Fine-scale genetic analysis of the exploited Nile monitor (Varanus niloticus) in Sahelian Africa

BACKGROUND: Overexploitation of wildlife populations results in direct consequences, such as extinction and local extirpation, as well as indirect effects including genetic diversity loss and changes in genetic structure. A clear understanding of the underlying genetic patterns of harvested species is necessary for sustainable management. The Nile monitor (Varanus niloticus) is a commercially valuable species in the international leather industry, with the highest levels of exploitation concentrated throughout Sahelian Africa. In this study, we examined the fine-scale genetic patterns of V. niloticus populations in the Sahel, with the expectation that the genetic structure would correspond to riverine drainage basins. The analyses were based on genotypes at 11 microsatellite loci for 318 individuals, spanning three separate watersheds throughout the Sahel. RESULTS: Our analyses identified four genetic clusters throughout the region, one of which (the westernmost population) exhibited very high levels of genetic differentiation (F(ST) = 0.47). Contrary to our expectation, the largest genetic break occurred within a single watershed, the Niger basin, rather than between watersheds. However, other localities displayed evidence of reduced gene flow between watershed boundaries. Across methods, the westernmost population exhibited lower estimates of N(e) as well as lower levels of genetic diversity compared to the other inferred populations. While we did not detect evidence for recent population bottlenecks, our analyses indicated historic population declines around 1,000–1,800 years ago. CONCLUSION: We found that the underlying genetic structure of Varanus niloticus across Sahelian Africa reflects historic as well as present-day patterns of riverine drainages. The high degree of differentiation found for the westernmost population indicates the presence of a separate lineage, and should be taken into consideration when setting harvest limits. The historic population decline for two of the populations corresponds to a drastic expansion of an ancient human civilization in the region, suggesting that human exploitation of V. niloticus has a longer history than previously thought. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0188-x) contains supplementary material, which is available to authorized users.