Phylogeography of Gerp’s mouse lemur highlights the importance of rivers and altitude as dispersal barriers in Madagascar’s humid rainforests

adagascar is a biodiversity hotspot with exceptionally high levels of endemic diversity. Historical variability in climate conditions likely played a crucial role in shaping the diversification and distribution of species in Madagascar by changing water and habitat availability and thus creating geographic barriers. However, the relative importance of such processes for different forest-adapted taxa in Madagascar is relatively poorly understood because empirical studies are lacking. Here, we combine RADseq-based population genomic inference, coalescent models and ecological niche modelling to reconstruct the phylogeographic history of the lowland specialist Gerp’s mouse lemur (Microcebus gerpi; Cheirogaleidae). We identify relevant mechanisms and drivers of diversification in humid rainforests of Madagascar’s east coast and show that M. gerpi diversified during the late Pleistocene, likely through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations. The inferred ecological niche, patterns of gene flow and genetic differentiation in M. gerpi suggest that the potential for rivers to act as biogeographic barriers depended on both their size and the elevation of headwaters. For instance, populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation comparable to that between its two sister species, whereas rivers with lower elevation headwaters have weaker barrier functions as indicated by higher migration rates and admixture. We present a scenario for the diversification of M. gerpi and argue that it serves as a model of diversification for other humid rainforest taxa that are similarly limited by geographic factors.