Supplementary files from the study "Comparative phylogeography of two specialist rodents in forest fragments in Kenya."

The following supporting information is associated with the study: - Data Table 1: List of field samples - Data Table 2: List of GenBank samples - Supplementary File 1: Descriptions of extended study areas - Supplementary File 2: Data processing for species distribution modeling - Supplementary File 3: Morphological characterization of species - Supplementary File 4: Phylogenetic trees - Supplementary File 5: Genetic distances at the genus level between species units. Abstract: The fragmented forests of the Kenya highlands, known for their exceptional species richness and endemism, are among the world’s most important biodiversity hotspots. However, detailed studies on the fauna of these ecosystems—especially specialist species that depend on moist forests, which are particularly threatened by habitat fragmentation—are still limited. In this study, we used mitochondrial genes (cytochrome b and the displacement loop) and a nuclear marker (retinol-binding protein 3) to investigate genetic and morphological diversity, phylogenetic associations, historical divergence, population dynamics, and phylogeographic patterns in two rodent species—the soft-furred mouse (Praomys jacksoni) and the African wood mouse (Hylomyscus endorobae)—across Kenya’s forest landscapes. We found a complex genetic structure, with P. jacksoni exhibiting greater genetic diversity than H. endorobae. The Mt. Kenya P. jacksoni populations are significantly genetically different from those in southwestern forests (Mau Forest, Kakamega Forest, and Loita Hills). In contrast, H. endorobae presented no observable biogeographic structuring across its range. The genetic diversity and geographic structuring patterns highlighted selectively strong effects of forest fragmentation and differing species’ ecological and evolutionary responses to these landscape changes. Our findings further underscore the need for expanded sampling across Kenya’s highland forests to better understand species’ changing diversity and distribution patterns in response to the impacts of human-mediated habitat changes. These insights are critical for informing conservation strategies to preserve biodiversity better in this globally important region. Keywords: Praomys jacksoni, Hylomyscus endorobae, Phylogeography, Genetic diversity, Habitat fragmentation, Tropical forests