Male and female adult zebra finch (Taeniopygia guttata) gonad RNAseq associated with: Relaxed purifying selection maintains a sex-linked supergene polymorphism in zebra finches

Recent years have seen an explosion in examples of inversion
polymorphisms, where recombination is suppressed between haplotypes,
acting as supergenes to control complex traits. However, an enduring
problem in evolutionary biology is understanding how these inversion
polymorphisms are maintained, often for long periods of time. Here, we
test alternate theories for how balancing selection maintains supergenes
and explore the molecular evolution and expression of a large, sex-linked
inversion polymorphism in a passerine bird, the zebra finch (Taeniopygia
guttata) responsible for most of the genetic variation in sperm
morphology. We find evidence for degeneration within the supergene
characterised by relaxed purifying selection and an excess of
nonsynonymous differences which, combined with signatures of balancing
selection, is indicative of associative overdominance protecting
heterozygotes from deleterious recessive alleles. Furthermore, we find
that the transcriptome acts to mitigate the negative consequences of
relaxed purifying selection through the more equal expression of those
most highly diverged, and potentially degenerated, alleles.