The Atavism

Friday, January 15, 2010

The why of the Y-Chromosome's amazing evolutionary rate

There is something faintly pathetic about the Y-chromosome when its lined up with its peers in a karyotype. Each of the 22 numbered chromosomes pair off with a near identical partner just their size while the Y has to shape up to the X which has more than twice as much DNA and 25 times as many functional genes.

The puny Y-chromosome only looks worse when you realise that mammalian sex chromosomes weren't always so mismatched. 160 million years ago the X and Y were just another pair of chromosomes, albeit the pair that the carried the sex determining gene SRY. Over time the chromosome that went on to become the Y stopped swapping genes with its partner, allowing it to maintain a suite of genes that are beneficial in male bodies but not in females. It's the lack of genetic recombination that sent the Y into its decline. Genes on any other chromosome can be swaped between pairs, meaning over many generations individual gene copies (called alleles) are exposed to natural selection independently of alleles either side of them. The same process doesn't apply to alleles on the Y-chromosome. Since the Y is always passed on as a single unit natural selection acts on the whole thing - a broken gene might make it into the next generation because it is attached to beneficial mutations. The efficiency of natural selection is further reduced in the Y-chromosome because it has a relatively small effective population size (less that one quarter of that for normal chromosomes since only males carry the Y and then in only one copy and even then a larger number of males than females don't contribute to the next generation) which makes genetic drift a strong force.

What we've known about the Y-chromosome's past has has shaped out ideas about what it is now and what it will become. Until quite recently the Y was seen as more or less a derelict chromosome, a few broken remnants of the genes still found on the X and a couple of male-specific genes hanging on the the sex determining gene SRY. People have even go so far as to extrapolate the Y's long slow decline to a future time at which the Y will simply disappear. The first clue that the Y-chromosome might be a little more resilient than that came in 2003. The publication of the complete sequence of the human Y-chromosome revealed more than fossils from the Y's more substantial ancestor. There are plenty of those so called "X-degenerate" segments but most of the active genes in the Y are in large repetitive runs of DNA called the "ampliconic regions". The genes in these regions are mainly made of DNA sequences unique to the Y chromosome and are expressed only in the testes - suggesting the Y has been making its own genes at the same time that its been losing the X-degenerate ones.

Untill this week it has been hard to test the idea of a regenerating Y-chromosome in an evolutionary framework. Those large repeated runs of DNA are very hard to sequence (the standard metaphor is putting together a jigsaw puzzle made entirely of sky) so we haven't had another Y-chromosome sequence to compare ours with. Now, thanks to Jeniffer Hughes and colleagues, we do and the result it stunning. Not only has the Y-chromosome been making genes, it's been making them at an outrageous rate. Thirty percent of our Y-chromosome sequences have no counterpart in the chimpanzee. As the authors say that's the sort of divergence you'd expect to see between humans and chickens, which are separated by 310 million years of evolution not humans and chimps which only split 6 million years ago!

It's evident that, far from being in the tail end of an inexorable decline, the Y-chromosome is evolving a good deal more quickly than the rest of the genome. So, the burning question is what is behind that evolutionary rate? There is probably no single answer to that question but it's safe to assume it results from some of the unique features of the Y-chromosome; a lack of genetic recombination, the presence of those large repetitive sections of DNA and the preponderance of male specific genes.

It's usually a good idea when trying to explain an evolutionary phenomenon to think of explanations that don't invoke natural selection as the main driver as a sort of null hypothesis against which to test other ideas. In this case the increased fixation of new genes on the Y-chromosome might simply reflect an increased rate of production of new genes. Those highly repetitive sections of the Y-chromosome are the perfect substrate for a process called ectopic gene conversion in which a Y-chromosome can recombine with itself and as a result duplicate streches of DNA. We know from human studies that a process like this has made wide scale structural changes in the last 100 000 years and it might be enough to explain the Y's unusual gene production.

