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.

Phylogenetic relationships among mtDNA and FIV Ple pol-RT sequences were assessed using Minimum evolution (ME), Maximum parsimony (MP), and Maximum likelihood (ML) approaches implemented in PAUP [78] . The ME analysis for mtDNA consisted of NJ trees constructed from Kimura two-parameter distances followed by a branch-swapping procedure and for FIV Ple data employed the same parameter estimates as were used in the ML analysis. The MP analysis was conducted using a heuristic search, with random additions of taxa and tree-bisection-reconnection branch swapping. The ML analysis was done after selecting the best evolutionary model fitting the data using MODELTEST 3.7 [79] . Tree topologies reliability was assessed by 100 bootstraps. For the FIV Ple data, the reliability of the tree topology was further assessed through additional analyses using 520 bp of FIV Ple pol-RT sequences in a representative subset of individuals.