Mitogenomes: genetic diversity, population structure, and
demographic inference
There were 36 unique mitochondrial haplotypes in the dataset that
included close relatives (n = 83), and 34 among the 58
“unrelated” individuals. All subsequent analyses were performed with
the unrelated dataset. H d was 0.977 (SD 0.008),
and π was 0.00583 (SD 0.0006). Phylogenetic analyses recovered mountain
treeshrews as a monophyletic group with two deeply divergent but
sympatric lineages. The average number of nucleotide substitutions per
site between the two lineages is 0.013 (Figure S2). Outgroup
relationships were consistent with the topology in Roberts et al.
(2011). The BEAST dating analysis suggests that the lineages diverged
ca. 450,000 ybp (95% Highest Posterior Density, HPD, 346,000–631,900
ybp) (Figure S3).
The median joining haplotype network (Figure 3) shows that the two
mountain treeshrew haplogroups are sympatric on both MT and MK. Three
haplotypes are found on both mountains (Table S3). Including related
individuals, haplogroups 1 and 2 are found in near equal proportion on
MK and MT (16 and 14 individuals, respectively), while haplogroup 1 is
more frequent on MT (46 out of 53 individuals) (Figure 4a). The AMOVA on
the unrelated dataset showed significant differentiation between the two
mountains (F ST = 0.133, p =.00812), with
13.3% of variance accounted for by differences between mountains and
86.7% within mountains. Dividing the population into high (≥ 2000 masl)
and low (< 2000 masl) elevation groups on each peak, 90.42%
of the total variance is accounted for by within-group variation, and
9.58% among (F ST = 0.096, p = 0.027).
Pairwise comparisons showed significant differences between high
elevation MK and low elevation MT (F ST = 0.15,p = 0.023) and high elevation MK and high elevation MT
(F ST = 0.18, p = 0.013).
Tajima’s D test was not significant, indicating a lack of
evidence for recent population contraction or expansion. In the Bayesian
skyline plot analysis, the 95% HPD of the population change parameter
included zero, meaning that we cannot reject the hypothesis of zero
demographic changes in the last 60,000 years.