Fig. 4: Divergence amongst core gene haplotypes in Europe is high and bimodal.

Neighbour-net networks were generated individually for the third-base position of 387 CEGs. a,b, A selection of networks built using three individual core genes are shown separately from European (a) and Japanese (b) H. fraxineus populations (see Supplementary Fig. 20 for combined networks). Encircled numbers are used in a to indicate numbers of individuals that share each haplotype. The three gene networks from the European population in a are the same genes as those from the Japanese population in b and drawn to the same scale. c,d, Density plots show the relative pairwise distance amongst haplotypes of all 387 CEGs in Europe (c) and Japan (d). In Japan, pairwise distances between haplotypes range in their divergence (d). In Europe, the majority of genes are either identical or at the complete opposite ends of the divergence range (c). The high level of divergence that separates European haplotypes, which are shared by many individuals, is visible in the three gene networks (a) but also in the measure of pairwise haplotype divergence of all 387 CEGs (c). This represents the presence of two major divergent haplotype groups in Europe.