Some time ago, the future of the human Y chromosome was called into question. After all, other species, such as mole voles and spiny rats, have lost their Y chromosomes, and sex-determination responsibilities have fallen to other chromosomes.

In fact, the human Y did not start off as a sex-determining chromosome either. Human X and Y chromosomes were once a pair of autosomes, like the 22 others we carry, and sex was determined by environmental factors rather than genetics. The ancient X and Y swapped gene copies during crossing-over, just like the other autosomes, to maintain genetic diversity and eliminate potentially harmful mutations. About 300 million years ago, however, one part of the X stopped swapping with the Y, then another, a third, a fourth and—about 30 million years ago—a fifth. As a result, the corresponding portions of the Y chromosome decayed, and it eventually lost ∼97% of the genes that it once shared with its partner, the X chromosome. It seemed that the Y was disappearing. Some said this was happening at an unsustainable rate, that it would be gone altogether within 10 million years. Prospects seemed dim for the withered Y.

But new research from Jennifer F. Hughes, David C. Page (both of Whitehead Institute, Massachusetts Institute of Technology, Cambridge) and colleagues suggests that reports of the Y's demise may be exaggerated. Hughes and Page specifically looked at recent degeneration of the human Y chromosome by comparing it with the Y of the rhesus macaque (Macaca mulatta); the two species shared a common ancestor that lived about 25 million years ago. Since that time, the macaque Y has not lost a single gene, and the human Y has lost only one (Nature doi:10.1038/nature10843; published online 22 February 2012). The lost gene is located in an unstable portion that makes up only 3% of the chromosome.

Hughes stated in a press release, “With no loss of genes on the rhesus Y and one gene lost on the human Y, it's clear the Y isn't going anywhere.” The results lead to a new understanding of the evolution of the human Y as a process featuring periods of decline separated by periods of stability. “We've been carefully developing this clearcut way of demystifying the evolution of the Y chromosome,” Hughes said. Page explained, “The Y was in free fall early on, and genes were lost at an incredibly rapid rate. But then it leveled off, and it's been doing just fine since.”