At several points in our tangled history, modern humans mated with Neanderthals.
It has left a telltale mark on the genomes of modern humans today, and this Neanderthal DNA affects our health in countless ways.
However, there is one part of our genome that lacks any Neanderthal DNA: the Y chromosome. But why?
Experts told Live Science that some of this could be a coincidence. But it is also possible that Neanderthal genes were incompatible with females Homo sapiens wearing them. This would mean that only female hybrids can reproduce.
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The Disappearing “Y”
The Y chromosome is one of two types sex chromosomes in humans. Females carry two copies of the X chromosome, while males carry one X and one Y chromosome. The Y chromosome can only be passed on from father to son.
Scientists first analyzed DNA taken from the fossilized remains of female Neanderthals. However, in 2016, a study published in American Journal of Genetics studied a Neanderthal Y chromosome from a 49,000-year-old man from Spain.
“We have never observed Neanderthal Y chromosome DNA in any human sample ever tested,” Carlos Bustamantestudy co-author and population geneticist at Stanford University, said in a statement at this time.
So why does this Neanderthal DNA seem to have disappeared without a trace?
The simplest answer may be that it was accidentally lost from the human gene pool over thousands of years.
“The amount of Neanderthal DNA in today’s humans is relatively low, so it may have been lost by drift,” Fernando Mendezthe study’s lead author, who was a postdoctoral fellow at Stanford at the time, said ABC News. In other words, it’s not that Neanderthal DNA was less “fit” than modern human DNA from an evolutionary perspective, but rather that it was simply lost to time.
Another possibility is that the Neanderthal Y-chromosome was incompatible with our own DNA. For example, the team found that three of the Neanderthal genes on the Y chromosome, which differed from those found in humans, functioned as part of immune system. These genes allow the immune system to distinguish between friend – ie. the body’s own cells – from the enemy. Failure to properly distinguish “self” from “invader” is the cause of male-to-female tissue transplants can be rejected or why a mother’s immune system might attack a male fetus during pregnancycausing miscarriage.
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It is therefore possible that modern women’s immune systems constantly attack male babies who carry Neanderthal DNA on their Y chromosome, leading to repeated miscarriages and eventually the loss of Neanderthal Y genes.
If modern women who interbred with Neanderthals had fewer boys than other couples, then systematically the boys who live are likely to have fewer boys, Mendes said ABC News. This hypothesis is consistent with an old theory called “Haldane’s rule,‘, suggesting that if breeding between genetically distinct populations results in infertility, it will most likely be in the sex—in this case, the male—carrying two different sex chromosomes.
A big loss
This is not the first time in our evolutionary history that the Neanderthal Y chromosome has failed to compete with its modern human counterpart.
Between 550,000 and 765,000 years agothe population that would lead to Homo sapiens diverged from the Neanderthals and another group of already extinct human relatives, the so-called Denisovans.
However, a study published in the journal Science in 2020 revealed that somewhere between 370,000 and 100,000 years ago, Neanderthals and early modern humans interbred. 100,000 years ago, the Neanderthal Y was completely replaced by that of Homo sapiens.
Scientists don’t know why this happened, Martin Petrco-senior study author and researcher and programmer at the University of Copenhagen in Denmark, told Live Science.
But one possible explanation, Petr’s hypothesis, is that for hundreds of thousands of years Neanderthals had a very small population size compared to early modern humans. Low population sizes allow harmful mutations to accumulate in the gene pool at a higher rate than within a larger population, he said.
If you then introduce “healthier” early modern human DNA into the mix, natural selection will favor that modern human DNA, which will then have passed through the Neanderthal population.
However, without much more genomic data from Neanderthals that would allow scientists to study the functional impact of inheriting this early modern human DNA, this is only a hypothesis, Petr said.
Connected: Scientists finally solve the mystery of why Europeans have less Neanderthal DNA than East Asians
Many unknowns
Unfortunately, it is still too early to say definitively why the Neanderthal Y DNA was lost in either case, Adam Sippelcomputational biologist at Cold Spring Harbor Laboratory in New York, told Live Science in an email.
It’s still possible the replacement occurred due to random genetic drift, he added.
Neanderthal DNA lives in us
Generally speaking, the loss of a Y chromosome line due to crossing over is not uncommon, Carles Lalueza-Foxco-author of the 2020 Science study and a paleogenomics researcher at the Institut de Biologia Evolutiva in Spain, told Live Science in an email.
That’s because the Y chromosome is inherited only through the father’s line, he said. This is in contrast to other chromosomes in the body, which are passed down to the next generation from both parents. That means the Y chromosome is more prone to “loss” over time, he said.
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