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.