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A comparison of Y chromosomes in eight African and eight European men dispels the common notion that Y genes are mostly unimportant or may even be destined to continue to dwindle and eventually disappear.
"The Y chromosome has lost 90 percent 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," adds evolutionary biologist Melissa A. Wilson Sayres, a Miller Postdoctoral Fellow in the Department of Integrative Biology 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. Last month, researchers reported shuffling some genes in mice to create Y-less males that could produce normal offspring. This lead some commentators to wonder whether the Y chromosome is superfluous.
Wilson-Sayres and coauthor Rasmus Nielsen, UC Berkeley professor of integrative biology, report in PLOS Genetics that patterns of variation on the Y chromosome, among 16 men, are consistent with natural selection. They maintain that much of the content of the Y gene plays a role in male fertility. Although puny – 27 unique genes versus thousands on other chromosomes – its size is simply a sign the Y is lean and stripped down to essentials.
"Wilson-Sayres's results are quite stunning. They show that because there is so much natural selection working on the Y chromosome, there has to be a lot more function on the chromosome than people previously thought," Nielsen said.
Variations in Y chromosomes are used to track how human populations moved around the globe, and according to Nielsen, the new research will help improve estimates of human evolutionary history.
"Melissa has shown that this strong negative selection – natural selection to remove deleterious genes – tends to make us think the dates are older than they actually are, which gives quite different estimates of our ancestors' history," Nielsen said.
Y has degraded over the past 200 million years
Before about 200 million years ago, when mammals were relatively new on Earth, early versions of both sex chromosomes, X and Y, were just like any other pair of chromosomes. With each generation, X and Y swap a few genes so that offspring are a mix of their parents' genes. Fertilized eggs that got two proto-X genes became female and eggs with one proto-X and one proto-Y became male.
But according to Dr. Wilson-Sayres, for some reason the gene that triggers a cascade of events resulting in male features became fixed on the Y chromosome. That attracted other male-specific genes, such as those that control development of the testes, sperm and semen. Many of these genes turned out to be harmful to females, so the X and Y stopped swapping genes and the two chromosomes began to evolve separately.
"Now that the X and Y do not swap DNA over most of their length, the Y cannot efficiently fix mistakes and has degraded over time," she adds. "In XX females, the X still has a partner to swap with and fix gene mistakes, which is why we think of the X as not degraded."
Wilson-Sayres was fascinated by the strange history of the sex chromosomes and in particular the lack of genetic variation worldwide on the Y chromosome. Gene variation markers seen in DNA on non-sex chromosomes, are used to chart human population migration through history — but are poorly characterized across the entire Y chromosome.
"Y chromosomes are more similar to each other than we expected," said Wilson-Sayres. "There has been some debate about whether this is because there are fewer males contributing to the next generation, or whether natural selection is acting to remove variation."
Did fewer males contribute genes to Y chromosome?
Wilson-Sayres: "We show a model of purifying selection acted on the Y chromosome, removing harmful mutations. That process, combined with a moderate reduction in the number of males passing on their Y chromosomes, can explain low Y diversity."
Researchers also found that all 27 genes on the Y chromosome –17 retained after 200 million years and 10 genes recently acquired (though poorly understood) – are likely the result of natural selection. Most of the newer genes, called ampliconic genes*, are present in multiple copies on the chromosome. Loss of one or more of these copies has been linked to male infertility.
*[From Wikipedia, the free encyclopedia: An amplicon is a piece of DNA or RNA that is the source and/or product of natural or artificial amplification or replication events. It can be formed using various methods including polymerase chain reactions (PCR), ligase chain reactions (LCR), or natural gene duplication. In this context, "amplification" refers to the production of one or more copies of a genetic fragment or target sequence, specifically the amplicon. As the product of an amplification reaction, amplicon is used interchangeably with common laboratory terms, such as PCR product.]
"These ampliconic regions that we haven't really understood until now are evidently very important and probably should be investigated and studied for issues of infertility," said Wilson-Sayres.
Wilson-Sayres was able to precisely measure Y variability by, for the first time, comparing Y's variation with variations found in that same person's other 22 chromosomes (autosomes), their X chromosome, and with their mitochondrial DNA. She compared whole genome data from 16 men whose DNA had been sequenced by the Mountain View-based company Complete Genomics Inc.
Most of the 1,000+ human genomes already sequenced do not have sufficient accurate coverage of the Y to make this type of comparison among individuals, but advances in technology to better characterize DNA will facilitate future analyses of the Y chromosome, Sayres concluded.
The work was funded by UC Berkeley's Miller Institute. Kirk Lohmueller of UCLA is a coauthor of the paper.