Diversification in a biodiversity hotspot: Genomic variation in the river frog Amietia nutti across the Ethiopian Highlands

Isolation is a major driver of population differentiation, due to long-term biogeographic barriers as well as habitat fragmentation across smaller geographic scales. East Africa is a highly heterogeneous and fragmented landscape and contains high numbers of endemic plants and animals, particularly in the Afromontane regions of the Eastern Arc Mountains, Albertine Rift Mountains and Ethiopian Highlands. Despite high levels of endemism, few studies have looked at intraspecific genetic variation in these regions, and fewer still within a genome-wide context. Here, we use two mitochondrial genes (ND2 and 16S) and large single nucleotide polymorphism panels to investigate patterns and processes of diversification in Ethiopian Highland populations of the river frog Amietia nutti. We identify a potential out-of-Ethiopia pattern of diversification, although further investigation is required to confirm this scenario. Within Ethiopia, regional populations diverged in isolation with little or no gene flow. Biogeographic barriers-including the Great Rift, Blue Nile and Omo River Valleys-and geographic distance, not environmental differences or watershed barriers, explain a large proportion of the genomic differentiation between populations. The timing of diversification in the group suggests genomic differentiation may have been facilitated by Pleistocene shifts of suitable habitat between glacial and interglacial periods. Strong regional genetic differences across A. nutti populations suggest that highland-adapted species harbour unique genetic variation across several regions of Ethiopia. This highlights the necessity for sampling many populations in phylogeographic analyses across this region to fully understand patterns of genetic variation and diversification across the complex topographical landscape of the Ethiopian Highlands.