Y chromosomes are genetically degenerate, having lost most of the active genes present in their ancestors. The causes of this degeneration have been studied by evolutionary theorists, with four major theories proposed: Muller's ratchet, background selection, the Hill–Robertson effect with weak selection, and the 'hitchhiking' of deleterious alleles by favourable mutations. These processes involve a reduction in effective population size due to selective events in non-recombining genomes, leading to weakened selection efficacy. The review discusses the consequences of these processes for molecular evolution and variation on Y chromosomes, and presents empirical studies on evolving Y and neo-Y systems. Results suggest that effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes are operative. However, it is unclear which process is most important, and future research is needed to resolve this. Y chromosomes have evolved independently in many animal and plant groups, with a common feature being the loss of most genes except those specific to the heterogametic sex. The evolution of sex chromosomes began with restricted recombination between proto-X and proto-Y chromosomes, which led to the loss of genetic activity on the Y chromosome. Once genetic sex determination evolved, selection for advantageous alleles in males but disadvantageous in females led to genetic differentiation between the two sex chromosomes and suppression of recombination. This sets the stage for the further evolution of an incipient Y chromosome. Several models of Y-chromosome degeneration have been proposed, including Muller's ratchet, background selection, the Hill–Robertson effect, and hitchhiking effects. Muller's ratchet involves the stochastic loss of chromosomes with the fewest deleterious mutations, leading to the accumulation of deleterious mutations. Background selection reduces genetic variability at neutral or weakly selected sites due to the elimination of chromosomes with strongly deleterious mutations. The Hill–Robertson effect involves interference between linked selected alleles, inhibiting the spread of favourable alleles and the elimination of deleterious ones. Hitchhiking effects involve the spread of favourable mutations leading to the fixation of deleterious mutations. Empirical studies on Y and neo-Y chromosomes, such as in Drosophila and plants, suggest reduced effective population sizes and genetic diversity on Y chromosomes. These findings support the hypothesis that processes like Muller's ratchet, background selection, and the Hill–Robertson effect contribute to Y-chromosome degeneration. However, the relative importance of these processes remains unclear, and further research is needed to determine which is most significant. The degeneration of Y chromosomes highlights the importance of recombination in maintaining the fitness of large genomic regions and the reduced ability of selection to maintain adaptation in asexual reproduction.Y chromosomes are genetically degenerate, having lost most of the active genes present in their ancestors. The causes of this degeneration have been studied by evolutionary theorists, with four major theories proposed: Muller's ratchet, background selection, the Hill–Robertson effect with weak selection, and the 'hitchhiking' of deleterious alleles by favourable mutations. These processes involve a reduction in effective population size due to selective events in non-recombining genomes, leading to weakened selection efficacy. The review discusses the consequences of these processes for molecular evolution and variation on Y chromosomes, and presents empirical studies on evolving Y and neo-Y systems. Results suggest that effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes are operative. However, it is unclear which process is most important, and future research is needed to resolve this. Y chromosomes have evolved independently in many animal and plant groups, with a common feature being the loss of most genes except those specific to the heterogametic sex. The evolution of sex chromosomes began with restricted recombination between proto-X and proto-Y chromosomes, which led to the loss of genetic activity on the Y chromosome. Once genetic sex determination evolved, selection for advantageous alleles in males but disadvantageous in females led to genetic differentiation between the two sex chromosomes and suppression of recombination. This sets the stage for the further evolution of an incipient Y chromosome. Several models of Y-chromosome degeneration have been proposed, including Muller's ratchet, background selection, the Hill–Robertson effect, and hitchhiking effects. Muller's ratchet involves the stochastic loss of chromosomes with the fewest deleterious mutations, leading to the accumulation of deleterious mutations. Background selection reduces genetic variability at neutral or weakly selected sites due to the elimination of chromosomes with strongly deleterious mutations. The Hill–Robertson effect involves interference between linked selected alleles, inhibiting the spread of favourable alleles and the elimination of deleterious ones. Hitchhiking effects involve the spread of favourable mutations leading to the fixation of deleterious mutations. Empirical studies on Y and neo-Y chromosomes, such as in Drosophila and plants, suggest reduced effective population sizes and genetic diversity on Y chromosomes. These findings support the hypothesis that processes like Muller's ratchet, background selection, and the Hill–Robertson effect contribute to Y-chromosome degeneration. However, the relative importance of these processes remains unclear, and further research is needed to determine which is most significant. The degeneration of Y chromosomes highlights the importance of recombination in maintaining the fitness of large genomic regions and the reduced ability of selection to maintain adaptation in asexual reproduction.