PT  - JOURNAL ARTICLE
AU  - Kenneth L. Chiou
AU  - Christina M. Bergey
AU  - Andrew S. Burrell
AU  - Todd R. Disotell
AU  - Jeffrey Rogers
AU  - Clifford J. Jolly
AU  - Jane E. Phillips-Conroy
TI  - Genome-wide ancestry and introgression in a Zambian baboon hybrid zone
AID  - 10.1101/578781
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 578781
4099  - http://biorxiv.org/content/early/2019/03/16/578781.short
4100  - http://biorxiv.org/content/early/2019/03/16/578781.full
AB  - 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.