Population genomic structure in Goodman’s mouse lemur reveals long-standing separation of Madagascar’s Central Highlands and eastern rainforests

The Central Highland Plateau of Madagascar is largely composed of grassland savanna, interspersed with patches of closed-canopy forest. Conventional wisdom has it that these grasslands are anthropogenic in nature, having been created very recently via human agricultural practices. Yet, the ancient origins of the endemic grasses suggest that the extensive savannas are natural biomes, similar to others found around the globe. We use a phylogeographic approach to compare these two competing scenarios. By sampling multiple populations of Goodman’s mouse lemur (Microcebus lehilahytsara), a small-bodied nocturnal primate, we reconstruct the phylogeographic and demographic history of these “environmental metronomes” to estimate the time at which their populations diverged, and thus proximally, when their habitats would have become fragmented. We applied coalescent methods to RADseq data to infer phylogenetic relationships, population structure, and migration corridors among sampling sites. These analyses indicate that forest fragmentation occurred rapidly during a period of decreased precipitation near the last glacial maximum and would have affected both the Central Highlands and eastern forests. Though there is clear genomic structure separating the populations of the Central Highland from those of the eastern rainforests, there is also evidence of historical migration between them. Findings support the hypothesis that the Central Highland savanna predates human arrival, indicating that it is a natural landscape that has long impacted the population dynamics of Goodman’s mouse lemur, and by extension, other forest-dwelling organisms in Madagascar.