Low levels of genetic differentiation and shared polymorphisms
To understand the level of genetic differentiation between morphologically defined taxa and genomic clusters, analyses of pairwiseF ST were performed between groups of specimens. Overall, there is low genetic differentiation between both morphological and genomic clusters with mean scaffold F STvalues well below 0.2 (Table 2). A large proportion of scaffolds show no differentiation (F ST=0), but a few scaffolds show high F ST-values (>0.5; Table 2 and Figures S5 and S6). Although M. × rotundifolia andM. spicata are overall more distant to M. suaveolens than to M. longifolia (Table 2), there is variation inF ST between the different genomic groups and the respective parental taxa (Table 2). In particular, the genomic cluster spi2 is very similar to M. longifolia (Table 2). Despite the detected difference in admixture history between M. spicata andM. × rotundifolia (Figure 2b) the genetic distance between them is small (Table 2).
Given the small genetic differences between groups of specimens, analyses of shared polymorphisms were conducted. Overall, there is a large overlap in the polymorphic sites between groups of specimens andM. spicata or M. × rotundifolia show no SNPs not found within either M. longifolia or M. suaveolens (Figure 3a). Despite the overall sharing of polymorphic sites, the site frequency spectra (SFS) for each morphological group do show differences in allele frequencies (Figure 3b). In particular, the SFS of M. spicata and M. × rotundifolia are shifted to higher proportions of sites with a higher frequency of the alternative allele (Figures 3b). However, a very low number of sites show complete fixation of an alternative allele (Figures 3b). This is not surprising forM. longifolia as such sites would be private SNPs in the reference genome. However, the low proportion of fixed differences in relation on the reference genome for the other analyzed taxa further supports their close relationships.