Comparative phylogeography, phylogenetics, and population genomics of East African montane small mammals

The Eastern Afromontane region of Africa is characterized by striking levels of endemism and species richness which rank it as a global biodiversity hotspot for diverse plants and animals including mammals, but has been poorly sampled and little studied to date. Using mtDNA and multi-locus nDNA sequence data, genome-wide RAD-Seq SNP data, and morphological data, I identify major cryptic biogeographic patterns within and between 11 co-distributed small mammal species/species groups across the Eastern Afromontane region. I focus on two endemic montane small mammal species complexes, Hylomyscus mice and Sylvisorex shrews, co-distributed across the Albertine Rift (AR) and Kenya Highlands (KH) of the Eastern Afromontane Biodiversity Hotspot. I characterize patterns of phylogeographic structure, demographic history, phylogenetic relationships and undescribed biodiversity across these taxa. Putative independently evolving lineages are inferred using a combination of distribution data, coalescent species delimitation and historical demographic inference. Hypotheses put forward to account for the high diversity of the region include both retention of older palaeo-endemic lineages across major regions in climatically stable refugia, as well as the accumulation of lineages associated with more recent differentiation between allopatric populations separated by unsuitable habitat at the LGM. Populations have persisted since the Pliocene to mid-Pleistocene across a climatic gradient from the AR in the west to the KH in the east for both focal taxa. Deeply divergent and sympatric cryptic lineages, previously unidentified, are strongly supported in both mice and shrews, highlighting the broad temporal scale at which cyclical climatic changes over the last 5 Ma may have contributed to high species diversity and endemism in the Eastern Afromontane Hotspot. Complete genome-wide SNP matrices for Hylomyscus and Sylvisorex are used in population genetic analyses that support lineages not uncovered by the 3-6 locus dataset. Graphs of population splits and admixture support substantial gene flow from AR into KH shrew populations subsequent to isolation that occurred 2.5-3.5 million years earlier, possibly by intermittent colonization. A new species, Hylomyscus kerbispeterhansi, is described from Kenya using combined morphological and multi-locus data sets.