Fig. 6: Neutral and adaptive genetic diversity in H. fraxineus genes and potential effectors.
From: The ash dieback invasion of Europe was founded by two genetically divergent individuals
a, The Japanese population contains an increased level of diversity to that in Europe but despite the founder effect, genes that are more polymorphic in Japan tend to be more polymorphic in Europe (Eu–Jp SNP density: gene, R2 = 0.664, n = 3214, p < 0.001; effector, R2 = 0.605, n = 369, p < 0.001). Linear model calculated using log–log data and plotted here on the original scale (see Supplementary Fig. 23 for log–log scale). b, The level of genetic diversity in Europe is not significantly different between potential effectors (Wilcoxon (π), Eu genes ~ Eu effectors: W(10,942) = 5,420,600, n = 10,943, p = 0.78 (not significant)) whereas, in Japan putative effectors carry significantly more genetic diversity (Wilcoxon (π), Jp genes < Jp effectors: W(10,942) = 5,671,200 n = 10943, *p = 0.041). Nucleotide diversity over all genes combined is significantly greater in Japan than in Europe (Wilcoxon (π), Jp all genes > Eu all genes: W(21,885) = 102,060,000 n = 21,886, ***p < 0.001). c, The signal of adaptive diversity (PN:PS) is significantly different between putative effectors and all other genes (permutation test of equality: n = 9,258, p < 0.001; joint kernel density shaded). The increase in effector PN:PS to other genes, over this range, is evidence for reduced efficacy of purifying selection in this classification of genes. For genes with a PN:PS greater than one and less than two (c, inset) effector genes again peak outside the joint kernel density, consistent with the operation of positive selection driving adaptive change in these effectors (permutation test of equality: n = 183, p = 0.01). d, The overall level of adaptive polymorphism is greater in effectors than other genes in both Japan and Europe (Wilcoxon (PN:PS), Jp genes < Jp effectors: W(9,510) = 4,891,800, n = 9,511, ***p < 0.001; Eu genes < Eu effectors: W(6,080) = 1,750,600, n = 6081, *p = 0.045). However, the strength of this signal has been reduced in the European population. Boxplots show the median, upper and lower quartiles with outliers plotted outside whiskers which extend 1.5 times beyond the interquartile range (see Supplementary Figs. 24,25 for outliers).
