Muller's ratchet and background selection are predicted to be strong degenerating forces when there are many genes on the nonrecombining region of the Y, while genetic hitchhiking will dominate the nonrecombining region of the Y when the genic content is smaller. Interestingly, these processes have different likelihood of operating at different times in the process of Y chromosome differentiation. The first two processes make the fitness of Y chromosomes worse on average as time goes by while genetic hitchhiking improves the Y on average. The long-term consequences for Y chromosome fitness are very different for each of these processes ( Figure 2). Genetic hitchhiking will occur when a beneficial mutation drags along the fixation of deleterious mutations in the nonrecombining region of the Y chromosome. Background selection will lead to the fixation of weakly deleterious mutations due to the reduction in effective population size brought about by the selection against strongly deleterious mutations in regions with reduced recombination. Muller's ratchet will operate when deleterious mutations occur, and the class of Y chromosomes with the least deleterious mutations is lost from the population by drift and cannot be recovered because of the lack of recombination. These three mechanisms are instances of the general Hill-Robertson effect that describes the reduction in the efficiency of selection in the presence of segregating mutations under selection when recombination is either absent or reduced. In the third phase of sex chromosome differentiation, three different processes-Muller's ratchet, background selection, and genetic hitchhiking-may contribute to degeneration of the Y (or W) chromosome once recombination is reduced in all or part of the nascent sex-specific chromosome. Close linkage between sexually antagonistic variation and the sex-determining gene has been proposed to start Y chromosome morphological differentiation from the X chromosome. We conclude by looking at ways to test the hypothesis that palindromes enhance the rate of adaptive evolution of Y-linked genes and whether this effect can be extended to palindromes on other chromosomes. This hypothesis helps reconcile two enigmatic features of the “palindromes as protectors” view: (1) genes that are not located in palindromes have been retained under purifying selection for tens of millions of years, and (2) under models that only consider deleterious mutations, gene conversion benefits duplicate gene maintenance but not initial fixation. Our paper emphasizes the latter, that palindromes may exist to accelerate adaptation by increasing the potential targets and fixation rates of incoming beneficial mutations. However, the adaptive significance of recombination resides in its ability to decouple the evolutionary fates of linked mutations, leading to both a decrease in degeneration rate and an increase in adaptation rate. Since palindromes enable intrachromosomal gene conversion that can help eliminate deleterious mutations, they are often highlighted as mechanisms to protect against Y degeneration. Y chromosome palindromes consist of inverted duplicates that allow for local recombination in an otherwise nonrecombining chromosome. We look at sex-limited chromosome (Y or W) evolution with particular emphasis on the importance of palindromes.
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