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 (genusPapio) 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 ofPapiobaboons, 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.

SummaryAdmixture graphs generalize phylogenetic trees by allowing genetic lineages to merge as well as split. In this paper we present the R package admixturegraph containing tools for building and visualizing admixture graphs, for fitting graph parameters to genetic data, for visualizing goodness of fit and for evaluating the relative goodness of fit between different graphs.Availability and ImplementationGitHub: https://github.com/mailund/admixture_graph and CRAN: https://cran.r-project.org/web/packages/admixturegraph.

are employees of deCODE genetics/ Amgen. Data availabilitySummary statistics with the results from the CUD GWAS is available on the iPSYCH website (https://ipsych.au.dk/downloads/). For access to genotypes from the the iPSYCH cohort, interested researchers should contact A.D. Børglum.

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