When landraces were compared to improved varieties using analysis of molecular variance (AMOVA), only 8.17% (P value < 0.0001) of the total genetic variance was due to differentiation between landraces and improved varieties.
Statistical comparisons between the ecotypes did not reveal significant differentiation (variation among ecotypes within sites using a hierarchical analysis of molecular variance: Φsc = 0.07, p = 0.07); therefore, we pooled ecotype data for all further analyses.
Strong and significant genetic structure was detected among regions by analysis of molecular variance (AMOVA ΦSTST = 0.81, p < 0.0001, Table 2a).
Under the AMOVA framework (including only identified Agaricia specimens), 60% of molecular variance (ΦSPP-TOT = 0.599; P < 0.001) was explained by morphotaxonomic species designation.
There was significant, though slight (3.9%), molecular variance between habitats in mtDNA (p = 0.047).
Analysis of molecular variance (AMOVA), Fst distances, and pairwise Fst p-values were estimated with Arlequin 3.1 software (Excoffier et al. 2005).
AMOVA indicated non-significant differentiation (1%) between north and south groups and significant population differentiation, with 4.5% (P < 0.001) of the molecular variance partitioned among populations (Table 2).
An analysis of molecular variance revealed that a large proportion (almost 50%, P < 0.001) of the total genetic variance could be explained by differences between two geographical regions, the southwestern and northeastern parts of the main islands of Japan.
Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91%%) than between populations (9 %).
The colonies showed only a moderate genetic differentiation with 74% of the molecular variance explained by within colonies diversity (ΦST = 0.257, p < 0.001).
