The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics

Antunes, Agostinho; Troyer, Jennifer L.; Roelke, Melody E.; Pecon-Slattery, Jill; Packer, Craig; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Frank, Laurence; Stander, Philip; Siefert, Ludwig; Driciru, Margaret; Funston, Paul J.; Alexander, Kathy A.; Prager, Katherine C.; Mills, Gus; Wildt, David; Bush, Mitch; O'Brien, Stephen J.; Johnson, Warren E.

Accurate interpretation of past and contemporary population demographic scenarios is a primary goal for the effective conservation of endangered species. In this study, we found substantial population subdivision, reduced gene flow, and large differences in FIV Ple sequence and sero-prevalence among lion populations, as well as evidence of historic secondary contact between populations ( Figure 3C ; Table S4 to S9). The very low population level of mtDNA nucleotide diversity, the number of haplotypes private to a single population (Figure 1) , and probably also the lack of SRY genetic variation across all male lions (haplotype S1, n = 183) suggests that lion numbers diminished considerably following the Late Pleistocene. The last century reduction in lion distribution further eroded its genomic diversity, and microsatellite variation suggested recent population bottlenecks in seven out of the 11 populations (standardized differences test, P,0.05; Table S5 ) [37] .