Fig. 3: Evidence of introgression and gene flow in European potato.
a, Multispecies coalescence phylogeny of 40 haplotypes of cultivated potatoes and 20 genomes of wild potato species. Consensus tree of 850 maximum likelihood phylogenies for each 100-kb window across the genome (branch support values and individual consensus trees for each chromosome are shown in Supplementary Fig. 24). Main clades are highlighted. b, Admixture analysis across 20 wild diploid potato species and the 40 haplotypes of the potato cultivars (other chromosomes in Supplementary Fig. 25). Each colour represents a different ancestral population. The asterisk indicates the best-fitting K. c, Sequence similarity between wild species and cultivars along chromosome 12 (other chromosomes shown in Supplementary Fig. 26). Colours indicate the clade of the closest wild species. Common haplotypes are highlighted with red dashed lines. d, Diagram illustrating the tests for introgression from the C4S clade. Each test involved four species (P1 to P3, and outgroup O), assessing introgression between P3 and either P1 or P2. The species names and clades are shown in panel a. e, Mean D-statistic results along chromosome 12 (Supplementary Fig. 27 for other chromosomes). Values are averaged across all tests within the clade. The total number of tests (maximum 4, see panel d) with statistically significant f4 statistics for the entire chromosome is indicated (individual f4 values in Supplementary Fig. 28). f, Diversity in haplotype ancestry along the genome from all 40 cultivar haplotypes. Green bars depict pericentromeric regions. Areas shaded in grey represent values below the 0.5 threshold, with the threshold level marked by a grey horizontal line along each chromosome.
