Population genomics of the African rainforest skink Trachylepis affinis

Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity integrate species' ability to adapt to changing environments, but regions with high biodiversity generated by mechanisms that are poorly understood represent significant challenges. Over 50 percent of the planet's biodiversity is centered in the tropics, making tropical rainforests crucial areas for integrating information on evolutionary processes into conservation planning. African rainforests in particular are severly at risk due to climate change and other anthropogenic activities. However, decadal debates over the mechanisms generating African rainforest biodiversity continue, hinging on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. We use RAD-seq of 14 populations of the rainforest skink Trachylepis affinis from Cameroon and Gabon to test alternative diversification hypotheses and find evidence for ecological speciation across the rainforest-savanna gradient. Our results provide compelling evidence for the role of ecological gradients in rainforest speciation and their importance in preserving evolutionary process in landscapes under increasing anthropogenic threats.