NEW YORK (GenomeWeb News) – The rapid gene loss and genetic "decay" that characterized early Y chromosome evolution has tapered off, with the male sex chromosome remaining relatively stable for tens of millions of years, according to a study published online today in Nature.
A Whitehead Institute for Biomedical Research-led group sequenced 11 million bases of the rhesus macaque's Y chromosome. By comparing this sequence to the same Y chromosome region in humans and chimpanzees, the team garnered evidence that the male sex chromosome has conserved almost all of its genes over the past 25 million years or so.
That pattern stands in stark contrast to the evolutionary decay that marked much of the Y chromosome's first 200 to 300 million years, researchers explained, suggesting its prospects are probably not as bleak as some had imagined.
"The Y [chromosome] was in free fall early on, and genes were lost at an incredibly rapid rate," the study's senior author David Page, director of the Whitehead Institute, said in a statement. "But then it leveled off, and it's been doing just fine since."
Once two members of an autosomal chromosome pair, X and Y chromosomes began morphing into distinct sex chromosomes around 200 to 300 million years ago, Page and his co-authors explained. Since then, a series of so-called "stratification events" curbed genetic exchange between the X and Y chromosomes, which had swapped bits of genetic material through the process of crossing over during their autosomal chromosome days.
As chunks of sequence in the male-specific region of the Y chromosome stopped trading genetic material with the X chromosome, these regions became prone to deletions and gene loss, the researchers explained. Over five such stratification events, the human male-specific region of the Y chromosome, or MSY, lost all but around 3 percent of the genes originally shared by the X and Y chromosomes' autosomal pre-cursors.
That evolutionary history fueled speculation by some that the Y chromosome might continue decaying to the point of extinction.
Still, while researchers had evidence for evolutionary decay on the Y chromosome as recently as 30 million years ago in the ancestors of Old World monkeys and primates in the human lineage, more recent Y chromosome patterns were less well understood.
"Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome, remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage," the study authors explained.
In an effort to retrace these more recent evolutionary patterns, the team used bacterial artificial chromosome sequencing and single-haplotype iterative mapping and sequencing to characterize 11 million bases of sequence from the rhesus macaque MSY.
They then compared this sequence to human and chimpanzee MSY regions to get a glimpse at the gene loss, if any, that has occurred on the male sex chromosome in the 25 million years since ancestors of the Old World monkeys diverged from the lineage leading to humans and chimpanzees.
While there were structural differences in the rhesus macaque MSY — along with less extensive gene family amplification and fewer palindromes — neither the rhesus macaque MSY nor the human MSY showed signs of significant gene loss or genetic decay.
In contrast, the researchers' results indicate that the rhesus macaque MSY has retained all of the ancestral genes believed to have been present in the common ancestor of rhesus macaques, chimpanzees, and humans.
The human MSY has lost one ancestral gene from a chunk of sequence representing the youngest "stratum," where crossing over ceased most recently. On the other hand, the team reported, all four of the older strata in the human MSY have remained stable and managed to hold on to their ancestral genes.
Based on these findings, the study's authors concluded that over the course of human MSY evolution "each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection."
"With no loss of genes on the rhesus Y [chromosome] and one gene lost on the human Y, it's clear the Y isn't going anywhere," first author Jennifer Hughes, a researcher in Page's Whitehead lab, said in a statement.