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Aim: To investigate models assessing the influence of geomorphology and climatic shifts on species diversification in sub-Saharan Africa by reconstructing the pattern and timing of phylogenetic relationships of rain frogs (Brevicipitidae: Breviceps).

Location: Sub-Saharan Africa, south of the Congo Basin.

Methods: Multilocus sequence data were generated for near complete species-level sampling of the genus Breviceps. Phylogenetic relationships were inferred via Bayesian inference and maximum likelihood analyses on both concatenated and single-gene datasets. Network analyses identified locus-specific reticulate relationships among taxa. Bayesian methods were used to infer dates of divergence among Breviceps lineages, and niche modelling was used to identify possible adaptive divergence.

Results: Breviceps is monophyletic and comprised of two major, largely allopatric subclades. Diversity within each subclade is concentrated in two areas with contrasting geologic and climatic histories: the arid/semiarid winter rainfall zone in the south-western (SW) Cape, and the semitropical East Coast that receives predominantly summer rainfall. Recognized species diversity in the SW Cape based on phenotypic variation is consistent with observed genetic patterns whereas the East Coast is shown to harbour unexpectedly high genetic diversity and up to seven putative, cryptic species. Niche models show significant overlap between closely related species.

Main conclusions: Dating analyses indicate that diversification of Breviceps occurred rapidly within the Miocene, with only a moderate decline over the Plio-Pleistocene, suggesting that this process might be slowed but ongoing. Our findings suggest that a combination of two models, a landscape barrier model and climate fluctuation model, can explain patterns of diversification in Breviceps. This demonstrates that Miocene epeirogenic events and climatic shifts may have had a considerable influence on contemporary patterns of biodiversity. Topographic complexity and relative geoclimatic stability in the East have promoted cryptic diversification in allopatry, and this area clearly harbours numerous undescribed taxa and is in need of detailed biotic investigation.