Genetic analysis of African lions (Panthera leo) in Zambia support movement across anthropogenic and geographical barriers

The Luangwa Valley in eastern Zambia is a transverse offshoot of the Great Rift Valley system. This region appears to have an isolating effect as evidenced by suspected endemic subspecies, such as the Cookson’s wildebeest and Thornicroft’s giraffe. Recent mitochondrial DNA studies demonstrated that African lions in Zambia consist of two highly diverse eastern and western sub-populations. Herein, we report nuclear and mitochondrial DNA results from 409 lions that support this population substructure across Zambia but proposes only partial isolation of the Luangwa Valley with more movement between the populations than previously thought. Population assignment analysis identifies two populations with little evidence of admixture assigning lions to either the eastern or western sub-populations. A high occurrence of private alleles and clear evidence for a Wahlund effect further justify the presence of a highly structured population. But, while mitochondrial DNA analysis still shows little to no matrilineal gene flow (F(ST) = 0.53) between sub-populations, microsatellite analysis suggests there is gene flow (F(ST) = 0.04) with low but significant isolation-by-distance and an average of 6 migrants per generation. Evidence of isolation-by-distance is also found in factorial correspondence analysis with the Lower Zambezi National Park and eastern corridor clusters overlapping isolated clusters of the Luangwa Valley and western sub-population. From this evidence, the Luangwa Valley appears separated from the western sub-population with some dispersal through the southern regions of the eastern sub-population. Both the eastern and western sub-populations have high heterozygosity (0.68 and 0.69, respectively) and genetic diversity (0.47 and 0.50, respectively) values, indicative of genetically healthy populations.