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. 2024 Aug 26;8(10):1933–1947. doi: 10.1038/s41559-024-02514-5

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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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Extended Data Fig. 8 — Panel A shows a simplified gene tree with 4 species (S1-S4), 3 duplications (D1-3), and 2 species-specific duplications (D2-3). Panel B shows depletion of duplications in orthogroups grouped according to their strongest evidence of repeatability. The mean duplication value is plotted for each repeatability decile. The black points and lines show a comparable analysis over 100 randomisations of all per gene ep-values_WZA. The black point shows the mean duplication metric per decile and the lines show the maximum and minimum values across the 100 randomisations. Panel C shows duplication results exclusively looking at contributing species within RAOs, compared with species with low ep-values_WZA (<0.1) within 10,000 draws of random orthogroup-climate sets. Lines show the observed mean relative to the distribution of random means, where green lines show permuted p-value < 0.05. The one-sided p-values for permutation tests = 0.153 (Mean Duplication N) and 0.035 (Mean Proportion of Duplicated Genes).