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.

A Bayesian clustering method implemented in the program STRUCTURE [22] was used to infer number of populations and assign individual lions to populations based on multilocus genotype (microsatellites) and sequence data (ADA, TF, and mtDNA genes) and without incorporating sample origin. For haploid mtDNA data, each observed haplotype was coded with a unique integer (e.g. 100, 110) for the first allele and missing data for the second (STRUCTURE [22] analyses with or without the mtDNA data were essentially identical). For K population clusters, the program estimates the probability of the data, Pr(X|K), and the probability of individual membership in each cluster using a Markov chain Monte Carlo method under the assumption of Hardy-Weinberg equilibrium (HWE) within each cluster. Initial testing of the HWE in each of the populations defined by the geographic origin of sampling revealed no significant deviation from HW expectations with the exception of SER and BOT population (later subdivided by STRUCTURE [22] in 3 and 2 clusters, respectively; such deviations from HW expectations were interpreted as evidence of further population structuring). We conducted six independent runs with K = 1-20 to guide an empirical estimate of the number of identifiable populations, assuming an admixture model with correlated allele frequencies and with burn-in and replication values set at 30,000 and 10 6 , respectively. STRUCTURE also estimates allele frequencies of a hypothetical ancestral population and an alpha value that measures admixed individuals in the data set. The assignment of admixed individuals to populations using STRUCTURE [22] has been considered in subsequent population analyses. For each population cluster k, the program estimates F k , a quantity analogous to Wright's F ST , but describing the degree of genetic differentiation of population k from the ancestral population.