Based on our phylogenomic and genetic structure analyses, we performed divergence time analysis using treePL and BEAST (Supplementary Data Figure S4) using one representative sample of each defined clade and genetic group: D. orientalis , DC1, DC2 and DC3. Both approaches reconstructed an early Oligocene origin for the crown node of the Tamus and Borderea clades (BEAST 28.5 MY and treePL 28.2 MY), and a late Miocene split for the two species of the Borderea clade (BEAST 8.1 MY and treePL 10.6 MY). The split of D. orientalis from D. communis was inferred to have occurred during the early Miocene; BEAST 18.2 MY and treePL 20.6 MY), and the Macaronesian clade (DC1) likely diverged from the Mediterranean lineage of D. communis during the mid-Miocene; BEAST 13.5 MY and treePL 16.0 MY). The most recent split between the clades DC2 and DC3 was estimated to have taken place during the late Miocene (BEAST 5.6 MY and treePL 6.6 MY).
The mean and median values of allelic ratios were >2 in all cases for D. orientalis and clade DC1, and only ten samples showed allelic ratio values <2: eight samples from clade DC2 and two samples from the eastern Mediterranean subclade of DC3 (Table 1). The lowest incidence of estimated polyploidy based on allelic ratio estimates was found in DC2, with 50% of the samples classified as diploids (Table 1).