According to Jenny Graves /Conversation
Neanderthals, the closest relatives of modern humans, lived in parts of Europe and Asia until their extinction about 30,000 years ago.
Genetic studies are revealing more and more about the links between modern humans and these long-gone relatives – most recently there was a flurry of interbreeding between our species in a relatively short period of time around 47,000 years ago. But one mystery still remains.
The Homo sapiens today’s genome contains some Neanderthal DNA. These genetic traces come from almost every part of the Neanderthal genome – except for the Y sex chromosome, which is responsible for making males.
So what happened to the Neanderthal Y chromosome? It could have been lost by accident or due to mating patterns or a worse function. But the answer may lie in a century-old theory about the health of interspecies hybrids.
Neanderthal sex, genes and chromosomes
Neanderthals and modern humans went their separate ways somewhere between 550,000 and 765,000 years ago in Africa, when Neanderthals wandered into Europe, but our ancestors stayed put. They did not meet again until H. sapiens migrated to Europe and Asia between 40,000 and 50,000 years ago.
Scientists obtained copies of the complete male and female Neanderthal genomes thanks to DNA from well-preserved bones and teeth of Neanderthal individuals in Europe and Asia. Unsurprisingly, the Neanderthal genome was very similar to ours, containing about 20,000 genes grouped into 23 chromosomes.
Like us, they had two copies of 22 of these chromosomes (one from each parent) as well as a pair of sex chromosomes. Females had two X chromosomes, while males had one X and one Y.
Y chromosomes are difficult to sequence because they contain a lot of repetitive “junk” DNA, so the Neanderthal Y genome has only been partially sequenced. However, the large chunk that has been sequenced contains versions of several of the same genes that are on the modern human Y chromosome.
In modern humans, a Y chromosome gene called SRY starts the process of developing an XY embryo into a male. The SRY gene plays this role in all great apes, so we assume it did in Neanderthals as well—even though we didn’t find the Neanderthal SRY gene itself.
Neanderthals lived alongside modern humans in the Negev desert. (Kovalenko I / Adobe Stock)
Interspecies mating left us with Neanderthal genes
There are lots of little gifts that mark the DNA sequence as coming from a Neanderthal or a H. sapiens. So we can look for bits of Neanderthal DNA sequence in the genomes of modern humans.
The genomes of all European-derived human lineages contain about 2% Neanderthal DNA sequences. Lineages from Asia and India contain even more, while lines restricted to Africa have none. Some ancient Homo sapiens genomes contained even more—about 6%—so it appears that Neanderthal genes are gradually disappearing.
Most of this Neanderthal DNA arrived in a 7,000-year period about 47,000 years ago, after modern humans arrived in Europe from Africa and before the extinction of Neanderthals about 30,000 years ago. During this time there must have been many matings between Neanderthals and humans.
At least half of the entire Neanderthal genome can be assembled from fragments found in the genomes of various modern humans. We owe traits including red hair, arthritis and resistance to certain diseases to our Neanderthal ancestors.
There is one glaring exception. No modern human has been found to have any part of the Neanderthal Y chromosome.
What happened to the Neanderthal Y chromosome?
Was it just bad luck that the Neanderthal Y chromosome was lost? Wasn’t she very good at her job of making males? Did Neanderthal women but not men engage in interspecies mating? Or was there something toxic about the Neanderthal Y to make it not work with human genes?
The AY chromosome comes to the end of the line if its carriers have no sons, so it could simply have been lost over thousands of generations.
Or maybe the Neanderthal Y was never present in interspecific mating. Maybe it was always modern human men who fell in love with (or traded, captured, or raped) Neanderthal women? All should have sons born to these women H. sapiens form of the Y chromosome. However, it is difficult to reconcile this idea with the finding that there is no trace of Neanderthal mitochondrial DNA (which is restricted to the female line) in modern humans.
Or maybe the Neanderthal Y chromosome just wasn’t as good at its job as he was H. sapiens compete. Neanderthal populations were always small, so harmful mutations would have been more likely to accumulate.
We know that Y chromosomes with a particularly useful gene (for example, for more or better or faster sperm) quickly replace other Y chromosomes in the population (the so-called hitchhiker effect).
We also know that the Y chromosome degrades in humans overall. It is even possible that SRY was lost from the Neanderthal Y and that Neanderthals were in the disruptive process of evolving a new sex-determining gene, as some rodents have.
Was the Neanderthal Y chromosome toxic in hybrid boys?
Another possibility is that the Neanderthal Y chromosome will not work with genes on other chromosomes of modern humans.
The missing Neanderthal Y can then be explained by “Haldane’s rule”. In the 1920s, the British biologist JBS Haldane noted that in hybrids between species, if one sex is infertile, rare, or unhealthy, it is always the sex with different sex chromosomes.
In mammals and other animals where females have XX chromosomes and males have XY chromosomes, there are disproportionately male hybrids that are unfit or infertile. In birds, butterflies and other animals where males have ZZ chromosomes and females have ZW, they are females.
Many crosses between different mouse species show this pattern, as do cat crosses. For example, in lion-tiger hybrids (ligers and tigons), the females are fertile, but the males are sterile.
We still lack a good explanation of Haldane’s rule. It is one of the enduring mysteries of classical genetics.
However, it seems reasonable that a Y chromosome from one species evolved to work with genes from other chromosomes of its own species, and may not work with genes from related species that contain even small changes.
We know that genes on the Y evolve much faster than genes on other chromosomes, and some have functions in sperm production, which may explain the infertility of male hybrids.
This could explain why Neanderthal Y got lost. It also raises the possibility that it was the fault of the Y chromosome that created the reproductive barrier that Neanderthals and humans became separate species.
Top image: An artist’s reconstruction of a Neanderthal on display at the ‘Britain: A Million Years of Human Story’ exhibition. Source: Trustees of the Natural History Museum, London
This article was originally published under the title ‘Modern Human DNA Contains bits of the entire Neanderthal genome – except for the Y chromosome. What happened?‘ from Jenny Graves on Conversationand has been republished under a Creative Commons license.