Extended Data Fig. 11. Compensatory evolution of X-linked genes.

a, b, examples of upregulation for the dosage reduction at the transcriptome layer. Species affected by upregulation are shown in olive, with arrows representing compensatory changes at the translatome layer. c, Median ratio of X-linked gene expression values in murine spermatogenic cell types to expression values of their 1:1 orthologues in chicken testis. In all cases log₂-ratio at the translatome layer is significantly (P < 0.05, Mann-Whitney U test, two-sided) higher than at the transcriptome layer (marked in bold). Solid vertical lines correspond to expression levels expected under no dosage reduction (i.e., log₂-ratio = -1). d, Median current to ancestral gene expression ratios at two expression layers for 1:1 orthologous autosomal genes located on chromosome 4 in chicken for brain, liver, and testis. Chicken orthologues were used as a proxy for ancestral expression. See Fig. 4a and main text for details. e, Normalized TEs for 1:1 orthologues of eutherian X-linked and autosomal genes across amniote organs. Mann-Whitney U tests (two-sided) were performed for statistical comparisons (non-significant, ns: P > 0.05, ***P = 0.00003, ****P < 0.0001). P values were adjusted for multiple testing using Bonferroni method. Box plots represent the median ± 25th and 75th percentiles, whiskers are at 1.5 times the interquartile range. Organ and species icons were previously used in ref. ²⁵.