Y Chromosome IV: Recombination Suppression

ResearchBlogging.orgLast time we discussed the discovery of “evolutionary strata” on the human X chromosome – there are distinct blocks on the X that stopped recombining with their Y-homologs at different times causing the Y chromosome’s genes to appear scrambled in order. How can this happen?

Note: I apologize for the lack of pictures. None of the figures presented in the articles were quite to my liking.

So why would recombination be suppressed between the X and Y chromosomes?

The prevailing hypothesis is sexual antagonism. A male-specific gene expressed in females could negatively impact female fitness, or vice versa – sexually antagonistic – and so natural selection will favor a way of keeping sex-specific genes from being expressed in the opposite sex. However, even if male-specific genes are located on the male sex chromosome, recombination can always move that gene to the female chromosome. Thus when a chromosomal inversion takes place around the male gene, the sequences between the sex chromosomes no longer align, and recombination can’t occur. Selection would further favor the translocation of other sexually antagonistic genes to the sex chromosomes and the cycle would repeat as recombination is suppressed down the chromosome. (Note that the recombination suppression helps cause Y chromsome degeneration – a byproduct of what was once selectively beneficial.)

This is heavily simplified but that’s the gist – natural selection favors the suppresion of sexually antagonistic gene expression in the wrong sex.

Are there any problems with the hypothesis? I was initially skeptical of all sexually antagonistic genes making their way to to the suppression regions but then I realized the translocation of a master control gene to the sex chromosome instead could solve the problem, like how SRY controls autosomal genes that control testis-differentiation. I’m also skeptical because sex chromosome systems are widely variant across taxa, especially in their initial evolution. I doubt proponents of the sexual antagonism believe this to be true anyway, so don’t accuse me of attacking a strawman!

Joseph Ironside (2010) is also skeptical.

One of Ironside’s qualms with the sexual antagonism hypothesis is that it only explains recombination suppression in the sex chromsomes but can’t explain similar phenomena in the autosomes. Instead, Ironside believes explanations of the latter could explain the former. These include:

1) Genetic drift. Perhaps the recombination suppression (chromsomal inversions) is selectively neutral in a small population. It becomes difficult to explain its spread into the larger population afterward, however.

2) Selection preventing homozygosity. I unfortunately do not understand this. I’ve read the article Ironside cites but it doesn’t make sense to me. I’ll just quote what Ironside says:

The hypothesis that chromosomal rearrangements spread through selection to prevent homozygosity of deleterious recessive genes at multiple loci was proposed by Charlesworth and Wall (1999). Their models demonstrate that, in populations with moderate levels of inbreeding, selection to maintain heterozygosity at two loci can favour the spread of neo-sex chromosomes generated by centric fusions or reciprocal translocations.

If anyone can explain that, please do! It almost sounds like sexual antagonism – does “deleterious recessive genes” mean sexually antagonistic in this context? If so, I presume heterozygosity indicates the recessive gene is now only found on one of the sex chromosomes? I think I almost get it. Anyway,

3) Dobzhansky’s “super gene.” Two loci may increase fitness to a higher degree when together rather than separated. In this case, if a chromosomal inversion occurs preventing recombination from breaking the pair, they would always be inherited together – a “supergene.” Note that this is similar to sexual antagonism and may in fact supercede that hypothesis – sexual antagonism is explained by the supergene.

Interestingly, Ironside notes that the supergene hypothesis assumes something called overdominance which is basically heterozygote advantage (think sickle cell anemia and malaria). At first I didn’t understand why overdominance was required but after some thought I realized that for the supergene/inversion to be maintained, both homologous chromosomes can’t have the inversion or else recombination could occur. Duh!

Ironside continues his article by investigating whether or not past experiments have validated the sexual antagonism hypothesis. He says no. While theoretically possible, the empirical support is lacking.

So what to take away from this?

– Recombination is really damn confusing.

– Chromosomal inversions prevent linked loci from being broken apart and as additional sexually antagonistic genes are translocated (and selectively favored to stay) to these regions, recombination suppression marches down the chromosome, creating “evolutionary strata.”

– However, why recombination suppression occurs is still debated.

Next time we will discuss the next region class – the ampliconic sequences. How big are the palindromes? and why are there palindromes anyway? will be the driving questions. Thanks for reading!

P.S. I apologize for the lack of scholarship in this post. Recombination at this depth is fairly new to me and the methods are currently beyond my understanding, although I try. I feel like a lot of assumptions of the reader’s knowledge are made (not a bad thing, necessarily) and so I cannot always connect the dots. Sometimes with some thought I can comprehend what the authors say, and sometimes I just cannot make sense of it. I’m not even sure where to look for background either.

Joseph E. Ironside (2010). No amicable divorce? Challenging the
notion that sexual antagonism drives
sex chromosome evolution Bioessays, 32, 718-726 : 10.1002/bies.200900124

5 thoughts on “Y Chromosome IV: Recombination Suppression

  1. Hey-

    I really enjoy your blog, I think I’m adding it to my google reader blog list. Keep posting interesting science at the rate you are doing now, and you will become far more well-known.


    • The 1999 Charlesworth / Wall paper addresses a specific situation: a population with high levels of inbreeding, and also an allele with significant heterozygote advantage.

      Normally, inbreeding leads to rapid loss of heterozygosity. However, if you suppress recombination across a portion of the sex chromosomes, it allows the population to fix one allele on the Y and the other on the X, thus enforcing heterozygosity. Since we’re postulating an allele with heterozygote advantage, this is thus favoured.


      Regarding the supergene model, there’s a simpler way to think about it.

      Consider a mutation somewhere in the pseudoautosomal region that happens to promote male fitness. Maybe it makes sperm swim faster, bind to the egg better, or some such. That allele is useless in a female context – it would be advantageous to maintain tight linkage between the “good sperm” gene and the sex determining gene. Hence, suppression of recombination to preserve that association. A supergene is just another term for a linkage group where the genes have related functions.

      It’s similar to the sexual antagonism model, but doesn’t require the gene to have a deleterious effect in females.


      • But it doesn’t strictly enforce heterozygosity. If it did, we’d all be male! What it can do is permit enforced heterozygosity in males if you fix one allele on the X and the other on the Y. The counterpart to that is that it enforces homozygosity in females.

        I’m not a modeller, but I think you need a quite special combination of circumstances to make it work – heterozygote advantage for the allele you’re selecting on, plus homozygosity in females needs to be not *too* disfavourable, plus high amounts of inbreeding to mean there’s a substantial risk of losing heterozygosity in the first place.

        (Note: I’m talking about enforeced hetero-/homozygosity for ease of illustrating the argument. You could also have a situation with one allele fixed on the Y and a mix of both alleles in the X population.)


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