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.

Both nDNA and mtDNA pairwise genetic distances among the 11 lion populations showed a significant relationship with geographic distance (R 2 = 0.75; Mantel's test, P = 0.0097; and R 2 = 0.15; Mantel's test, P = 0.0369; respectively) ( Figure 3 ). The significant positive and monotonic correlation across all the scatterplot pairwise comparisons for the nDNA markers (biparental) was consistent with isolation-by-distance across the sampled region. However, the correlation between nDNA F ST and geographic distance considerably decreased when the Asian GIR population was removed (R 2 = 0.19; Mantel's test, P = 0.0065) suggesting that caution should be taken in interpreting the pattern of isolation-by-distance in lions. We further compared linearized F ST estimates [24] plotted both against the geographic distance (model assuming habitat to be arrayed in an infinite onedimensional lattice) and the log geographic distance (model assuming an infinite two-dimensional lattice). The broad distribution of lions might suggest a priori that a two-dimensional isolationby-distance model would provide the best fit for the nDNA data (R 2 = 0.25; Mantel's test, P = 0.0022), but instead the onedimensional isolation-by-distance model performed better (R 2 = 0.71; Mantel's test, P = 0.0476) ( Figure S2 ). The pattern observed for the mtDNA (maternal) was more complex. While there was a significant relationship between mtDNA F ST and geographic distance, there was an inconsistent pattern across broader geographic distances ( Figure 3 ). This is partly due to the fixation or near fixation of haplotype H11 in six populations and the fixation of a very divergent haplotype H4 in KEN population ( Figure 1B and 1C). The removal of the KEN population considerably increased the correlation between mtDNA F ST and geographic distance (R 2 = 0.27; Mantel's test, P = 0.0035). Thus, the null hypothesis of regional equilibrium for mtDNA across the entire sampled region is rejected despite the possibility that isolation-by-distance may occur regionally.