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.
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.
Cryptic species present a challenge for conservation, as undetected diversity may be lost. DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) has become a useful heuristic tool for delimiting species boundaries and detecting cryptic speciation across different animal taxa. Despite concerted efforts to genetically barcode bats and birds, comprehensive assessments have yet to be undertaken across the Afrotropics. We retrieved available DNA barcodes of bat and bird species naturally breeding within the Afrotropics. Using Bayesian phylogenetic modelling, we assessed DNA barcode performance at species identification, and to detect instances of non-monophyly (indicating potential cryptic speciation). Available DNA barcodes represent only 42.3 % and 23.6 % of the relevant bat and bird species diversity, respectively, with only 18.7 % of bat species and 7.2 % of bird species having geographic coverage. DNA barcodes afforded greater taxonomic resolution of Afrotropical bird species than of bats (96.8 % vs 84.0 %), with the bats reporting a higher species non-monophyly (25.5 % vs 4.8 %). Twenty-one bat species and fifteen bird species exhibited well-supported phylogenetic complexity. Additionally, deep intraspecific divergences (>2.0 %) were observed in one bat species and fifteen bird species. These instances of non-monophyly and deep intraspecific divergences may represent cryptic speciation within these volant taxa, suggesting greater hidden diversity of more sedentary African fauna. They also highlight the importance of areas such as the Congo-Guinean lowland forests to endemic vertebrate diversity. The current taxonomic status of birds is better supported by this molecular evidence than that of bats.
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