Let's turn to research on X and Y chromosome evolution to explain some of what we saw in Part 1. Once upon a time, the Y chromosome used to be just another X chromosome. But at some point, the X-that-would-be-Y (I'll call it pseudo-Y for now) suffered a major inversion; that is, a big chunk of the chromosome was broken off, flipped around, and stuck back on. This causes a problem with recombination. During meiosis, homologous chromosomes line up and swap pieces of DNA. This can only occur if the pieces being swapped are pretty much the same. Recombination is an important means of swapping around alleles (different versions of genes) and therefore a big player in evolution.
The inversion event threw a wrench into X chromosome recombination. The un-inverted sections could still recombine, but the inverted section couldn't, and therefore these formerly homologous stretches of DNA diverged, each gradually mutating in different ways. The pseudo-Y experienced a number of other inversion events, each time taking another chunk of the homologous region and rendering it incapable of recombination with X.
How do we know this? Because the inversion events left behind fingerprints:
This image is from a 1999 paper by Lahn & Page. We would expect that inverted sections of the pseudo-Y would diverge from the corresponding regions on the X. The more time has passed since the inversion, the more divergence we should expect.
Lahn & Page looked at 19 X-linked genes that were known to have homologous sections of DNA on the Y chromosome. For each of these DNA regions, they measured the differences between the X and Y versions. The x-axis in the figure shows location on the chromosome. The y-axis shows the estimated mean number of substitutions per synonymous site. What we see are four main age blocks; genes in Group 1 are more diverged from their Y counterparts than those in Group 2, which suggests the Group 1 region of DNA inverted earlier.
Next time, we'll look at how these evolutionary regions of the X chromosome relate to which genes escape X-inactivation.