Niche dynamics modulate population connectivity between disjunct ranges of the Cape Robin-chat (Cossypha caffra) supporting an aridlands species pump

Southern Africa boasts an extraordinary diversity of birds, posited to have at least in part been driven by a “species pump” model, facilitated by an intermittent arid corridor connecting it with northeast Africa. This arid corridor arose and disappeared in concert with Plio-Pleistocene climate fluctuations, providing a means for northern, primarily arid-adapted lineages, to disperse to and subsequently colonize Southern Africa. Here, we test this “species pump” at the intra-specific level. We focus on Cape Robin-chats (Cossypha caffra) which have disjunct resident populations in the forested mountains of East Africa and in the aridlands of Southern Africa. We use multi-locus data to estimate gene flow between these populations, model spatial connectivity across this region contemporaneously and over the past 120 thousand years, and test niche differentiation. We found evidence for highly asymmetric gene flow (north to south) among Cape Robin-chat populations, and niche differentiation coupled with an inferred niche-based environmental filter limiting gene flow from southern to northern populations. Habitat suitability supports the presence of an intermittent corridor stretching from the Horn of Africa to Southern Africa. We propose that a modified species pump incorporating niche divergence and subsequent dispersal limitation driven by environmental filters has contributed to population differentiation among northern and southern populations of Cape Robin-chats, and that this same mechanism over time may have contributed to the rich avifaunal diversity of Southern Africa. Southern Africa has rich avifauna with high endemicity driven in part by in situ speciation. Using a combination of genetic analyses, niche models, and dispersal models, we find support for an intermittent aridlands corridor between disjunct populations of Cape Robin-chats modulated by Plio-Pleistocene climatic oscillations. This study shows niche divergence and asymmetric gene flow between southern and northern populations, providing a mechanism for population divergence. This supports the existence of an aridlands species pump that drives population divergence and may have contributed to species diversification in the Southern Africa avifauna.