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. 2023 Jan 26;7(3):414–423. doi: 10.1038/s41559-022-01975-w

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a, Independent origins of the tolerant populations: a maximum-likelihood phylogenetic tree based on 15,285 SNPs; all inter-population relationships had bootstrap support ≥99%. b, PCA of variance-stabilizing transformed counts (Methods) of all 27,970 genes for all populations in the control treatment, summarizing constitutive expression differences between populations. Point fill corresponds to zinc tolerance (orange, tolerant; blue, sensitive); point border corresponds to geographic pair (red, Wales (T1/S1); dark blue, England (T2/S2)). Arrows are drawn from the centroid of susceptible populations (S1 and S2) to the centroid of corresponding tolerant populations (T1 and T2, respectively). c, For CEC genes, boxplot of absolute values of log₂-transformed fold changes (|FC|; y axis) between pairs of populations (x axis) in the control treatment (box, interquartile range; line, median; whiskers, the largest value no further than 1.5× the interquartile range). N = 413 for each box. Values above/below whiskers not plotted. d, PCA of variance-stabilizing transformed counts in both treatments across all genes. Point fill and border as in b. Circles correspond to control treatment, triangles to zinc treatment. Dashed line, plastic change; solid arrow, evolutionary change. e, Heat map of log₂-transformed shrunken fold changes between control and zinc treatments for genes that were differentially expressed between control and zinc in both T1 (x axis) and T2 (y axis; that is, DP genes). f, PCA of variance-transformed counts for DP genes only, in both treatments (legend as in b).

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