Phylogenetic tree of carrot. Phylogenetic analysis was based on the combined datasets of 622-SNP and 89-SNP. Different Daucus species were used as outgroup to D. carota. Numbers at the nodes indicate posterior probabilities (%). Sample names beginning with “W” are wild species and those with “C” are cultivars; the middle name of each sample indicates species name (for outgroup) or subspecies name of wild species, or root type/accession name of cultivars; the sampling country is indicated at the end. For more details of the samples see Table 1 and Additional file 1: Table S1. Group 1–5 were designed to represent the main phylogeographic structure of the tree. Note that the grouping is somewhat arbitrary because there is no distinct boundary between groups, for instance a few wild carrots are within the Group 4 of Eastern Cultivars.