The chapter discusses the degeneration of Y chromosomes, which have lost most of their active genes due to various evolutionary processes. Four major theories explaining this degeneration are reviewed: Muller’s ratchet, background selection, the Hill–Robertson effect with weak selection, and hitchhiking of deleterious alleles by favorable mutations. These theories involve a reduction in effective population size and a weakening of selection efficacy in non-recombining genomes. The authors review the consequences of these processes on molecular evolution and variation at Y chromosome loci, and discuss empirical studies of evolving Y-chromosome and neo-Y-chromosome systems. Results suggest that effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, supporting the hypothesized processes. However, it is unclear which process is most significant, and future work is needed to resolve this question. The chapter also highlights the importance of recombination in maintaining genetic fitness and the broader pattern of reduced adaptation under asexual reproduction.The chapter discusses the degeneration of Y chromosomes, which have lost most of their active genes due to various evolutionary processes. Four major theories explaining this degeneration are reviewed: Muller’s ratchet, background selection, the Hill–Robertson effect with weak selection, and hitchhiking of deleterious alleles by favorable mutations. These theories involve a reduction in effective population size and a weakening of selection efficacy in non-recombining genomes. The authors review the consequences of these processes on molecular evolution and variation at Y chromosome loci, and discuss empirical studies of evolving Y-chromosome and neo-Y-chromosome systems. Results suggest that effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, supporting the hypothesized processes. However, it is unclear which process is most significant, and future work is needed to resolve this question. The chapter also highlights the importance of recombination in maintaining genetic fitness and the broader pattern of reduced adaptation under asexual reproduction.