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.