Is The Y Chromosome Vanishing? A New Sex Gene May Be The Future of Men

Is The Y Chromosome Vanishing? A New Sex Gene May Be The Future of Men

Carly Cassella

Sat, December 6, 2025 at 12:00 PM UTC

5 min read

Is The Y Chromosome Vanishing? A New Sex Gene May Be The Future of Men

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In 2002, evolutionary biologist Jenny Graves shared a controversial calculation. The human Y chromosome, she wrote two years later in a commentary, "is running out of time."

The male-determining sex chromosome has lost 97 percent of its ancestral genes in the last 300 million years. If that rate continues, Graves calculated, it could vanish in several million more.

The doomed fate of the Y chromosome quickly took the media by storm, in many cases without the nuance Graves had intended.

Her evolutionary musings were not supposed to predict the 'end of males', or the termination of the human species; they were a 'back-of-the-envelope' calculation in an academic paper that nevertheless produced a "hysterical reaction".

"It really amazes me that anyone is concerned that men will become extinct in 5 or 6 million years," Graves told ScienceAlert. "After all, we have only been human for 0.1 million years. I think we'll be lucky to make it through the next century!"

Genetic Inheritance Humans — Typical genetic inheritance in humans. (ttsz/Getty Images)

But if Graves' calculation is correct, what does that mean for the Y chromosome – and what does it mean for the future of men?

The good news is that similar chromosomes in other mammals, as well as fish and amphibians, have lost their sex-determining status in genetic shuffles, with species continuing to tell the tale.

In some rodents, for instance, the Y chromosome has been completely and silently replaced. Three species of Y-less mole vole, for instance, Ellobius talpinus, Ellobius tancrei, and Ellobius alaicus, now have only X chromosomes. Sex-determining genes on their Y chromosomes were shifted elsewhere.

Spiny rats (Tokudaia osimensis), meanwhile, lost their Y chromosome to a new version, which now acts as a sex-determiner in its stead.

"If a new variant … should arise that works better than our poor old Y, it could take over very rapidly," predicted Graves. "Maybe it already has in some human population somewhere – how would we know?"

After all, sex-determining variants aren't routinely screened for in genome studies, and if the Y chromosome's role transferred to another chromosome in a population, there'd be no obvious differences. There would still be males, and they'd still be able to reproduce.

The fate of the Y chromosome has captured the world's attention for years now, and yet beneath the surface of sensationalized headlines, many don't realize a potent scientific debate is brewing, throwing two incompatible views of evolution into direct conflict.

One school of thought, which Graves subscribes to, frames the sex chromosome as a crumbling old-timer that is doomed to vanish and could be replaced at any moment. The other school positions the Y chromosome as a tenacious survivor, at last safe and stable.

Evolutionary biologist Jenn Hughes from MIT's Whitehead Institute agrees with this latter interpretation. For over a decade now, Hughes and Graves have respectfully disagreed over how to interpret the same evidence, partaking in open academic argument.

In 2012, Hughes and her colleagues found that very few core Y genes have been lost in the human lineage over the past roughly 25 million years.

More recent evidence has strengthened that argument, suggesting there is deep conservation of core Y genes in primates – compared to fish and amphibians, which display gradual deterioration of their Y chromosomes – and some scientists, such as Hughes, interpret this as long-term evolutionary stability of the Y chromosome in primates.

"Our work comparing Y gene content across many mammals showed that the gene loss was rapid at first, but quickly leveled off, and gene loss has essentially stopped," Hughes told ScienceAlert.

"The genes that are retained on the Y serve crucial functions across the whole body, so the selective pressure to maintain those genes is too great for them to be lost."

Graves disagrees with these interpretations. Just because a gene is deeply conserved does not mean it can't be replaced, she argues.

Plus, the additional genes found in the human Y sequence in recent years are largely repeat copies, she says, some of which could be inactive.

Y Chromosome Repair — How a Y chromosome repairs itself without a second copy, as there are with two X chromosomes. (Silber, Middle East Fertility Society Journal, 2011)

In the past, Graves has called the Y chromosome the "DNA junkyard". Creating lots of copies of a gene can boost the odds that at least one survives, Graves explains, but it can also create evolutionary 'duds' by accident.

It's sort of like a game of telephone. The more a message is shared, the more likely it is to last, but it is also more likely to become distorted.

So why is the Y chromosome like this?

Evolution is to blame.

"In the ancestor of placental mammals, the X and Y chromosomes were identical and had about 800 genes," Hughes told ScienceAlert.

"Once the Y became specialized for male sex determination (about 200 million years ago), the X and Y stopped recombining in males, and the Y started losing genes. Meanwhile, the X could still recombine in XX females, so it remained largely unchanged."

Today, the human Y chromosome has only 3 percent of the genes it once shared with X. But these genes weren't lost at a constant rate. That's the biggest misconception, argues Hughes.

Graves agrees.

Her projected extinction date of 6 million years or so is based on a straight, unflappable deterioration of the Y chromosome, but she says that is highly unlikely, which means the estimate has a wide range of error.

"Anything from now to never," Graves told ScienceAlert. "I was surprised it was taken so seriously!"

While at certain moments it may look like the Y chromosome is stabilizing, Graves argues that these snapshots won't last, even if they have seemingly persisted for 25 million years.

"I don't see any reason to suppose that Y degradation has, or could halt in primates, or any other mammal group," Graves said. "It's slow and proceeds in fits and starts, for reasons we well understand."

After a public debate between Hughes and Graves in 2011 on whether the Y chromosome is stable or doomed, the audience at the 18th International Chromosome Conference voted 50/50. They were split right down the middle on which hypothesis was correct.

Let's hope it doesn't take 6 million years for a tie-breaker.

Is The Y Chromosome Vanishing? A New Sex Gene May Be The Future of Men

Is The Y Chromosome Vanishing? A New Sex Gene May Be The Future of Men

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