Fig. 4. Evolutionary and demographic history for Papio baboons.

(A) Analyses using f-statistics indicate that P. kindae was formed via input from both a southern clade lineage and a northern clade lineage, with contributions estimated to be 52 and 48%. P. papio is inferred to have been produced through 10% introgression from an unidentified ancient northern lineage into a population related to P. anubis. Dates for divergence and admixture events were inferred through CoalHMM, and internal nodes representing those divergence or admixture events are labeled A through K. Our analyses of asymmetric haplotype sharing also inferred admixture from P. cynocephalus into P. anubis approximately 21 generations ago. (B) Reconstruction of baboon demographic history using PSMC methods. A prolonged bottleneck was observed in the lineage ancestral to P. papio beginning ~400 thousand years (ka) ago, while the populations ancestral to P. hamadryas and P. anubis increased between ~280 and ~160 ka ago. After diverging, P. anubis followed an upward trend whereas P. hamadryas declined. At ~400 ka ago, N_e for P. ursinus diverged from estimates for the populations ancestral to P. cynocephalus and P. kindae, and underwent a species-specific prolonged bottleneck. At ~300 ka ago, the N_e reconstructed for both P. cynocephalus and P. kindae increased, peaking ~150 ka ago before experiencing a subsequent decline. PSMC methods are not always reliable for the most recent time periods.