Phylogenetic analysis and modeling demographic history
We performed phylogenetic analyses to place the mitochondrial lineages detected in our mountain treeshrew samples within an evolutionary framework with respect to other Bornean treeshrew species (i.e. the large treeshrew, pygmy treeshrew, and ruddy treeshrew). We used PartitionFinder v2.0 (Lanfear et al. 2012) to select partitions and substitution models (Table S2) and estimated a phylogeny using MrBayes v3.2.6 (Ronquist & Huelsenbeck 2003). We then used BEAST v.1.8.4 (Drummond & Rambaut 2007) to estimate the timing of divergence between the mountain treeshrew mitochondrial lineages we identified.
To infer demographic history, we performed a Bayesian coalescent skyline plot analysis using BEAST v2.0 (Bouckaert et al. 2014). We used a time to most recent common ancestor (TMRCA) prior of 450,000 years before present (lognormal distribution, µ = 0.45, σ = 0.2), the estimated date of divergence between the two mitochondrial lineages as determined by the dating analysis performed in BEAST. Analytical details are provided in Supplemental Information.