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A Rat Without a Y Chromosome Could Reveal Human’s Genetic Future

Ferreira's spiny Tree Rat
A Rat Without a Y Chromosome Could Reveal Human Genetic Future Credit: Antoine Baglan CC-BY-4.0 / Wikimedia Commons

A spiny rat  that has lost its Y chromosome has been discovered by researchers in the Amami Islands. The finding could reveal the future of human genetics.

The rattus – its scientific name – from the island in the Ryukyu archipelago of Japan, perplexed biologists for decades as the loss of Y chromosome implies the loss of males and with, the species demise.

According to the researchers, the Y chromosomes in many mammals including humans has, over the past tens of millions of years, drastically reduced, which could possibly lead to extinction.

Asato Kuroiwa from the Hokkaido University in Japan stated that the spiny rat shows how such an event might happen which, by consequence, indicates that humans may be prone to the same fate. Kuroiwa and her colleagues have also determined that one of the rat’s normal chromosomes has effectively evolved into a totally new male sex chromosome.

What is the Y chromosome?

A sex chromosome pair is composed of a combination of X and Y chromosomes. The X chromosome is the female sex-determining chromosome and the Y the male sex-determining chromosome.

Y chromosome
Y chromosome. Credit: Christinelle Miller, CC-BY-SA-4.0 / Wikimedia Commons

The Y chromosome contains a gene called SRY that activates the “male” genes on other chromosomes and, most importantly, the SOX9 gene that triggers the development of testes.

The Amami spiny rat (Tokudaia osimensis) is one of just a handful of mammals that lack Y chromosomes. What’s more, females as well as males have only one X chromosome. However, the existence of female mammals shows that the shrunken Y doesn’t contain any crucial genes, so cells and individuals can survive its loss.

In fact, recent studies show it is often lost from cells as men age, although the loss of the chromosome from an entire population should have resulted in their eventual eradication due to the fact that there were no more males.

How male spiny rats still exist without the Y chromosome

Whiteheads Spiny Rat
Spiny Rat Credit: Konstans Wells CC BY 4.0 / Wikimedia Commons

In order for the researchers to identify how male spiny rats still exist, the team first sequenced the genomes of several males and females, which didn’t reveal any variants unique to males. Kuroiwa and her team then looked more closely, and found that one of the two copies of chromosome 3 in the male rates has a duplicated region that is right next to SOX9.

They therefore carried out several experiments, including adding the duplicated region to mice – to show that this duplication boosts the activity of SOX9 and thus effectively replaces SRY. What this implied was that during duplication, the chromosome 3 becomes a “proto-Y”, while the version without duplication a “proto-X”.

According to Robin Lovell-Badge at the Francis Crick Institute in London, one of the researchers who discovered the SRY gene, the team deleted the duplication in the rodents to show that no males develop in order to prove it beyond doubt.

Yet because they are an endangered species, such experiments are not allowed. Nevertheless, Lovell-Badge said, “…the evidence they have is all quite convincing.”

That being said, since duplications of that type are difficult to spot, it could explain why previous attempts to explain how male spiny rats became male had been futile. One theory is thus that duplication must have started to arise sometime 2 million years ago when the mammals diverged from a related species that still had the Y chromosome.

What it implies if so is that once the duplication has happened, the loss of the Y chromosome would no longer result in the loss of all males. Still, it is the belief of Kuroiwa  that a mixed population of males with and without Y chromosomes probably existed together on the island for some time.

The chromosome controversy in humans and rats

During the study, Kuroiwa noted that the male rats with the Y chromosome were fewer on the island, though that fact was most likely due to rising seas. This left only the males without.

“At some point in the past, the sea level rose and the land area was much smaller,” she said.

“I think this is a brilliant piece of work. The evidence is very compelling,” Jenny Graves at La Trobe University in Melbourne, Australia, stated. “There’s no reason to think our Y chromosome is any more robust than the spiny rat’s.”

In 2002 however, Graves controversially claimed that the human Y chromosome would eventually fade out in around 10 million years.

XY Chromosomes
XY Sex determination chromosomes. Credit: Yassin Mrabet, CC-BY-SA-4.0 / Wikimedia Commons

Kuroiwa also concurs with Graves. In her words,  “I absolutely agree with Jenny, I also believe that the Y chromosome will disappear.”

Kuroiwa further noted that because both sexes in the Amami spiny rat now have only a single X chromosome, it’s possible that they could as well vanish over time.

“Since it is unstable and mutations are accumulating, I think that X will eventually disappear.”

There is though the chance that, if the descendants of the Amami spiny rat survive long enough, its proto-X and proto-Y chromosomes are likely to evolve along the same lines as the X and Y, with the proto-Y shrinking and becoming distinct from the proto-X.

In contrast, Lovell-Badge points to a number of studies which suggest that the Y chromosome is doing just fine and is in absolute yno danger of disappearing from either humans or other mammals.

“I think the paper makes it pretty clear that the loss of a Y chromosome in mammalian evolution is a very rare event,” he declared.

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