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Crazy Y Chromosomes

A few weeks ago, I set myself some 2010 goals. One of which was to make sure that I fit in reading at least one paper every month. What I didn’t say though, was that I would try to do a quick blog post on each (to help keep me honest).

I forgot exactly how I found this paper, but the subject immediately caught my eye:

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

What? I had always been taught that the genomic differences between chimpanzees and humans were extraordinarily small, and since I’m male, I was also drawn to the fact that it would talk about a chromosome that was very near and dear to me.

What I read was pretty amazing. Despite the fact that we are very genetically similar to chimpanzees the Y chromosomes of our two species are actually very different. The best depiction of this that I can point to is from Figure 2 of the paper (below). The two charts below are dot plots which show where the human and chimpanzee chromosomes “line up”, so to speak. The right-hand chart shows how closely related the human chromosome 21 is to the analogous chimpanzee chromosome. You can see this from the nearly perfect diagonal line, showing that the two chromosomes are pretty close to identical as you move from one end of the chromosome to the other. The left-hand chart shows a similar comparison of a human Y chromosome and a chipmanzee Y chromosome. Notice the difference?


While it was fascinating to read what specifically was different (i.e. repeats, ectopic homologous recombination, introduction of nonsense mutations and open reading frames), what I found most interesting was the speculation as to why the Y chromosomes of two very similar species would diverge so much in such a narrow period of time. The research group’s hypothesis is that the Y chromosome holds a great deal of influence over sperm production, and because a Y chromosome will never have a “partner” chromosome the way that every other non-sex-determining chromosome does, changes in the Y chromosome are likely to have very significant changes in sperm characteristics. Because female chimpanzees oftentimes mate with multiple males, there is strong sperm competition and hence strong selective pressure for chimpanzees to have rapid evolution in the Y chromosome.

Of course, this is all just a guess. One way to test it would be to compare the human Y chromosome sequence with further primate species and see if primates where sperm competition is less intense have more similar chromosomes as humans. Another would be to see if any of the genetic changes resulted in clear sperm/testes genetic or transcriptional control differences.

But, all in all, a very cool start to what I’m hoping will be a fun 12 months!

(Figure 2 from paper)

Paper: Hughes, Jennifer F. et al. “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.” Nature 463, 536-539 (28 January 2010) – doi:10.1038/nature08700

Published in Blog


  1. I think a lot of the claimed similarities between human and chimp genomes doesn't take into account structural and copy number variation, especially since we're discovering more and more intraspecies variation as we analyze new genomes for more than just SNPs.

    For example, human chromosome 2 is a fusion of two chimpanzee chromosomes.

  2. […] It was the end of February yesterday – which means its time to read/blog about another paper! […]

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