The plastid tree was generally congruent with the nuclear tree. However,
the plastid topology differed in the resolution of the most recent
Mediterranean subclades. In addition, one DC2 sample (R32) was placed in
a different subclade (see Figure 1). The remaining MediterraneanD. communis samples (DC3) were intermingled in three plastid
subclades (I, II and III in Figure 1). In the nuclear tree, the subclade
DC3 from the eastern Mediterranean contained samples with plastid
haplotypes from all plastid subclades I, II and III, and the subclades
of DC3 from central Mediterranean and western Europe contained samples
with those from plastid subclades I and II, and II and III, respectively
(Figure 1).
To better understand the source of topological incongruence between the
nuclear and plastid phylogenetic trees of the Mediterranean samples ofD. communis , we used STRUCTURE to investigate whether
introgression between samples from different subclades may have
occurred. The highest deltaK value (15821.9) was obtained forK = 3 genetic groups (Supplementary Data Figure S2). All samples
in clade DC2 of D. communis showed genetic profiles corresponding
to one genetic group (Cluster 1), and five samples also showed a
percentage of membership <20% to Cluster 2 (i.e., samples
R16, R17, S69 and S70) or Cluster 3 (sample R32, 26%). The samples ofD. communis in clade DC3 showed genetic profiles corresponding
predominantly to Cluster 3 and multiple patterns of admixture with
Clusters 1 and 2 (Figure 2). The genetic profile of one DC3 sample from
the eastern Mediterranean subclade showed a percentage of membership
>20% to Cluster 1, and nine DC3 samples had membership
percentages of >20% to Cluster 2 (five from the eastern
Mediterranean, one from the central Mediterranean and three from the
western Europe subclades). Other alternative K groups did not
increase the number of clusters in DC2 and showed higher admixture in
the DC3 subclades (Supplementary Data Figure S3). In all cases, the
sample R32 was always resolved with ca. 20% admixture with the main
genetic cluster of the DC3.