Genomic clusters represent different admixture histories
In accordance with previous results, Mentha is resolved as
monophyletic in relation to Salvia in the plastome phylogeny
(Figure S3a; Li et al., 2016). However, the taxa within Menthaare polyphyletic although M. longifolia and M. suaveolensare mostly separated into different lineages (Figure S3b). Specimens
identified as the hybrid M. × rotundifolia are found
intermingled with both M. longifolia and M. suaveolens(Figure S3b). In contrast, with the exception of a single specimen, all
specimens identified as M. spicata are monophyletic and found
together with a subset of the M. longifolia specimens (Figure
S3b).
Genomic clustering was performed by means of PCA, and similar to the
morphological analyses there is a separation of M. longifolia(long) and M. suaveolens (sua) on the first PC (11%; Figure 2a).
Intermediate to these taxa there are three relatively distinct groups of
specimens that are consistent with the hybrid M. ×rotundifolia although a few samples of M. longifolia are
also found in these clusters (rot1-3; Figure 2a). The genetic
distinction between M. longifolia and M. spicata is more
elusive with specimens only somewhat separating along the second PC
(4%; Figure 2a). Some specimens mostly morphologically identified asM. spicata (spi1) do however, form a separate cluster on the
positive extremes of the second PC (spi1; Figure 2a).
Overall, the admixture analysis reflects the genomic clustering with the
best-fit number of population groups (K ) being two with other
smaller optima at four and six (Figures 2 and S4). The specimens
separating on the first genomic PC form five groups with distinct
admixture profiles (Figure 2b). Based on the morphology of these
specimens the three admixed groups genomically resemble F1 crosses
between M. longifolia and M. suaveolens (M. ×rotundifolia ) as well as backcrosses to either parent (Figure
2b). Most specimens morphologically recognized as M. spicata are
also admixed (Figures 2b). However, when the number of populations
(K ) is increased it is clear that the admixture histories ofM. × rotundifolia and M. spicata are different
(Figure 2b and S4b). When three respective four populations are
considered, the two M. spicata clusters (spi1 and spi2; Figure
2a) forms separate populations but a few specimens morphologically
identified as M. spicata still appear admixed (Figure 2b). The
specimens with more central positions in the genomic PCA show admixture
proportions consistent with mixing of all gene pools (Figures 2 and S4).
However, our admixture analyses cannot decisively exclude that some
patterns are caused by admixture with other species not included in our
study.
Although, there is an overall agreement between the morphological and
genomic analyses there are also a few cases of miss-matches. In
particular a few specimens morphologically identified as M. ×rotundifolia are found intermingled with other genomic groups, as
well as intermediate to the two groups of M. spicata (rot4;
Figure 2a) and these specimens show admixture proportions consistent
with their genomic cluster assignments (Figure 2b). In addition, a few
specimens morphologically identified as M. spicata are
genomically indistinguishable from M. longifolia and a few
specimens morphologically identified as M. longifolia were found
to be admixed (Figure 2b).