Figure 1.
Analyses of 21 chloroplast (cp) DNA haplotypes of Scrophularia ningpoensis.
(A) The maximum likelihood tree of 21 chloroplast (cp) DNA haplotypes of S. ningpoensis, S. buergeriana, S. spicata and S. dentata were used as the outgroup. Statistical supports (Bayesian posterior probability ≥80/maximum likelihood bootstrap value ≥50/maximum parsimony bootstrap value ≥50) are indicated on the branches. (B) 95% plausible network of the 21 cpDNA haplotypes of S. ningpoensis (A–E11). The size of circles corresponds to the frequency of each haplotype. Each solid line represents one mutational step that interconnects two haplotypes for which parsimony is supported at the 95% level. The small open circles indicate inferred intermediate haplotypes not detected in this investigation. (C) A geographic distribution of 21 cpDNA haplotypes (A–E11) detected in Scrophularia ningpoensis. The populations correspond to those detailed in Table 1. Squares represent cultivated populations and circles represent wild populations.
Table 1.
Details of sample locations and sample sizes (N) of Scrophularia ningpoensis.
Table 2.
Chloroplast DNA sequence polymorphisms detected in two intergenic spacer (IGS) regions of Scrophularia ningpoensis identifying 21 haplotypes (A-E11).
Table 3.
Comparisons of genetic diversity and genetic structure between wild and cultivated Scrophularia ningpoensis populations based on chloroplast DNA sequences.
Table 4.
Hierarchical analysis of molecular variance for 28 populations of Scrophularia ningpoensis based on chloroplast DNA sequences.
Table 5.
Genetic diversity in 24 populations of S. ningpoensis based on AFLP.
Table 6.
Hierarchical analysis of molecular variance for 24 populations of S. ningpoensis based on AFLP.
Figure 2.
Principal coordinate analysis (PCoA) of 306 individuals from 24 populations of S. ningpoensis based on the Euclidean distance generated from AFLP data.
To simplify comparison, cultivated S. ningpoensis are indicated by triangles, while wild S. ningpoensis are indicated by circles.
Figure 3.
Neighbor-Joining and STRUCTURE analyses of the AFLP data.
(A) Neighbor-Joining analysis of the AFLP data for all individuals of S.ningpoensis based on Nei's (1979) genetic distances with S. buergeriana as the outgroup. (B) Result of the model from clustering (K = 2) of all wild individuals and 10 cultivated individuals of S. ningpoensis using STRUCTURE based on the AFLP data set.
Figure 4.
The estimated mean logarithmic likelihood of K values ranging from 2 to 14 with 10 replicates for each K calculated using the R-script Structure–sum.