Relationship of the mouse taxa and numbers of sex-biased genes for each organ comparison.

Numbers of sex-biased genes are presented as bar plots, female-biased in red, male-biased in blue. DOM = M.m. domesticus, MUS = M. m. musculus, SPR = M. spretus, SPI = M. spicilegus. The X-axis show the number of genes. Note that there are two different scales for the non-gonadal organs and gonadal organs. The gonadal comparisons were done between ovary and testis (OvaTes), oviduct and epididymis (OviEpi) and uterus and vas deferens (UteVas). Full numbers are provided in suppl. Table S2.

Percentages of shared genes with sex-biased expression between the mouse taxa.

The plots show the percentages of genes that are shared as sex-biased across the four taxa for each organ comparison. Numbers are normalized to “1 taxon” which represents the sum of all genes in a single taxon (set to 100%), “2 taxa”, “3 taxa” and “4 taxa” represent the percentages of the sums of shared genes for any pairwise comparison.

Variances and positive selection on sex-biased genes.

(A) Variances of expression in sex-biased and non-biased genes for each organ. The ranges of relative variances (IQR/median ratios for tpm counts) for the four taxa are displayed as quartile plots; note that these constitute the range of the four values from the four taxa. (B) Results of the McDonald-Kreitman (MK) test for positive selection at coding positions for the sex-biased genes in DOM and MUS. The alpha values represent the fraction of amino acid substitutions that are predicted to be driven by positive selection. CI_low and CI_high represent the lowest and highest estimates respectively. Note that the range of these values depends on the number of analyzed genes/SNPs. The “reciprocal” values are for the orthologous genes that are sex-biased in one taxon, but not in the other. Note that this corresponds to different gene sets in DOM and MUS, since they have different sets of sex-biased genes each.

Density plots of individual variation values of the sex-biased gene expression index (SBI) for mouse organs.

Plots for all organs are grouped according to organ for each taxon. Males are represented by blue shading, females by red shading. The taxon designations are on the top, the organ designations to the left. The Y-axis represents the density scale of the smoothed distribution, the X-axis represents the relative maleness <--> femaleness scores. Note that the X-axis is partly shifted to accommodate the breadth of the variances. All individual SBI values are included in suppl. Table S3.

Sex-biased genes and SBIs for data from human tissues.

(A) and (B) Bar plots representing the number of sex-biased genes in tissues that show at least five such genes per sex (excluding the Y-chromosomally encoded genes). Note the different Y-axis scale for the numbers of genes in (B). (C) SBI plots for the nine individuals of each sex based on the set of organs and genes shown in (A) and (B). The Y-axis represents the density scale, the X-axis represents the relative maleness <--> femaleness scores centered around zero. The absolute scale is the same for all plots, but partly shifted towards positive or negative to center the actual distributions. (D) SBI plots for the same individuals and organs as in (C), but based on the sex-biased gene lists from (Oliva et al., 2020). Note that these authors have not included a comparison for OvaTes. All SBI values are listed in suppl. Table S6

Number of genes with sex-biased expression in human single cell data.

Genes with conserved sex-biased gene expression between mice and humans.

The different organs analysed are listed to the left. The green boxes designate sex-biased expression in the respective tissues.