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Genome-wide ancestry and introgression in a Zambian baboon hybrid zone

View ORCID ProfileKenneth L. Chiou, View ORCID ProfileChristina M. Bergey, Andrew S. Burrell, Todd R. Disotell, View ORCID ProfileJeffrey Rogers, Clifford J. Jolly, Jane E. Phillips-Conroy
doi: https://doi.org/10.1101/578781
Kenneth L. Chiou
1Department of Anthropology, Washington University, St. Louis, MO 63130, USA
2Department of Psychology, University of Washington, Seattle, WA 98195, USA
3Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Washington, Seattle, WA 98195, USA
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Christina M. Bergey
4Department of Anthropology, New York University, New York, NY 10003, USA
5New York Consortium in Evolutionary Primatology, New York, NY, USA
6Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
7Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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Andrew S. Burrell
4Department of Anthropology, New York University, New York, NY 10003, USA
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Todd R. Disotell
4Department of Anthropology, New York University, New York, NY 10003, USA
5New York Consortium in Evolutionary Primatology, New York, NY, USA
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Jeffrey Rogers
8Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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Clifford J. Jolly
4Department of Anthropology, New York University, New York, NY 10003, USA
5New York Consortium in Evolutionary Primatology, New York, NY, USA
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Jane E. Phillips-Conroy
1Department of Anthropology, Washington University, St. Louis, MO 63130, USA
9Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
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Abstract

Hybridization in nature offers unique insights into the process of natural selection in incipient species and their hybrids. In order to evaluate the patterns and targets of selection, we examine a recently discovered ba-boon hybrid zone in the Kafue River valley of Zambia, where Kinda baboons (Papio kindae) and gray-footed chacma baboons (P. ursinus griseipes) coexist with hybridization. We genotyped baboons at 14,962 variable genome-wide autosomal markers using double-digest RADseq. We compare ancestry patterns from this genome-wide dataset to previously reported ancestry from mitochondrial-DNA and Y-chromosome sources. We also fit a Bayesian genomic cline model to scan for genes with extreme patterns of introgression. We show that the Kinda baboon Y chromosome has penetrated the species boundary to a greater extent than either mitochondrial DNA or the autosomal chromosomes. We also find evidence for overall restricted introgression in the JAK/STAT signaling pathway. Echoing results in other species including humans, we find evidence for enhanced and/or directional introgression of immune-related genes or pathways including the toll-like receptor pathway, the blood coagulation pathway, and the LY96 gene. Finally we show enhanced introgression and excess chacma baboon ancestry in the sperm tail gene ODF2. Together, our results eluci-date the dynamics of introgressive hybridization in a primate system while highlighting genes and pathways under selection.

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Posted March 16, 2019.
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Genome-wide ancestry and introgression in a Zambian baboon hybrid zone
Kenneth L. Chiou, Christina M. Bergey, Andrew S. Burrell, Todd R. Disotell, Jeffrey Rogers, Clifford J. Jolly, Jane E. Phillips-Conroy
bioRxiv 578781; doi: https://doi.org/10.1101/578781
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Genome-wide ancestry and introgression in a Zambian baboon hybrid zone
Kenneth L. Chiou, Christina M. Bergey, Andrew S. Burrell, Todd R. Disotell, Jeffrey Rogers, Clifford J. Jolly, Jane E. Phillips-Conroy
bioRxiv 578781; doi: https://doi.org/10.1101/578781

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