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. 2024 May 22;56(6):1278–1287. doi: 10.1038/s41588-024-01769-9

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a,b, Isolate-level clustering using t-SNE based on the expression of 1,797 coexpressed genes (a) and 2,209 DEGs (b). Isolates belonging to each annotated subpopulation are color-coded. c–k, Examples of subpopulation-specific domestication signatures. Three examples are shown. c, 5. French dairy. d, 5. French dairy GAL1. e, 5. French dairy UIP3. f, 11. Ale beer. g, 11. Ale beer MAL32. h, 11. Ale beer AAD6. i, 1. Wine/European. j, 1. Wine/European SSU1. k, 1. Wine/European VTH1. In c,f,i, the volcano plots show upregulated (orange) and downregulated (blue) genes and biological processes, with the x axis showing the log₂ fold change when the subpopulation was compared with the rest of the isolates, and the y axis showing the Benjamini–Hochberg-adjusted −log₁₀P_adj. The dot sizes were scaled according to the FDR. The variance-stabilized expression levels for specific upregulated (d,g,j) and downregulated (e,h,k) genes were overlapped over the t-SNE plot, with expression levels scaled as different color intensities. The colored scales are shown on the side of the plots.