Climate refugia for three Afromontane forest-dependent bird species in south-eastern South Africa

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.