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.

Species-landscape interactions drive divergent population trajectories in four forest-dependent Afromontane forest songbird species within a biodiversity hotspot in South Africa

Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest-dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest-dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost-distances along least-cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest-thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors- where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land-cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest-dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.