Phylogenetic analyses of lion sequence data. A) Median network of 1051 bp of cytb for all 88 lion individuals identified from GenBank plus those generated in this study. Panthera leo spelaea was used as an outgroup. Circles are proportional to haplotype frequencies and black circles represent hypothesized intermediate haplotypes. The number of links represent the number of mutations between haplotypes. Haplotypes are labelled from A to S and correspond to sequences labelled in Table 1 and Additional file 3: Table S1. B) Phylogenetic tree from a Bayesian analysis of combined cytb and control region data for all lion taxa where available (n = 54). Posterior probabilities of supported clades are shown at nodes. Estimates of divergence times: (a) 124,200 years (95% credibility: 81,800-183,500); (b) 61,500 years (32,700-97,300); (c) 51,000 years (26,600-83,100); (d) 81,900 years (45,700-122,200); (e) 57,800 years (26,800-96,600); (f) 21,100 years (8300–38,800). Branch colours correspond to reconstructed ancestral geographic states (Purple, South Africa; Yellow, East Africa; Orange, West Africa; Red, Central Africa; Teal, North Africa; Blue, South Asia; Green, Near-East). Tip colours correspond to origins of samples.