In order to support effective conservation and sustainable land management, it is important to understand the population structure and rates of population differentiation in lesser-known species. Biogeographers, evolutionary biologists and ecologist share an interest in learning about patterns of species diversity, and the identification of such a pattern (e.g. the effects of Pleistocene glacial cycles) can help predict levels of diversity according to the most likely evolutionary history of a species. A phylogenetic study focusing on the population genetics and phylogeography of two sympatric Indonesian murids (Maxomys hellwaldi & Bunomys andrewsi) was performed on different populations on the islands of Sulawesi and Buton. Indicators for population differentiation due to genetic structure were calculated using RAD-tagged Illumina sequencing data. Phylogenetic consensus trees were created using BEAST and MrBayes and dated on the basis of published references. Two hypotheses were tested, firstly that the putative populations are cryptic species, secondly that a defined geological event equally affected the evolutionary biology of both species of interest. A significant amount of differentiation was found between populations of each species on the different islands over a small geographic range. It was concluded that island colonisations during the early Pleistocene associated with the Pliocene to Pleistocene transition and its impact on sea level had resulted in incipient speciation in each genus in parallel
