Analysis of genetic diversity
Statistical parameters including sequence diversity, nucleotide diversity (Nei & Tajima, 1983; Nei, 1987), A+T content, and substitution, inversion, and transversion rates (Rozas & Rozas, 1997; Librado & Rozas, 2009; Baier, 2011; Chiu et al., 2013) were computed using DnaSP software version 5.10.01 (Librado & Rozas, 2009; Chiu et al., 2013). Pairwise intra- and inter-specific sequence divergences for each chloroplast region were computed as the mean number of nucleotide differences per site, following the formula:
100 x (Tv + Ts + ID)/L
where Tv is the number of transversions, Ts is the number of transitions, ID is the number of insertions/deletions, and L is the total length of the sequence (O’donnell, 1992; Dane et al., 2007). We used the PERMUT software package (Pons & Petit, 1996) to calculate the mean within-population gene diversity (Ching-Yi et al.) and the total gene diversity (hT) (Martin et al., 2003; Guicking et al., 2011; Chiu et al., 2013; Sun et al., 2019; Zhao et al., 2019). Other intra-population metrics such as the number of haplotypes per population, the number of singleton haplotypes (haplotype that occurs only once in the study), the number of effective haplotypes, and the overall haplotype diversity were also estimated (Baier, 2011).