Phylogeography of the critically endangered Gerp‘s mouse lemur has been shaped by rivers, altitude and paleoclimate

Madagascar has great potential to study the diversification of species due to its numerous endemic radiations and steep environmental gradients. Here, we reconstruct the phylogeographic history and patterns of gene flow in the critically endangered mouse lemur Microcebus gerpi to understand the principles underlying the diversification of small mammals in Madagascar’s rainforests. Using genome‑wide RADseq data of 67 individuals across seven locations, we infer that M. gerpi diversified in the Late Quaternary, potentially through cycles of connectivity and isolation during paleoclimatic fluctuations. Populations in different inter-river systems are well differentiated and do not show signs of admixture. The deepest divergence (~ 270 kya) is found between M. gerpi populations north and south of two major rivers with headwaters at high altitudes and is comparable to that between its two sister species. These rivers have likely long been a major barrier to gene flow that cannot be crossed by the lowland specialist M. gerpi. Two other rivers coincide with more recent divergences (< 50 kya), potentially because their smaller size or lower headwaters permitted higher migration rates at mid elevations. Our findings provide empirical evidence for the interacting effects of rivers, altitude, and paleoclimate in shaping the evolution of biodiversity in Madagascar. We further highlight important conservation implications considering extreme habitat loss and fragmentation in the region.