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Abstract
Sex chromosomes have evolved independently many times across the tree of life. Ancient sex chromosomes have been a powerful model to understand both the evolution of sex chromosomes, as well as improve our understanding of fundamental genetics. But the sequencing of recently evolved sex chromosomes provides the opportunity to identify how selection operates on sex chromosomes in earlier stages of sex chromosome evolution and how testis genes accumulate on Y chromosomes. My dissertation focused on two projects; the first was to identify how cis-regulatory elements have evolved on the X and Y chromosome and the second was to identify how gene content and gene expression has evolved for testis genes across different stages of spermatogenesis. I utilized a combination of transcriptomics and epigenomics, overlayed with molecular evolution between species and within populations to identify patterns of regulatory evolution on the X and Y chromosomes. I found that cis-regulatory elements shared between the X and Y chromosome harbor molecular signatures of rapid evolution consistent with adaptive loss of expression on the Y chromosome. These findings help provide empirical evidence for theoretical predictions about Y chromosome evolution. I also showed that threespine stickleback sex chromosomes have evolved post-meiotic sex chromosome repression, perhaps in response to intragenomic conflicts evolving on between the X and Y chromosome. Together, my dissertation provides insight into the evolution of sex chromosomes in stickleback fish, and advances our understanding of sex chromosome evolutionary theory.