Phylogeography of the mesic-adapted striped mouse, Rhabdomys dilectus chakae (Rodentia: Muridae) in forest margins of the Eastern Cape and southern KwaZulu-Natal provinces of South Africa

Rhabdomys is a genus that occupies a variety of habitats, including forest margins. Among the Rhabdomys taxa, Rhabdomys dilectus chakae has a distribution that covers the eastern seaboard of South Africa, with a poorly defined divergence date from its sister taxon Rhabdomys dilectus dilectus. Here, we study three mitochondrial markers (cytochrome b, cytochrome c oxidase I and partial control region) of R. d. chakae across the Eastern Cape and KwaZulu-Natal forests of South Africa, aiming to determine the cladogenesis (molecular dating) and effective population size of this subspecies through time, in addition to its cladogenesis in relationship to other species within the genus. A phylogenetic analysis revealed six clades within Rhabdomys, confirming that our study area is occupied solely by R. d. chakae, to the exclusion of other recognized sibling species. A fossil-calibrated Bayesian relaxed molecular clock estimated a recent split between R. d. chakae and R. d. dilectus ~1.4 ± 0.35 Mya and between two Rhabdomys pumilio groups, coastal A and B, at 1.16 ± 0.44 Mya. Coalescent Bayesian skyline plots revealed a stable population of R. d. chakae in the study area that was in slow decline until 2500 years ago, when there was an expansion in the late Holocene. Radiation within Rhabdomys dates as far back as 4.27 Mya, and subsequent demographic fluctuations primarily reflect palaeoclimatic changes.