DEATH OF THE Y: Does the human Y-chromosome have a future?

They are enriched in high-, middle- and low-copy repetitive sequences and contain only a few functional genes. ,,, Y chromosomes: born to be destroyed.

There has been a large accumulation of “junk” in the human genome – about 42% is “retrotransposons” – jumping non-functional genes that easily form multiple copies, amplifying themselves and possibly destroying other genes when they jump. Most of this junk is archaic DNA which through mutation is no longer able to jump or duplicate.

The amount of this retrotansposon junk is very much greater in non-recombinant DNA suh as the human Y-chromosome since it is not removed by evolutionary pressure and, is not cleaned out by the recombination process, which employs a range of protective safeguards against bad copying and intrusive elements).

Hypothetical formation of the Y-chromosome – after Steinemann and Steinemann (2005)

The Y chromosome formed around 160 million years ago when an ancestral mammal developed a sex locus, now called the SRY gene, which causes testicular development. This gene sat on one of two copies of the X chromosome. Subsequently during recombination, a number of other genes useful to males translocated near to SRY in this chromosome or were created there. After that, recombination between X and Y proved harmful, and recombination on this region was suppressed. About 95% of the chromosome – all except for a small area at the tips – was then unable to recombine and was passed on virtually intact to sons.

The Y chromosome has very high rates of mutation because it comes entirely from the sperm, which have to split and rearrange three times during meiosis, with limited chance to check and repair against a duplicate. Natural selection against intrusive elements does not occur very well in non-recombinant DNA. Individual alleles cannot be exposed to natural selection, so that deleterious alleles can hitchhike easily on a good gene. The reverse can also occur – good genes can be lost if they are surrounded by bad ones. Also many perfectly viable lines die out randomly when terninated by girls. This all contributes to the degeneration of Y (in that lines with good Y die out while lines with bad Y live on); and of non-recombinant DNA more generally.

During the lifetime of men, the splitting of sperm cells in mitosis is particularly subject to damage, which is why the fertility of males deteriorates with age and the likelihood of birth defects is greater for older men.

In April 2013 Prof Jenny Graves of Melbourne attracted a good deal of attention when she announced that because of the inherent fragility of the male Y-chromosome and the lossof almost all its functional genes, it would “soon” crumble, making men extinct.

Subsequent investigation has shown that in fact we have not lost any functional genes on the Y chromosome from the time of our branching with chimpanzees 6 million years ago, and only one since diversion with the rhesus monkey 35 million years ago. That is, almost all  of the gene loss from Y took place before 35 million years ago, and quite possibly in the “early” years of the Y. 

In the 58 million base pairs oif the Y-chromoisome, it appears we do not need more than the 86 or so functional genes coding for only 23 distinct proteins to handle our sex differences. It may be that these 86 genes, surviving as they have for 35 million years, have “learned” to defend themselves living in a tangle of useless DNA, which might even act like some sort of styrofoam  packaging protecting the vital materials.

One mechanism by which the Y-chromosome protects itself is by built-in palindromes over critical areas important for male fertility. The Y-chromosome is able to recombine with itself using these palindromes to edit out mistakes and maintain the integrity of the few functional genes. It apparently uses  reversed copies of these genes on itself as a template for verification instead of having a second homologous chromosome.

One wonders from all this if our hard discs could use a clean – if we knew how to do it. The primary driver of our existence is so flawed, random and inefficient it is astonishing it works at all – no machine of our devising could work carrying this kind of useless load. It is not surprising that some are calling the genome  “Unintelligent Design”.

References 

Graves, J. A. M. (2004). "The degenerate Y chromosome—can conversion save it?". Reproduction Fertility and Development 16 (5): 527–534

Graves, J. A. M. (2006). "Sex chromosome specialization and degeneration in mammals". Cell 124 (5)

Steinemann, S&M (2005). Y-chromosomes: born to be destroyed. Bioessays 27.