Mito-nuclear discordance
The population genetic pattern inferred from our mitogenome data is discordant with the nuclear SNP dataset, although it is not inconsistent with a scenario of two colonization events to KNP. Phylogenetic analyses revealed two divergent mitochondrial lineages within mountain treeshrews; both lineages are found on both mountains, but haplogroups 1 and 2 are equally represented on MK while haplogroup 1 is more frequent on MT (Figures 3 & 4). As mentioned above, MT provided montane habitat earlier than MK. If KNP were colonized a second time by mountain treeshrews from another part of their range, such as the southern portion of the Crocker Range, this would explain the presence of two sympatric divergent lineages within Kinabalu Park. The greater frequency of haplogroup 2 on MK could be explained by the closer geographic proximity of MK to the Crocker Range (Figure 7) combined with male-biased dispersal limiting the movement of haplogroup 2 from MK to MT. Lack of recombination in the mitochondrial genome would have retained the divergence between these the two lineages whereas recombination in nuclear SNPs would result in genetic admixture between the two groups. However, as noted above, the cluster on high elevation MT has maintained a moderate level of differentiation.
As an alternative explanation, this pattern could have been caused by a single colonization event of two sympatric lineages that diverged elsewhere in Borneo, for example, due to isolation in interglacial refugia and mixing during glacial maxima when montane forest was at its maximum extent (Cannon, Morley, & Bush, 2009; den Tex et al, 2010). However, this scenario implies that the colonization of KNP by mountain treeshrews would have occurred after the divergence between the two lineages ca. 450,000 ybp, which is relatively recent compared to the age of MT (at least 7 million years) and the age of the species (ca. 4 million years). Multiple colonization events to MK have been inferred in other taxa, including plants in the genus Rhododendron (Merckx et al., 2015).
Gawin et al. (2014) documented a similar pattern in mountain blackeyes (Chlorocharis emiliae ) in Borneo; they found two divergent mitochondrial haplogroups on MK, with one lineage sister to a lineage found on Mt. Trus Madi, a mountain south of MK within the Crocker Range (Figure 7). The pattern inferred from SNP data in a subsequent study was not concordant, with a single lineage found on MK (Manthey et al., 2017). This similar pattern may indicate a common colonization history between mountain blackeyes and mountain treeeshrews. Future studies should include broader geographic sampling of mountain treeshrews, including individuals from across the Crocker Range, to test the hypothesis of multiple colonization events and to determine the phylogeographic history of this species in Borneo.