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. 2024 May 29;630(8016):401–411. doi: 10.1038/s41586-024-07473-2

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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. 3 — (a) DNA methylation levels in 100-kb bins in Pseudoautosomal region 1 (PAR1; teal), non-PAR chromosome X (orange), and non-PAR chromosome Y (periwinkle). (b) Differences in DNA methylation levels between different repeat categories as well as protein-coding genes (after excluding repetitive sequences). (c) Differences in methylation levels between ampliconic and ancestral regions in the X and the Y chromosomes (in 100 kb bins). All box plots (a-c) show the median and first and third quartiles. Those in b-c also have whiskers extending to the closer of the minimum/maximum value or 1.5 times the interquartile range, and outliers (beyond the whiskers) are plotted as individual points. p-values were determined using two-sided Wilcoxon rank-sum tests (* p < 0.05; ** p < 10⁻³; *** p < 10⁻⁶) and are shown in Table S28. No correction for multiple testing was applied. Sample sizes (i.e., number of 100 kb bins (a,c) or number of repeats, genes, etc. (b)) are shown in Table S28.