Genetic diversity and phylogeographic analysis
The sequences were checked visually and edited manually by BioEditor
ver. 7.09 (Hall, 1999), and then aligned by Clustal W in MEGA ver. 5.0
(Tamura et al., 2011). The three cpDNA sequences were concatenated for
subsequent analysis. Identification of cpDNA haplotypes (H) and ITS
ribotypes (R), and calculation of their diversities
(H d/R d) as well as
nucleotide diversity (P i) were performed by DnaSP
v. 5.0 (Librado & Rozas, 2009). Analysis of molecular variance (AMOVA)
was conducted to estimate the genetic variances within and between
populations and groups by Arlequin ver. 3.1 (Laurent et al. ,
2005). Network of cpDNA haplotypes and ITS ribotypes were drew by
TCS1.2.1 (Clement et al. , 2000). Phylogenetic analysis, takingPrunus salicina , Cerasus tomentosa and C. yedoensisas outgroups, was constructed based on maximum parsimony (MP), maximum
likelihood (ML) and Bayesian(BI) to make the best use of the CIPRES
Science Gateway V. 3.3. (Miller & Gross, 2011). The robustness of each
internal branch of the genealogical trees was evaluated with 1,000
bootstrap replicates. All the above analysis involved both cpDNA and ITS
sequences.
GST, representing haplotype frequency, and
NST, representing haplotype difference, were calculated
to examine the existence of population structure by PERMUT v. 2.0 with
10,000 permutations (Pons & Petit, 1996). N ST> G ST, P < 0.05
indicates the presence of a phylogeographic structure. Mismatch
distribution analyses and neutrality tests were conducted to test
population expansion using ARLEQUIN v. 3.5 with 10,000 permutations.
These analysis were only conducted with cpDNA sequences.