Widespread intersex differentiation across the stickleback genome – the signature of sexually antagonistic selection?

Females and males within a species commonly have distinct reproductive
roles, and the associated traits may be under perpetual divergent natural
selection between the sexes if their sex-specific control has not yet
evolved. We here explore whether such sexually antagonistic selection can
be detected based on the magnitude of differentiation between the sexes
across genome-wide genetic polymorphisms by whole-genome sequencing of
large pools of female and male threespine stickleback fish. We find
numerous autosomal genome regions exhibiting intersex allele frequency
differences beyond the range plausible under pure sampling stochasticity.
Alternative sequence alignment strategies rule out that these
high-differentiation regions represent sex chromosome segments
misassembled into the autosomes. Instead, comparing allele frequencies and
sequence read depth between the sexes reveals that regions of high
intersex differentiation arise because autosomal chromosome segments got
copied into the male-specific sex chromosome (Y), where they acquired new
mutations. Because the Y chromosome is missing in the stickleback
reference genome, sequence reads from derived DNA copies on the Y
chromosome still align to the original homologous regions on the
autosomes. We argue that this phenomenon hampers the identification of
sexually antagonistic selection within a genome, and can lead to spurious
conclusions from population genomic analyses when the underlying samples
differ in sex ratios. Because the hemizygous sex chromosome sequence (Y or
W) is not represented in most reference genomes, these problems may apply
broadly.