Functional degeneration of neo-Y genes.

A. Composition of neo-Y linked genes. We show numbers of putative functional genes (‘Intact’), genes with premature stop codons (‘PTC’) and/or frameshift (‘Shift’) mutations on the neo-Y. B. Boxplots of gene expression level on each chromosome. We divide neo-sex linked genes according to the functional status of the neo-Y genes: functional (func) neo-Y genes, and their diploid (dpd) neo-X homologs; non-functional (psd) neo-Y genes and their hemizygous (hmz) neo-X homologs. The former group of neo-sex linked genes shows a higher expression level than the latter. C. Allelic expression bias of neo-sex linked genes in male adults. Shown are the log ratios of neo-X expression vs. neo-Y expression along the neo-sex chromosome, with putatively functional neo-Y genes in red and pseudogenes in green. We also plot the loess smooth lines separately for the two categories of genes, in order to show the local variation of the log ratio along the chromosome position. Any genes above 0 have higher neo-X expression relative to the neo-Y. D. Sex-bias expression of neo-sex linked genes. We show the expression difference between sexes for neo-sex linked genes, with neo-X/Y gene expression level combined in male, and only neo-X gene expression in female. E. Correlation between relative neo-sex allelic expression vs. sex-biased expression and relative neo-X expression. Shown are the ratios of neo-X vs. neo-Y expression level for neo-sex linked genes, vs. their expression ratio between sexes (in blue), and the ratio of neo-X expression in male vs. that in female (in orange), as well as their linear regression lines. F. Density plot of the ratios of male neo-sex alleles (neo-X in orange, neo-Y in blue) vs. female expression levels. Assuming an equal expression level between sexes, we expect the distribution of relative neo-X alleles’ expression to be around half of the female expression level (dashed line).