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Sci Adv. 2019 Jan 30;5(1):eaau6947. doi: 10.1126/sciadv.aau6947. eCollection 2019 Jan.

The comparative genomics and complex population history of Papio baboons.

Author information

1
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
2
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
3
Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark.
4
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
5
Department of Genetics and Biochemistry, 105 Collings Street, Clemson University, Clemson, SC 29634, USA.
6
Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
7
Departments of Anthropology and Biology, Pennsylvania State University, 514 Carpenter Building, University Park, PA 16802, USA.
8
Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria.
9
Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
10
Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
11
Department of Biology, University of Konstanz, Universitätsstr. 10, 78467 Konstanz, Germany.
12
Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg 1, 78315 Radolfzell, Germany.
13
Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA.
14
Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA.
15
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
16
Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military Drive, San Antonio, TX 78227, USA.
17
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.
18
Department of Pathology and Laboratory Medicine and Yerkes Primate Research Center, 954 Gatewood Road, Emory University, Atlanta, GA 30322, USA.
19
Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
20
Department of Anthropology, Washington University, McMillan Hall, 1 Brookings Drive, St. Louis, MO 63130, USA.
21
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader, 88. 08003, Barcelona, Spain.
22
Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.
23
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri Reixac, 4, 08028, Barcelona, Spain.
24
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.
25
Centre for Biological Diversity, School of Biology, University of St. Andrews, Dyers Brae House, Greenside Place, St Andrews, Fife, KY16 9TH, UK.
26
Department of Biology and Department of Computer Science, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA.
27
Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA.
28
Duke Population Research Institute, Duke University, Box 90989, Durham, NC 27708, USA.
29
Institute of Primate Research, P.O. Box 24481, Nairobi, Kenya.

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.

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