Molecular Evolution of a Sex-Linked Inversion Polymorphism in Zebra Finches

Recent years have seen an explosion in examples of supergenes, where recombination is suppressed between haplotypes, often via inversion polymorphisms, to control complex traits. However, an enduring problem in evolutionary biology is understanding the molecular consequences of recombination suppression, especially when it has been present for long periods. Here, we explore the molecular evolution of the A and B haplotypes 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 reduced efficacy of purifying selection acting on the coding sequence of the Z-linked haplotypes and an increase in mutational load. However, we fail to find a positive association between expression and sequence divergence, consistent with an absence of any compensatory expression evolution for the accumulation of deleterious alleles.