SNPs: Genetic diversity
The nucleotide diversity of phased UCE pseudo-haplotypes (1,664 alignments concatenated end-to-end) for all 58 unrelated mountain treeshrews was 0.001732 (SE 0.000022). Using the SNP dataset with no missing data, average individual heterozygosity for all 80 individuals was 0.2297 (SD 0.027), and the average inbreeding coefficient (F IS) was 0.0121 (SD 0.12). For the 58 unrelated individuals, average heterozygosity was 0.2260 (SD 0.027), andF IS was 0.0187 (SD 0.12). Bartlett’s test revealed that the variances in observed and expected heterozygosity were not significantly different (K2 = 1.676,p = 0.195). Average F IS was higher on MK than MT, but the difference was not significant (0.04 and 0.01 respectively, Welch two-sample t-test p = 0.2). Using the dataset with 10% missing data, the probability of two individuals having identical genotypes assuming siblings are present (PIDsib ) was 1.54 × 10-199 .