Originally the X and Y chromosome were identical chromosomes. At some point in the evolutionary process a sex differentiating gene appears on one of the chromosomes, and genetic recombination becomes inhibited around this gene. In humans this is the SRY gene on the Y chromosome.
Inhibition of recombination spreads to cover all but the very ends of the Y chromosome.
Over time, without benefit of genetic recombination, the Y chromosome begins to degrade.
As the Y chromosome loses active genes, each organism must develop a method for equalizing genetic expression in males and females. For this reason one of the X chromosomes in every female mammal becomes inactive and curls up into a structure known as a Barr Body.

Y: THE DRIVING FORCE

SPEAKING of the evolution of X inactivation without speaking of the history of the X and Y chromosomes leaves out critical context, something like cataloguing the rarefied structures of orchids without considering the habits of insects which evolved in concert with the flowers.
      The X and Y chromosomes hardly look like a pair. Textbooks have considered the mammalian X and Y fully differentiated from each other.
      Yet the X and the Y descended from a pair of identical sister chromosomes. Early in the evolution of mammals, before monotremes (echidnas and the platypus) and marsupials (opossum, kangaroos and other Australian mammals) diverged from the placental mammals about 130 to 150 million years ago, the sex chromosomes arose. We can reconstruct how this happened. Probably, a gene variant appeared that influenced sex determination. In mammals the gene on the Y that triggers male development was discovered a decade ago.
      This evolutionary history applies generally when sex chromosomes arise. A sex-affecting variant appears on a chromosome that contains a haphazard collection of genes, most of which have nothing to do with sex determination or differentiation.
      Once a sex-determining gene appeared, recombination became restricted around that gene, as if to ensure that it remained confined to the male line. Eventually, the region of suppressed recombination expanded to include nearly the whole Y. How recombination between sex chromosomes becomes suppressed and how the suppression spreads remain some of the most mysterious steps in sex chromosome evolution. Now, the human X and Y chromosomes recombine only at their very tips.

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