Computational protocol: Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)

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Protocol publication

[…] Sequences were aligned using Clustal_X version 1.81 [], and all indels were coded as substitutions following Caicedo and Schaal []. All individuals were characterized for cpDNA haplotype. Sequence variation was tested for deviations from neutrality by Tajima's D statistic [], and by Fu and Li's D* and F* statistics [] using DNASP 4.00 []. A haplotype network depicting the mutational relationships among distinct haplotypes was drawn following the principle of parsimony by TCS version 1.13 [,], positing S. rehderiana as outgroup. The geographical distribution of haplotypes was plotted on a map of China using Arcmap 8.3 (ESRI, Inc.). Significant difference of haplotype frequencies between wild and cultivated populations was quantified using x2 test. Total diversity (hT), within-population diversity (hS) and level of population differentiation (GST) were calculated using the program HAPLONST, treating wild and cultivated populations as separate groups. The significance of the parameter comparisons (Number of haplotype; Total diversity, hT; Within-population diversity, hS; Population differentiation, GST) between wild and cultivated groups were estimated by x2 test and Wilcoxon two-group tests, being implemented in the statistical package SPSS17.0 (SPSS Inc.).Hierarchical structure of genetic variation in S. baicalensis was determined by an analysis of molecular variance (AMOVA) with ARLEQUIN version 2.000, partitioning genetic variance into three levels: among groups (cultivated and wild groups), among-population within groups, and within-population. Genetic differentiation between cultivated and wild groups was also evaluated using DNASP 4.00 []. To examine the effect of geographical distance on genetic structure, correlations between pairwise genetic distances (Kimura 2-parameter distance generated with Kimura's two parameter model in MEGA 3) [-] and pairwise geographic distances were tested using a Mantel test implemented by Isolation By Distance Web Service []. […]

Pipeline specifications

Software tools Clustal W, DnaSP, Arlequin, MEGA, IBDWS
Application Population genetic analysis
Organisms Scutellaria baicalensis, Leuciscus baicalensis, Homo sapiens