Analysis of genome-wide data from 2 Cape lions and 53 other lions. These lions were from 14 countries (panel A) from across Africa (panel B) and from India (panel B—insert). In panel B, the numbers indicate the sample sizes for each country. In a principal component analysis (PCA) of genome-wide genetic variation (panel C), PC1 separated Asiatic lions from all other lions and positioned individuals from DRC and CAR as intermediate to Asiatic and other African lions, while PC2 separated two of four individuals from DRC from all other lions. Panel D shows an enlargement of the African lion cluster. Cape lion 1 and Cape lion 2 (panel D filled black squares) have distinct genomic profiles that were also evident in the admixture analysis (panel E). The two Cape lions did not have depleted genome-wide heterozygosity or higher inbreeding coefficients compared with other historical populations (panel F). Colors in panels A–D consistently correspond to geographic location, while colors in panel E correspond to the probability of belonging to an admixture cluster (K).