Molecular characterization of Acomys louisae from Somaliland: a deep divergence and contrasting genetic patterns in a rift zone

Phylogeographic patterns in the Horn of Africa have recently attracted researchers searching for hidden diversity and explaining the evolutionary history of this region. In this paper, we focus on spiny mouse Acomys louisae. We examined 88 samples from 13 localities across Somaliland and sequenced CYTB, control region and IRBP genes. Phylogenetic analysis confirmed clear distinctness of A. louisae from the other clades of Acomys, but it also revealed deep splits within A. louisae clade. Samples from Central and Eastern Somaliland, including those from the type locality, form a clearly distinct Somaliland clade while remaining ones from the very NW of Somaliland and 5 previously published sequences from Djibouti and E Ethiopia form a Djibouti group. At two localities in the contact zone, we detected sympatric occurrence of both. The clades exhibit sharply contrasting patterns of variability, the Somaliland clade is characterized by a sufficient mitochondrial haplotype diversity, but low sequence divergence. The population parameters and haplotype networks suggest that the populations belonging to the Somaliland clade probably underwent a recent expansion of its range and population size. It may be explained by a repopulation after the interglacial period providing poor environmental conditions for spiny mice in E and C Somaliland. In contrast, the Djibouti group shows extremely high nucleotide diversity besides that of haplotype one. This suggests a long-term persistence of large and/or structured populations. It may be attributed to a specific history of the Ethiopian Rift and Afar. The results emphasize the importance of the Horn of Africa as a region preserving high endemism.