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:
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).