetics Humans Hybridization, Genetic Male Papio/genetics Phylogeny Polymorphism, Genetic Whole Genome Sequencing
Authors & Affiliations
43 authors, click to expand affiliations / ORCID
Rogers Jeffrey ORCID
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. | Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Raveendran Muthuswamy ORCID
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Harris R Alan ORCID
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. | Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Mailund Thomas
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
Leppälä Kalle ORCID
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
Athanasiadis Georgios ORCID
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
Schierup Mikkel Heide ORCID
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
Cheng Jade
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
Munch Kasper ORCID
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
Walker Jerilyn A
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
Konkel Miriam K ORCID
Department of Genetics and Biochemistry, 105 Collings Street, Clemson University, Clemson, SC 29634, USA.
Jordan Vallmer ORCID
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
Steely Cody J
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
Beckstrom Thomas O ORCID
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
Bergey Christina ORCID
Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA. | Departments of Anthropology and Biology, Pennsylvania State University, 514 Carpenter Building, University Park, PA 16802, USA.
Burrell Andrew
Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
Schrempf Dominik
Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria.
Noll Angela ORCID
Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
Kothe Maximillian
Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
Kopp Gisela H ORCID
Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany. | Department of Biology, University of Konstanz, Universitätsstr. 10, 78467 Konstanz, Germany. | Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg 1, 78315 Radolfzell, Germany.
Liu Yue
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Murali Shwetha
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. | Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA. | Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA.
Billis Konstantinos ORCID
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Martin Fergal J ORCID
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Muffato Matthieu ORCID
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Cox Laura ORCID
Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military Drive, San Antonio, TX 78227, USA. | Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, 475 Vine Street, Winston-Salem, NC 27101, USA.
Else James
Department of Pathology and Laboratory Medicine and Yerkes Primate Research Center, 954 Gatewood Road, Emory University, Atlanta, GA 30322, USA.
Disotell Todd
Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
Muzny Donna M
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. | Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Phillips-Conroy Jane ORCID
Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA. | Department of Anthropology, Washington University, McMillan Hall, 1 Brookings Drive, St. Louis, MO 63130, USA.
Aken Bronwen ORCID
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Eichler Evan E ORCID
Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA. | Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA.
Marques-Bonet Tomas ORCID
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader, 88. 08003, Barcelona, Spain. | Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain. | CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri Reixac, 4, 08028, Barcelona, Spain. | Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, c/de les Columnes, s/n. Campus de la UAB. 08193-Cerdanyola del Vallès, Barcelona, Spain.
Kosiol Carolin ORCID
Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria. | Centre for Biological Diversity, School of Biology, University of St. Andrews, Dyers Brae House, Greenside Place, St Andrews, Fife, KY16 9TH, UK.
Batzer Mark A
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
Hahn Matthew W ORCID
Department of Biology and Department of Computer Science, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA.
Tung Jenny ORCID
Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA. | Duke Population Research Institute, Duke University, Box 90989, Durham, NC 27708, USA. | Institute of Primate Research, P.O. Box 24481, Nairobi, Kenya.
Zinner Dietmar ORCID
Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
Roos Christian ORCID
Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
Jolly Clifford J
Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
Gibbs Richard A ORCID
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. | Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Worley Kim C ORCID
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. | Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Baboon Genome Analysis Consortium
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Article Info
Journal
Science advances
Abbr.
Sci Adv
ISSN
2375-2548
DOI
10.1126/sciadv.aau6947
Published
2019-00-00
Epub
2019-00-30
Pages
eaau6947
Language
English
Region
United States
NLM ID
101653440
PMCID
PMC6401983
Subset
IM
Grants
NIH HHS · P51 OD011133 · United States
NIGMS NIH HHS · R01 GM059290 · United States
NIGMS NIH HHS · R35 GM118335 · United States
External Links
PubMed source DOI: 10.1126/sciadv.aau6947 PMC Full Text View journal details
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