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.

The time to the most recent common ancestor (TMRCA) for the ADA and TF haplotypes was estimated following Takahata et al. [80] , where we calculate the ratio of the average nucleotide differences within the lion sample to one-half the average nucleotide difference between leopards (P. pardus) and lions and multiplying the ratio by an estimate of the divergence time between lions and leopards (2 million years based on undisputed lion fossils in Africa) [81, 82] . The mtDNA TMRCA was estimated with a linearized tree method in LINTREE [83] and using the equation H = 2mT, where H was the branch height (correlated to the average pairwise distance among haplotypes), m the substitution rate, and T the divergence time. Leopard and snow leopard (P. uncia) sequences were used as outgroups. Inference of the TMRCA for microsatellite loci followed Driscoll et al. [6] where the estimate of microsatellite variance in average allele repeat-size was used as a surrogate for evolutionary time based on the rate of allele range reconstitution subsequent to a severe founder effect. Microsatellite allele variance has been shown to be a reliable estimator for microsatellite evolution and demographic inference in felid species [6] . [24] for lion (nDNA and mtDNA) and FIV Ple (pol-RT) genetic data plotted both against the geographic distance (model assuming habitat to be arrayed in an infinite one-dimensional lattice; one-dimension isolation-by-distance [IBD]) and the log geographic distance (model assuming an infinite two-dimensional lattice; twodimension isolation-by-distance) on geographic distance. Found at: doi:10.1371/journal.pgen.1000251.s002 (0.13 MB PDF) Figure S3 Phylogenetic relationships of the 12S-16S mtDNA lion haplotypes. Neighbour-joining tree of the 1,882 bp 12S-16S mtDNA sequences. Bootstrap values are placed at each branchpoint for the minimum evolution/maximum parsimony/maximum likelihood analyses, respectively (ME/MP/ML). Outgroups: Ppaleopard, Panthera pardus; Pun -snow-leopard, Panthera uncia. The symbol (N) represents nodes with bootstrap support ,50 or an inferred polytomy in the bootstrap 50% majority-rule consensus tree.