"The Y chromosome has lost 90 per cent of the genes it once shared with the X chromosome, and some scientists have speculated that the Y chromosome will disappear in less than 5 million years," said evolutionary biologist Melissa A Wilson Sayres at the University of California, Berkeley, and lead author of the new analysis.
Some mammals have already lost their Y chromosome, though they still have males and females and reproduce normally.
Also, last month, researchers reported shuffling some genes in mice to create Y-less males that could produce normal offspring, leading some commentators to wonder whether the chromosome is superfluous, the new study said.
"Our study demonstrates that the genes that have been maintained, and those that migrated from the X to the Y, are important, and the human Y is going to stick around for a long while," Wilson Sayres said.
Wilson Sayres and colleagues compared Y chromosomes in eight African and eight European men and found that patterns of variation on the Y chromosome among the 16 men are consistent with natural selection acting to maintain the gene content there, much of which plays a role in male fertility.
The Y chromosome's puny size - it contains 27 unique genes versus thousands on the other chromosomes - is a sign it is lean and stripped down to essentials, researchers said.
As the X and Y chromosomes evolved, male-specific genes became fixed on the Y chromosome. Some of these genes were detrimental to females, so the X and Y chromosomes stopped swapping genes.
This meant the Y chromosome was no longer able to correct mistakes efficiently and has thus degraded over time.
There is low genetic diversity in the human Y chromosome, and researchers were able to precisely measure this by comparing variation on a person's Y chromosome with variation on that person's other 22 chromosomes, the X chromosome and the mitochondrial DNA.
The researchers then showed that this low genetic diversity cannot be explained solely by a reduction in the number of males passing on their Y chromosome.
Instead, the low diversity must also result from natural selection, in this case purifying selection (the selective removal of deleterious alleles).
"We show that a model of purifying selection acting on the Y chromosome to remove harmful mutations, in combination with a moderate reduction in the number of males that are passing on their Y chromosomes, can explain low Y diversity," added Wilson Sayres.
The study was published in the journal PLOS Genetics.