Shortly after mammals branched off from reptiles, approximately 300 million years ago, a regular pair of autosomes began evolving into what would become the modern X and Y chromosomes. By comparing the number of mutations between the X form and the Y form of a pair of X-Y genes, Lahn and Page came up with rough estimates of when they were last alike, giving them a 'geologic' snapshot of sex chromosomes. Without it, the two chromosomes would diverge into distinct forms. But, says Lahn, recombination between X and Y was suppressed in a step-wise fashion during evolution, so that discrete chunks of chromosomal material suddenly were unable to recombine. Today, the human X and Y chromosomes hardly recombine at all.
Inversions occur when a large chunk of DNA gets turned upside down on the chromosome.
Instead, each inversion drove the sex chromosomes farther apart as they evolved. Each piece of the chromosomes that inverted added to the length of DNA that could no longer align and recombine. On the Y chromosome, this led to degeneration and shrinking, since deleterious mutations were able to build up faster on this non-recombining chromosome. No other pair of chromosomes is as diverse as the sex chromosomes. In the October 29 issue of Science, Bruce Lahn and David Page describe how the sex chromosomes became so different, evolving from a pair of identical chromosomes into X and Y in several discrete stages over 300-million years.