Genetic diversity and population structure
Because the inclusion of close relatives can bias estimates of genetic
diversity and structure (Goldberg & Waits, 2010), we removed sequences
representing first-order relatives identified by our SNP dataset
(methods described below) and performed all subsequent mitogenome
analyses with the reduced data, which we refer to as the “unrelated
dataset”. We defined haplotypes and calculated haplotype diversity
(H d), nucleotide diversity \((\pi\)), and
Tajima’s D using DNAsp (Librado & Rozas 2009). We estimated the
differentiation between MK and MT and between high and low elevations
within each peak through analysis of molecular variance (AMOVA) in
Arlequin v3.5 (Excoffier & Lischer, 2010) with a permutation test of
10,000 replicates to assess statistical significance. We visualized
relationships among haplotypes by generating a median-joining network
with the PopART software (Leigh & Bryant, 2015).