Chimp and human Y chromosomes radically different?

Very interesting article in Nature today:

Hughes et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536-539.

From the abstract:
Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, achieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years.
Wow. "Remarkably divergent?" "Differ radically?" That's impressive. Given creationists' general obsession with the similarity of the chimp and human genomes, I expect this report will become a hot topic on creationist websites and in upcoming issues of creationist journals.

But how radical is radical? Well... pretty radical. The diagram at the top of this post is from Figure 1 in the Hughes et al. paper. It illustrates undeniable and significant differences in the organization of the human and chimp MSY. The authors claim that 30% of the chimp MSY lacks an alignable homologue in the human MSY and vice versa. That's amazing, definitely "radical" and "remarkable."

Does it change any of my conclusions in my chimp genome paper (sadly enough, the most popular thing I've ever written)? Not really. On the one hand, this is yet another example of a part of the human genome that really does significantly differ from the chimp genome. I documented some of those in the article, including the size difference in the Y chromosomes. I concluded that these differences are quite minor features that are overwhelmed by the near-identity of the rest of the human and chimp genomes. In the case of the MSY, it's important to keep in mind that the chimp MSY sequence reported by Hughes et al. is only 25.8 Mb. That's slightly less than 1% of the entire genome. Given that fixed nucleotide differences between the human and chimp genomes are around 1%, having yet another 1% difference in the very different Y chromosomes doesn't make the genomes that much more different than they already were.

One other point I made in the chimp genome paper is relevant here: is signifcant that the regions of highest variation between the genomes are also sites of the highest polymorphism rates.
The Y chromosome certainly fits that bill. Variations in the human Y chromosome are known to be much higher than in the human autosomes, and there are lots of segmental duplications on the human Y chromosome. It's not terribly surprising that such variable regions of human DNA would also be quite different from their chimpanzee counterparts.

Unfortunately, I'm sure none of this will dampen the enthusiasm of those bent on denying the similarity of the human and chimp genomes.