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

Abstract

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.

Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa

“…2014b ; VanHooft et al. 2018 ; Curry et al. 2019 ) levels of gene flow, but this was largely dependent on the amount of connectivity present between sampling locations, for example, isolated populations such as those in the Kainji Lake National Park and Yankari Game Reserve in Nigeria ( Tende et al.…”

“…2019 ) levels of gene flow, but this was largely dependent on the amount of connectivity present between sampling locations, for example, isolated populations such as those in the Kainji Lake National Park and Yankari Game Reserve in Nigeria ( Tende et al. 2014b ) and Kafue National Park and the Luangwa Valley Ecosystem in Zambia ( Curry et al. 2019 ).…”

A kingdom in decline: Holocene range contraction of the lion (Panthera leo) modelled with global environmental stratification

“…The position of major rivers through Africa, in addition to contractions of suitable habitat driven by climate change, are the likely causes of vicariance over 100ka. Suture zones and parapatric (sub)speciation are likely important in maintaining genetic variation ( Bertola et al, 2016 ; Curry et al, 2020 ; Curry, White & Derr, 2019 ; Dures et al, 2020 ). The persistence of major river barriers/corridors in the region, appears to have major biogeographical legacies in terms of defining boundaries between populations and linkage between areas.…”

Spatiotemporal Genetic Diversity of Lions

“…Although nuclear diversity has decreased significantly, mtDNA diversity has remained constant over time ( Table 1). Mitochondrial DNA is matrilineally inherited, and localized studies show there is little or no female-mediated gene flow between subpopulations across Africa (32,46,47). Female lions primarily remain with their natal pride while males disperse (48,49).…”

“…Previous studies that sampled nuclear genetic diversity reported both high (28)(29)(30) and low (31-33) levels of gene flow, but this was largely dependent on the amount of connectivity present between sampling locations. For example, isolated populations such as those in the Kainji Lake National Park from Yankari Game Reserve in Nigeria (31) and Kafue National Park from the Luangwa Valley Ecosystem in Zambia (32). Genetic differentiation can even be seen between populations within national parks (33).…”