Search

Aim: Pleistocene climate shifts were influential in shaping biodiversity patterns for forest‐dependent species. Within southern Africa, palaeoclimatic shifts possibly homogenised subtropical Afromontane forest biodiversity, yet these forests continue to harbour unique diversity. For the three songbird species with different natural histories, we investigated the refugial role of subtropical Afromontane and scarp forests and explored specifically how palaeoclimatic events impacted genetic connectivity among forest patches. Location: Maputaland‐Pondoland‐Albany Biodiversity Hotspot, south‐eastern South Africa. Taxon: Batis capensis, Phylloscopus ruficapilla and Pogonocichla stellata. Methods: Mitochondrial control region sequences and microsatellite data were used to assess genetic diversity and population structure among 406 birds. Demographic change was inferred using Bayesian skyline plots (BSPs), and approximate Bayesian computations (ABCs) were used to identify gene flow trends among putative refugia. Environmental niche models (ENMs) were used to infer past occurrence probabilities. Results: Species BSPs supported regional presence predating the Last Glacial Maximum (21 kya) and indicated post‐glacial population expansions. ABC modelling revealed that present‐day gene flow trends emerged largely during the current interglacial (<12 kya), suggesting that thermal maxima promote regional forest expansion. The north‐eastern source of gene flow in all the three species suggested a post‐glacial influx from refugia further north, while southern scarp forests sustained secondary source populations for B. capensis and P. ruficapilla. High gene flow signatures from south‐western forests in B. capensis and especially P. stellata alluded to hidden source populations in the under‐surveyed southern Afrotemperate forests—the southernmost Afromontane forest bloc. ENMs corroborated both scarp and southern Afrotemperate forests as glacial refugia and demonstrated persistent regional population presence over the past 120 kya. Main Conclusions: The population genetics and palaeodistribution of the three bird species indicate their regional persistence throughout the late Pleistocene, suggesting that Afromontane and scarp forests of south‐eastern South Africa served as refugia for subtropical African avian forest biota. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization. [ABSTRACT FROM AUTHOR]

In this study, we examined the phylogeographical structure of three frog species (Anhydrophryne rattrayi , Arthroleptis wageri and Cacosternum nanum) in the Eastern and Western Cape provinces of South Africa. The first two species are forest dwelling and exhibit direct development, whereas the last species is a habitat generalist, breeding in open freshwater bodies and exhibiting rapid metamorphosis. Evolutionary relationships were inferred using combined mitochondrial DNA (mtDNA) sequence data [16S rRNA and cytochrome b (Cytb)]. Divergence times were estimated for each species using the combined mtDNA dataset, and population genetic structuring was inferred using haplotype networks and analysis of molecular variance using the rapidly evolving Cytb locus. The two forest-dwelling species (Anhydrophryne rattrayi and Arthroleptis wageri) each revealed two statistically well-supported clades and were characterized by marked genetic differentiation and the general absence of shared maternal haplotypes, indicating no maternal gene flow between conspecific populations; a result corroborated by moderate values of pairwise genetic distance. In contrast, for the generalist species C. nanum , two shallow clades were observed and several haplotypes were shared between localities, indicating moderate maternal gene flow. Diversification in the two forest-dwelling species occurred during the Plio-Pleistocene climatic oscillations and was associated with increased xeric conditions, whereas in C. nanum a recent, Holocene divergence was inferred. Ancient climatic factors thought to be causal in the divergences within each of the three species are discussed. The marked mtDNA differentiation in the two forest specialist species suggests the presence of distinct management units that should be considered in future conservation management decisions. [ABSTRACT FROM AUTHOR]