Phylogeographic patterns of Greater cane rat populations from East and West African regions inferred from maternal lineages

The African Greater Cane rat (AGC) populations in East and West Africa bear single ancestral origin. However, to date, information is lacking on their genetic differentiation due to long-time geographical isolation and the environmental and anthropogenic pressures the populations face in each region. This gap limits our ability to understanding potential speciation in these populations. We analysed the genetic sequences of cane rat samples from Tanzania and Ghana to characterize the phylogeographic patterns of the two populations based on the mt-DNA. The D-loop sequences used comprised samples collected from two Eastern Arc Mountains in Tanzania and three agro-ecological zones in Ghana. We found a high nucleotide diversity in AGC population from Tanzania (0.022±0.003) and low nucleotide diversity in Ghana (0.013±0.003). Analysis of Molecular variance (AMOVA) showed significant genetic differentiation between AGC population from Tanzania and Ghana (Fst=0.85938, p<0.00001). Further, analysing the genetic differentiation, we found high variation by 85.94% in AGC populations between Tanzania and Ghana and low variation (14.06%) within any AGC population at individual region. Reconstructing past history of the population in each region based on the neutrality test revealed a positive (0.006) Harpending’s raggedness index for Tanzania and negative (-0.009) for Ghana. Also, Tajima’s D was negative (-0.798) for Tanzania and positive (0.041) for Ghana, indicating that the population of Tanzania is increasing while the Ghanaian is decreasing. This is the first study to compare maternal lineages of the AGC population from two regions in Africa, and provides a basis for future studies.