Gene Conversion Drives the Evolution of HINTW, an Ampliconic Gene on the Female-Specific Avian W Chromosome

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Abstract
The HINTW gene on the female-specific W chromosome of chicken and other birds is amplified and present in numerous copies. Moreover, as HINTW is distinctly different from its homolog on the Z chromosome (HINTZ), is a candidate gene in avian sex determination, and evolves rapidly under positive selection, it shows several common features to ampliconic and testis-specific genes on the mammalian Y chromosome. A phylogenetic analysis within galliform birds (chicken, turkey, quail, and pheasant) shows that individual HINTW copies within each species are more similar to each other than to gene copies of related species. Such convergent evolution is most easily explained by recurrent events of gene conversion, the rate of which we estimated at 10−6–10−5 per site and generation. A significantly higher GC content of HINTW than of other W-linked genes is consistent with biased gene conversion increasing the fixation probability of mutations involving G and C nucleotides. Furthermore, and as a likely consequence, the neutral substitution rate is almost twice as high in HINTW as in other W-linked genes. The region on W encompassing the HINTW gene cluster is not covered in the initial assembly of the chicken genome, but analysis of raw sequence reads indicates that gene copy number is significantly higher than a previous estimate of 40. While sexual selection is one of several factors that potentially affect the evolution of ampliconic, male-specific genes on the mammalian Y chromosome, data from HINTW provide evidence that gene amplification followed by gene conversion can evolve in female-specific chromosomes in the absence of sexual selection. The presence of multiple and highly similar copies of HINTW may be related to protein function, but, more generally, amplification and conversion offers a means to the avoidance of accumulation of deleterious mutations in nonrecombining chromosomes.