I think it's very likely that natural selection also plays a role in the number of of those new genes that become fixed in the human and especially the chimp lineage. Most of the active genes on the Y-chromosome are expressed in the testes and involved in sperm production. Chimpanzees are highly polygynous polygynandrous [Thanks to Harvest Bird for pulling me up on this,], in most cases a female will mate with each of several dominant males in a troop, and a result sperm competition is an important level of selection. Although humans aren't as polygamous as chimps (and likely haven't been in our recent history) it's clear that fertility selection is still an important force and we know for sure that mutations in the Y-chromosome can lead to infertility so, again, the fate of new genes on the Y-chromosome are likely to be driven by selection.

Both the adaptive and non-adaptive explanations above might will be influenced by the lack of recombination in the Y-chromosome. The reduction in the efficiency of natural selection described above will stop very slightly deleterious mutations from being driven to extinction which might mean new genes that would be selected against on any other chromosome become fixed on the Y. This phenomenon can be enhanced when it is coupled with selection producing a 'selective sweep'. If a new beneficial mutation, perhaps associated with sperm competition or fertitily selection, pops up in on a chromosome with a bunch of other mutations that whole thing will be selected for and driven to fixation which has the potential to make for large scale changes quickly.

It is likely that the amazing evolutionary rate of the Y-chromosome is a result of some combination of all these factors but it should be possible to disentangle at least some of their contributions. If sperm competition is a major driver of Y-chromosome evolution then it follows that animals that go in for purely monogamous relationships will have comparatively low rates. Evolution has furnished us a natural experiment to test this idea, all gibbon species form pair bonds and are highly monogamous. We could test the sperm production hypothesis by sequencing the Y-chromosome of two gibbon species and calculating the rate of evolution of a Y-chromosome in a monogamous species. .Although I'm happy to present the test of this idea I'm not going to line up to do it, those repetitive sections of DNA make sequencing Y-chromosome so hard that it took 13 years to do the human one and 8 to finish the chimp one.

Hughes, J., Skaletsky, H., Pyntikova, T., Graves, T., van Daalen, S., Minx, P., Fulton, R., McGrath, S., Locke, D., Friedman, C., Trask, B., Mardis, E., Warren, W., Repping, S., Rozen, S., Wilson, R., & Page, D. (2010). Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content Nature DOI: 10.1038/nature08700

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Posted by David Winter 2:24 PM


I enjoyed this from the most self-interested perspective, since I don't yet know if my passenger is travelling with a Y-chromosome or not.

One minor point: you mention the polygyny of chimpanzees, the former a term which I understand to mean a single male with multiple female partners. Given that you explain how "a female [chimp] will mate with each of several dominant males in a troop", do you mean polyandry (single female, multiple male partners)? Or have I misunderstood?
Oh no, I've been schooled! The sad truth is that I, typically, misspelled 'polygamy' in such a way as to fox my spell check! I'll edit the text accordingly

Have you made a decision to not know about your passenger's chromosomal compliment or is yet to make itself clear?
Consider it spelling For Science!

The passenger is a few weeks shy of discernible sexual characteristics, and assuming s/he is facing the right way at the next scan, I am keen to know (and the Y-Chromosome bearer who put me in this condition is happy enough to go along with this plan).
hi! really liked your blog.. very cool findings.. but you meant polyandrous right? and not polygynandrous? they both have slightly different meanings.
Hi Athena.

Sorry for taking such a long time to reply to your comment. It's been on my TODO list, but when "write your god damned thesis" is #1 then the later ones tend to get ignored!

You can tell I got a bit tangled up in those words, *I think* polygynandrous is right in that only the dominate males mate with females and both males and females mate with mutliple partners.

Of course, the sensible thing would have been just describing the relationship and why it makes sperm competition relevant. If adding a word doesn't add to the readers understanding then what's it doing there? ;)

Actually, I might propose those words for Carl Zimmers black list.
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