Fig. 2

GNP baboon genomic variation and Papio diversity. A Phylogeny of Papio mitogenomes using Theropithecus gelada as an outgroup; codes refer to the specimen identifiers used in Zinner et al. [10]. GNP: baboon sample collected in Gorongosa National Park (code: bf146); colors indicate the different species listed in the legend. All nodes have a posterior probability of 1. Divergence times are reported (confidence intervals shown as gray boxes; values in Tables S2). B Y chromosome Papio phylogeny based on six concatenated genes (see main text); codes as in Additional file 2: Table S1; Hap refers to a P. cynocephalus male sample from Wall et al. [15]; colors refer to legend in panel A. All nodes have a posterior probability of 1. Divergence times are reported (confidence intervals shown as gray boxes; values in Tables S3). Macaca mulatta was used as an outgroup. C Heterozygosity estimates across Papio; colors as legend in panel A; sample codes as reported in Additional file 2: Table S1. D Principal component analysis (PCA) of Papio autosomal genomic data; codes and colors as in panel legend in panel A