title: Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons.
abstract: Naturally occurring admixture has now been documented in every major primate lineage, suggesting its key role in primate evolutionary history. Active primate hybrid zones can provide valuable insight into this process. Here, we investigate the history of admixture in one of the best-studied natural primate hybrid zones, between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in the Amboseli ecosystem of Kenya. We generated a new genome assembly for yellow baboon and low-coverage genomewide resequencing data from yellow baboons, anubis baboons and known hybrids (n = 44). Using a novel composite likelihood method for estimating local ancestry from low-coverage data, we found high levels of genetic diversity and genetic differentiation between the parent taxa, and excellent agreement between genome-scale ancestry estimates and a priori pedigree, life history and morphology-based estimates (r(2)  = 0.899). However, even putatively unadmixed Amboseli yellow individuals carried a substantial proportion of anubis ancestry, presumably due to historical admixture. Further, the distribution of shared vs. fixed differences between a putatively unadmixed Amboseli yellow baboon and an unadmixed anubis baboon, both sequenced at high coverage, is inconsistent with simple isolation-migration or equilibrium migration models. Our findings suggest a complex process of intermittent contact that has occurred multiple times in baboon evolutionary history, despite no obvious fitness costs to hybrids or major geographic or behavioural barriers. In combination with the extensive phenotypic data available for baboon hybrids, our results provide valuable context for understanding the history of admixture in primates, including in our own lineage.
authors.affiliation: Institute for Human Genetics, University of California-San Francisco, Box 0794, San Francisco, CA, 94143, USA.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Wall
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7701, South Africa.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Schlebusch
authors.affiliation: Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC, 27708, USA.|Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.|Institute of Primate Research, National Museums of Kenya, PO Box 24481, Nairobi, 00502, Kenya.
authors.forename: Susan C
authors.initials: SC
authors.lastname: Alberts
authors.affiliation: Department of Genetics and Southwest National Primate Research Center, Texas Biomedical Research Institute, Box 760549, San Antonio, TX, 78245, USA.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Cox
authors.affiliation: Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC, 27708, USA.
authors.forename: Noah
authors.initials: N
authors.lastname: Snyder-Mackler
authors.affiliation: Division of Neuroscience, Primate Genetics Section, Oregon National Primate Research Center, 505 NW 185th Ave, Beaverton, OR, 97006, USA.|Behavioral Neuroscience Department, Oregon Health Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Nevonen
authors.affiliation: Division of Neuroscience, Primate Genetics Section, Oregon National Primate Research Center, 505 NW 185th Ave, Beaverton, OR, 97006, USA.|Behavioral Neuroscience Department, Oregon Health Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
authors.forename: Lucia
authors.initials: L
authors.lastname: Carbone
authors.affiliation: Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC, 27708, USA.|Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.|Institute of Primate Research, National Museums of Kenya, PO Box 24481, Nairobi, 00502, Kenya.|Duke University Population Research Institute, Duke University, Box 90420, Durham, NC, 27708, USA.
authors.forename: Jenny
authors.initials: J
authors.lastname: Tung
mesh_terms: D000818:Animals; D005075:Biological Evolution; D051456:Gene Flow; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006824:Hybridization, Genetic; D007630:Kenya; D016013:Likelihood Functions; D008957:Models, Genetic; D048530:Papio anubis / Q000235:genetics*; D048548:Papio cynocephalus / Q000235:genetics*; D010375:Pedigree; D010641:Phenotype
keywords: Amboseli baboons; admixture; genome resequencing; hybridization; local ancestry