Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Background and aim: African Greater Cane (ACG) rat populations are widely distributed across Africa but the ancestral origin of populations inhabiting different geographical regions is unknown. There is currently no information available on the genetic differentiation of these populations resulting from long-time geographical isolation, environmental and anthropogenic pressures they face in each region. This limits our ability to understand potential speciation processes in AGC and their implications for their conservation and of other small wild mammals exposed to similar ecological conditions in the savannah biomes in Africa. Methods: We analyzed mitochondrial genes targeting the D-loop region of AGC samples from two blocks of the Eastern Arc Mountains in Tanzania (eastern), three agro-ecological zones in Ghana (western) and four sites in South Africa (southern) to characterize the phylogeographical patterns of the species. Results: AGC populations from Tanzania revealed higher haplotype diversity than those from the two other régions. Analysis of variance (AMOVA) revealed higher genetic variations within than between populations in all geographic regions. Demographic history analysis revealed a negative and significant Tajima’s D for a single southern African population as well as close relatedness with the Eastern Africa populations, suggesting a common ancestral origin. Conclusion: This is the first study to compare maternal lineages of AGC populations from eastern, western and southern Africa and provides a basis for future genetic studies of the species, its evolutionary ecology and the conservation of these populations across their range. Conservation implications: Evidence of recent population size expansion underpinned by high genetic diversity observed in the Uluguru urban (Tanzania) Guinea savannah (Ghana) and Kwazulu Natal (South Africa) populations suggest that the AGC populations are not currently threatened, consistent with the current IUCN status. Also, the distinct haplotypes observed in each region suggest that the populations can be managed as meta-populations, thus providing opportunities for potential local game-farming programs.