Mitochondrial genetic diversity of the Greater Cane rat (Thryonomys swinderianus) populations from the Eastern Arc Mountains ecosystem, Tanzania.

Abstract

Management of most herbivorous small mammal species considered to be pests in Africa is still challenging partly because of the paucity of information on their biological traits that would help to manage their destructive impacts. This gap also precludes the potential for tapping species with potential food-value to improving the economy of rural communities through, for example, sustainable game farming programs in Africa. This study investigates the genetic diversity and population demography of the African Greater Cane rat (AGC), a rodent pest of crops and game species inhabiting two isolated blocks of the Eastern Arc Mountains (EAMs), Tanzania to contribute to the species management and conservation. We used non-invasive sampling techniques and DNA sequencing of the D-loop region of MtDNA (515bp) from 46 cane rats (Thryonomys swinderianus) samples to characterize the genetic diversity and structure of the species and potential population threats faced in natural habitats. We found 25 haplotypes:15 from Uluguru and 9 from Udzungwa mountains populations, containing 49 polymorphic regions (32 parsimoniously informative and 17 singleton sites). Haplotype diversity (range: 0.849-0.995) did not differ substantially across populations but the median haplotype diversity for Udzungwa South was overall lower than for other populations. Nucleotide diversity averaged 0.00641, 0.01528, 0.0111 and 0.01313, respectively for Udzungwa South, Udzungwa North, Uluguru Rural and Uluguru Urban, suggesting high genetic diversity within the four populations. Analysis of molecular variance (AMOVA) indicated significantly high genetic differences between the four populations (FST = 0.16, p = 0.00098) whereas neutrality test (FU's Fs) values were negative, indicating historical population expansion. Similarly, the Bayesian skyline analysis indicated a recent demographic expansion suggesting limited bottlenecks in the recent past in this population. Our results show the AGC population in EAMs consists of four distinct populations which have experienced a recent population expansion, especially among the urban population due perhaps to influence of urbanization process that may have favored assisted species movements across the rural-urban landscapes. Future research should focus on understanding impact of geographical isolation on the genetic structure and diversity of this species.