Data from: Variant files for genotypic and sex-reversed males

X and Y chromosomes are usually derived from a pair of homologous
autosomes, which then diverge from each other over time. Although
Y-specific features have been characterized in sex chromosomes of various
ages, the earliest stages of Y chromosome evolution remain elusive. In
particular, we do not know whether early stages of Y chromosome evolution
consist of changes to individual genes or happen via chromosome-scale
divergence from the X. To address this question, we quantified divergence
between young proto-X and proto-Y chromosomes in the house
fly, Musca domestica. We compared proto-sex chromosome sequence
and gene expression between genotypic (XY) and sex-reversed (XX) males. We
find evidence for sequence divergence between genes on the proto-X and
proto-Y, including five genes with mitochondrial functions. There is also
an excess of genes with divergent expression between the proto-X and
proto-Y, but the number of genes is small. This suggests that individual
proto-Y genes, but not the entire proto-Y chromosome, have diverged from
the proto-X. We identified one gene, encoding an axonemal dynein assembly
factor (which functions in sperm motility), that has higher expression in
XY males than XX males because of a disproportionate contribution of the
proto-Y allele to gene expression. The up-regulation of the proto-Y allele
may be favored in males because of this gene’s function in
spermatogenesis. The evolutionary divergence between proto-X and proto-Y
copies of this gene, as well as the mitochondrial genes, is consistent
with selection in males affecting the evolution of individual genes during
early Y chromosome evolution.