Modern human DNA has traces of the Neanderthal – except for the Y chromosome

from Jenny Graves /Conversation

Neanderthals, the closest cousins ​​of modern humans, lived in parts of Europe and Asia until their extinction about 30,000 years ago.

Genetic studies are increasingly revealing links between modern humans and these long-extinct relatives – most recently that a rush of interbreeding between our species occurred in a relatively short burst of time around 47,000 years ago. But a mystery still remains.

of Homo sapiens The genome today contains little Neanderthal DNA. These genetic traces come from almost every part of the Neanderthal genome – except for the Y sex chromosome, which is responsible for creating males.

So what happened to the Neanderthal Y chromosome? It could have been lost by chance, or due to mating patterns or inferior function. However, the answer may lie in a centuries-old theory about the health of interspecies hybrids.

Neanderthal sex, genes and chromosomes

Neanderthals and modern humans went their separate ways sometime between 550,000 and 765,000 years ago in Africa, when Neanderthals wandered into Europe, but our ancestors stayed put. They would not meet again until H. sapiens migrated to Europe and Asia between 40,000 and 50,000 years ago.

Scientists have found 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. Amazingly, the Neanderthal genome was very similar to ours, containing about 20,000 genes strung together on 23 chromosomes.

Like us, they had two copies of 22 of those chromosomes (one from each parent), and also 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 majority that have been sequenced contain versions of some of the same genes that are on the modern human Y chromosome.

In modern humans, a gene on the Y chromosome called SRY initiates the process of developing the XY embryo into a male. The SRY gene plays this role in all apes, so we assume it did for Neanderthals as well—even though we haven’t found the Neanderthal SRY gene itself.

Neanderthals coexisted with modern humans in the Negev desert. (Kovalenko I / Adobe Stock)

Mating between species left us with Neanderthal genes

There are many small gifts that mark a DNA sequence as coming from a Neanderthal or a H. sapiens. So we can look for parts of the Neanderthal DNA sequence in the genomes of modern humans.

The genomes of all human lineages originating in Europe contain about 2% Neanderthal DNA sequences. Bloodlines from Asia and India contain even more, while lineages restricted to Africa have none. Some ancient ones Homo sapiens genomes contained even more – 6% or more – so it looks like Neanderthal genes are gradually dying out.

Most of this Neanderthal DNA arrived over a 7,000-year period about 47,000 years ago, after modern humans moved out of Africa into Europe, and before Neanderthals became extinct 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 pieced together from fragments found in the genomes of various contemporary humans. We have our Neanderthal ancestors to thank for traits including red hair, arthritis and resistance to certain diseases.

There is one notable exception. No modern humans have 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 men? Did Neanderthal females, but not males, indulge in interspecies mating? Or was there something toxic about Neanderthal Y that didn’t work with human genes?

The AY chromosome comes at the end of the line if its carriers have no sons, so it may simply have been lost over thousands of generations.

Or maybe the Neanderthal Y was never present in interspecies mating. Perhaps it was always modern men who fell in love with (or traded, captured or raped) Neanderthal women? The sons born to these women would have all 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’s Y chromosome wasn’t as good at its job as he was H. sapiens rival Neanderthal populations were always small, so deleterious mutations would be more likely to accumulate.

We know that Y chromosomes with a particularly useful gene (for example for more or better or faster sperm) rapidly replace other Y chromosomes in a population (called the hitchhiking effect).

We also know that the Y chromosome is generally degrading in humans. It is even possible that SRY was lost from Neanderthal Y and that Neanderthals were in the destructive 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 did not work with genes on other chromosomes from modern humans.

The missing Neanderthal Y can then be explained by “Haldane’s rule”. In the 1920s, 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, it is disproportionately the 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 rat species show this pattern, as do cat crosses. For example, in lion-tiger crosses (liger and tigon), females are fertile, but males are sterile.

We still lack a good explanation of Haldane’s rule. It is one of the enduring mysteries of classical genetics.

But it seems reasonable that the Y chromosome from one species has evolved to work with genes from other chromosomes of its species and may not work with genes from a related species that contain even minor 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.

So this could explain why Neanderthal Y was lost. It also raises the possibility that it was the Y chromosome’s fault, in establishing a reproductive barrier, that Neanderthals and humans became separate species in the first place.

Top image: An artist’s reconstruction of a Neanderthal, on display at the ‘Britain: A Million Years of Human History’ exhibition. Source: The Trustees of the Natural History Museum, London

This article was originally published under the title ‘Modern human DNA contains parts of the entire Neanderthal genome – except for the Y chromosome. What happened?from Jenny Graves IN Conversationand is republished under a Creative Commons license.