Abstract Admixture has profoundly influenced evolution across the tree of life, including in humans and other primates 1,2 . However, we have limited insight into the genetic and phenotypic consequences of admixture in primates, especially during its key early stages. Here, we address this gap by combining 50 years of field observations with population and functional genomic data from yellow ( Papio cynocephalus ) and anubis ( P. anubis ) baboons in Kenya, in a longitudinally studied population that has experienced both historical and recent admixture 3 . We use whole-genome sequencing to characterize the extent of the hybrid zone, estimate local ancestry for 442 known individuals, and predict the landscape of introgression across the genome. Despite no major fitness costs to hybrids, we identify signatures of selection against introgression that are strikingly similar to those described for archaic hominins 4–6 . These signatures are strongest near loci with large ancestry effects on gene expression, supporting the importance of gene regulation in primate evolution and the idea that selection targeted large regulatory effects following archaic hominin admixture 7,8 . Our results show that genomic data and field observations of hybrids are important and mutually informative. They therefore demonstrate the value of other primates as living models for phenomena that we cannot observe in our own lineage.

Selection against admixture and gene regulatory divergence in a long-term primate field study