A new look at the human Y chromosome has overturned longstanding ideas about its evolutionary history. Far from being in a state of decay, the Y chromosome is the fastest-changing part of the human genome and is constantly renewing itself.
The Y chromosome’s rapid rate of evolutionary change does not mean that men are evolving faster than women. But its furious innovation is likely to be having reverberations elsewhere in the human genome.
The finding was reported online on Wednesday in the journal Nature by a team led by Jennifer Hughes and David Page of the Whitehead Institute in Cambridge, Mass. In 2003, Dr. Page, working with scientists at the Washington University School of Medicine, decoded the DNA sequence of the human Y chromosome. He and the same Washington University genome team have now decoded the chimpanzee Y chromosome, providing for the first time a reference against which to assess the evolutionary history of the human Y.
The chimpanzee and human lineages shared a common ancestor just six million years ago, a short slice of evolutionary time. Over all, the genomes of the two species are very similar and differ in less than 1 percent of their DNA. But the Y chromosomes differ in 30 percent of their DNA, meaning that these chromosomes are changing far faster in both species than the rest of the genome.
In the case of chimps, their mating habits are probably the source of the fierce evolutionary pressure on their Y chromosome. When a female comes into heat, she mates with all the males in the group, setting up competition within her reproductive tract between the sperm of different males.
Many genes that govern sperm production are situated on the Y chromosome, and any genetic variation that improves a chimp’s chances of fatherhood will be favored and quickly spread through the population.
Sperm competition may have been important in the earliest humans, too, for some years after the chimp and human lineages split. Sperm competition could still play a role in human reproduction, some experts think, given the trickle of cases of heteropaternity, the birth of twins with different fathers.
Another reason for the intensity of selective pressures on the Y chromosome in both chimps and humans may be that natural selection sees it as a single unit, so a change in any one of its genes affects the survival of all the rest. On the other chromosomes, selection is more focused on individual genes because chunks of DNA are swapped between the members of each pair of chromosomes before the generation of eggs and sperm.
This DNA swapping process is forbidden between the X and the Y pair, keeping the male-determining gene from being transferred into the X chromosome, creating gender chaos.
But this prohibition has caused most of the genes on the Y chromosome to decay for lack of fitness. In the rest of the genome, a gene damaged by a mutation can be swapped out for the good copy on the other chromosome.
In the Y, which originally had the same set of genes as the X, most of the X-related genes have disappeared over the last 200 million years. Until now, many biologists have assumed either that the Y chromosome was headed for eventual extinction, or that its evolutionary downslide was largely over and it has sunk into stagnation.
Dr. Page’s new finding is surprising because it shows that the Y chromosome has achieved an unexpected salvation. The hallmark of the Y chromosome now turns out to be renewal and reinvigoration, once the unnecessary burden of X-related genes has been shed.
“Natural selection is shaping the Y and keeping it vital to a degree that is really at odds with the idea of the last 50 years of a rotting Y chromosome,” Dr. Page said. “It is now clear that the Y chromosome is by far the most rapidly evolving part of the human and chimp genomes.”
This does not mean that men are evolving faster than women, given that the two belong to the same species, but it could be that the Y’s rate of change drives or influences the evolution of the rest of the human genome in ways that now need to be assessed. It would be “hard to imagine that these dramatic changes in the Y don’t have broader consequences,” Dr. Page said.
Andrew Clark, a geneticist who works on the Y chromosome at Cornell University, said the Y’s fast turnover of DNA could effect the activity of genes throughout the genome, because just such an effect has been detected in laboratory fruit flies.
The decoding of the Y chromosome’s DNA was particularly difficult because the chromosome is full of palindromes — runs of DNA that read the same backward as forward — and repetitive sequences that confuse the decoding systems. Decoding the human Y took 13 years, and the chimp Y took eight years, Dr. Page said.
