Palindromes on the Y chromosome
- The organization and evolution of the human Y chromosome
A startling finding is that, with one exception, the Y chromosome repeats are organized as palindromes, with two very similar long sequences pointing in opposite directions, connected by a 'spacer' (Figure 2) . A companion paper  shows that at least some of the palindromes are present in chimpanzees and gorillas, so their origin predates the split between humans and their closest relatives. There is very little sequence divergence between the arms of the palindromes, compared to the divergence between human and chimpanzee sequences. This strongly suggests that there is ongoing gene conversion between the arms, maintaining their sequence similarity. A simple population genetics argument yields an estimate of the rate of conversion as 2.2 × 10-4 per nucleotide per generation, comparable with values from other sources . The MSY therefore experiences recombination, although of a type that does not affect its divergence from the X.
A consequence, though probably not a cause (given that evolution has no foresight), of the existence of the palindromes is that ongoing gene conversion will inhibit the spread by genetic drift of a deleterious mutation through just one of the two arms, allowing selection to preserve the functionality of both copies . It is possible that the unusual abundance of palindromes among functional duplications on the Y reflects the fact that unequal crossovers between sister chromatids cannot occur among palindromes without causing disruptive chromosome rearrangements; this will prevent their loss through the generation of single-copy units by unequal crossing over, as can happen with tandem duplications .
The organization of the human Y chromosome thus reflects a combination of several evolutionary processes: the degeneration of the bulk of the genes, which were originally common to the primeval X/Y chromosome pair; the accumulation of genes with male-specific functions by sporadic transpositions from the X chromosome and autosomes; and a unique recent transposition of a large piece of X chromosomal material. It is therefore probably premature to predict the ultimate demise of the human Y chromosome, as has recently been done . Some species have indeed lost all trace of the Y chromosome, so that males are Xo, not XY . But this can happen only if the male-determining function of the Y chromosome is abolished and is replaced by an X/autosome-balance sex-determination system of the kind found in Drosophila and Caenorhabditis, which is probably rather hard to pull off . Together with the presence of several genes required for male fertility on the human Y chromosome, these considerations imply that human males are likely to be stuck with their bizarre genetic make-up for the foreseeable evolutionary future.
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