The size difference between the X and Y chromosome can be seen in an image of the whole chromosome set for a human male. (National Human Genome Research Institute/Wikimedia Commons)

The popular theory that the Y chromosome is well on its way to losing all its genes is wrong, a new study suggests.

"Our empirical data fly in the face of the other theories out there," said Jennifer Hughes, lead author of the study, in a statement. "It's clear the Y isn't going anywhere."

Hughes, a biology researcher at the Massachussets Institute of Technology, and her colleagues, published their findings online in the journal Nature Wednesday.

The "rotting Y" theory is based on the fact that the tiny human Y chromosome, found just in males, has lost about 97 per cent of the 600 genes it once shared with the bigger, beefier human X chromosome, which is found in both males and females. The paired chromosomes were once identical and regularly traded genes with one another like the other 22 pairs of human chromosomes. But larger and larger sections of the X and Y stopped that kind of swapping starting around 300 million years ago, and the Y began losing genes.

David Page, director of the Whitehead Institute at MIT and a co-author of the new paper, said the rotting Y theory went viral and is now so pervasive that he can't give a public talk without being asked about it.

Hughes, Page and their colleagues decided to test the theory by comparing human and chimpanzee Y chromosomes with the Y chromosome of the rhesus macaque, a monkey that shared a common ancestor with humans 25 million years ago.

They found that all 18 genes on the oldest portions of the chromosome, which were inherited from that common ancestor, remained on the Y chromosome of both species — that is, they have remained stable for 25 million years. In a slightly newer part of the chromosome that formed about 30 million years ago, one gene has been lost in humans since they split from rhesus monkeys. All other differences between the Y chromosomes in the two species arose in the past 25 million years.

"The Y was in free fall early on, and genes were lost at an incredibly rapid rate," Page acknowledged in a statement. "But then it levelled off, and it's been doing just fine since."