Mitochondrial DNA diversity and population structure of a forest-dependent rodent, Praomys taitae (Rodentia: Muridae) Heller 1911, in the fragmented forest patches of Taita Hills, Kenya

The population genetic structure of the forest-dependent rodent, Praomys taitae, sampled from nine indigenous forest fragments distributed over three ranges of the Taita Hills in Kenya, was determined using mitochondrial DNA (mtDNA) control region sequence variation. Thirty-three unique haplotypes were observed in a total sample of 132 individuals, whereas the number of different haplotypes per population ranged from two to 10. An overall low nucleotide diversity of 0.9% was observed in the total sample but varied widely between populations (0.2-1.3%). Significant genetic differentiation was observed in 30 of the 36 possible pair-wise comparisons between populations, while a hierarchical AMOVA revealed significant genetic subdivision between groups of populations on the three hill ranges of Dabida, Mbololo and Kyulu (F CT = 0.404, P < 0.01), among populations on each of the hill ranges (Fsc = 0.112, P < 0.01) and among populations in the total sample (FST = 0.471, P < 0.001). Demographic history analyses based on pair-wise nucleotide sequence mismatch distributions revealed that all the populations were in mutation-drift disequilibrium except the populations of the Kyulu and Ronge forest fragments.