Modern human DNA contains bits from all over the Neanderthal genome – except the Y chromosome. What happened, Jenny Graves, June 16, 2024:

‘Genetic studies are revealing ever more about the links between modern humans and [Neanderthals]… But one mystery still remains.

The Homo sapiens genome today contains a little bit of Neanderthal DNA. These genetic traces come from almost every part of the Neanderthal genome – except 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 because of mating patterns or inferior function. However, the answer may lie in a century-old theory about the health of interspecies hybrids.

Scientists have recovered copies of the full 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 bundled into 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 hard 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 in the modern human Y chromosome.

In modern humans, a Y chromosome gene called SRY kickstarts the process of an XY embryo developing 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.

There are lots of little giveaways that mark a 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 human lineages originating in Europe contain about 2% Neanderthal DNA sequences. Lineages from Asia and India contain even more, while lineages restricted to Africa have [little to] none. Some ancient Homo sapiens genomes contained even more – 6% or so – so it looks like the Neanderthal genes are gradually fading out.

At least half of the whole Neanderthal genome can be pieced together from fragments found in the genomes of different contemporary humans. There is one glaring exception. No contemporary humans have been found to harbour any part of the Neanderthal Y chromosome.

Was it just bad luck that the Neanderthal Y chromosome got lost? Was it not very good at its job of making males? Did Neanderthal women, but not men, indulge in interspecies mating? Or was there something toxic about the Neanderthal Y so it wouldn’t work with human genes?

A Y chromosome comes to the end of the line if its bearers have no sons, so it may simply have been lost over thousands of generations. Or maybe the Neanderthal Y was never present in interspecies matings. Perhaps it was always modern human men who fell in love with (or traded, seized or raped) Neanderthal women? Sons born to these women would all have the H. sapiens form of the Y chromosome. However, it’s hard to reconcile this idea with the finding that there is no trace of Neanderthal mitochondria DNA (which is limited to the female line) in modern humans.’

Ancient DNA and Neanderthals, Robin Teague, Ryan McRae and Briana Pobiner:

‘Researchers compared the Neanderthal mtDNA to modern human and chimpanzee mtDNA sequences and found that the Neanderthal mtDNA sequences were substantially different from both (Krings et al. 1997, 1999). Most human sequences differ from each other by an average of 8.0 substitutions, while the human and chimpanzee sequences differ by about 55.0 substitutions. The Neanderthal and modern human sequences differed by approximately 27.2 substitutions. 

There is evidence that some other hominin contributed to the Neanderthal mtDNA gene pool… (Posth et al., 2017). A femur discovered in Germany had its mtDNA genotyped and it was found that there was introgression from a non-Neanderthal African hominin, either Homo sapiens or closely related to us… This mitochondrial genome is also highly divergent from the Neanderthal average discussed previously, indicating that Neanderthals may have been much more genetically diverse in their more distant past. 

As for Neanderthal introgression into the modern human mtDNA genome, it is possible that the evidence of such admixture is obscured for a variety of reasons (Wang et al 2013). Primary among these reasons is sample size: There are to date only a dozen or so Neanderthal mtDNA sequences that have been sampled. Because the current sample of Neanderthal mtDNA is so small, it is possible that researchers simply have not yet found the mtDNA in Neanderthals that corresponds to that of modern humans.’

Graves: ‘Or perhaps the Neanderthal Y chromosome was just not as good at is job as its H. sapiens rival. 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 instance for more or better or faster sperm) rapidly replace other Y chromosomes in a population (called the hitchhiker effect). We also know the Y chromosome is degrading overall in humans. 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, like some rodents have.

Another possibility is that the Neanderthal Y chromosome won’t work with genes on other chromosomes from modern humans. The missing Neanderthal Y may then be explained by “Haldanes rule”. In the 1920s, British biologist J.B.S. Haldane noted that, in hybrids between species, if one sex is infertile, rare or unhealthy, it is always the sex with unlike sex chromosomes.

In mammals and other animals where females have XX chromosomes and males have XY, it is disproportionately male hybrids that are unfit or infertile. In birds, butterflies and other animals where males have ZZ chromosomes and females have ZW, it is the females.

Many crosses between different species of mice show this pattern, as do feline crosses. For example, in lion–tiger crosses (ligers and tigons), 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 classic genetics.

But it seems reasonable that the Y chromosome from one species has evolved to work with genes from the other chromosomes of its own species, and might not work with genes from a related species that contain even small changes. We know that genes on the Y evolve much faster than genes on other chromosomes, and several have functions in making sperm, which may explain the infertility of male hybrids.

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

Constant readers having read the first three articles in this series will be conversant with this writer’s explanation regarding Neanderthal man. For new readers or those who have skipped articles, it is briefly the following. 

The Genesis account in the Bible discusses a creation of a human on what is referred to as Day Six, not a literal day but meaning an epoch of time. A pause of a ‘Day’ occurred where the Creator ‘rested’ and then Adam and Eve were created on Day ‘Eight’ – article: The Sabbath Secrecy; and Chapter XXII Alpha & Omega. 

The people of Day Six equate to Homo neanderthalensis and those of Day Eight to Homo sapiens. A genetic bottleneck occurred during the Great Deluge in 10,837 BCE, whereby a handful of people survived – Article: The Younger Dryas Stadial: Ending of the Earth… Beginning of the World.

The Bible says eight people survived to then reproduce in the post-diluvian world. From this family, all the ethnicities in the world have evolved – Article: Y-DNA Adam & mtDNA Eve: The Genesis & Evolution of Homo sapiens. 

Noah had three sons before the Flood, Japheth, Ham and Shem. They in turn had three wives. This was the advent of Homo sapiens sapiens. At least one of Noah’s daughters-in-law had Neanderthal DNA. 

This perhaps answers why the Neanderthal Y Chromosome is missing; as every son born after the flood would have a Homo sapiens Y sex chromosome.  

With regard to “no trace of Neanderthal mitochondria DNA in modern humans”; yet “evidence that some other hominin contributed to the Neanderthal mtDNA gene pool.” 

There is a theory – as postulated by the late Alan Alford – that the DNA of Homo erectus was used in the formation of Homo sapiens. It is possible Homo erectus contributed the mystery genetic material in the Homo neanderthalensis mtDNA.

The descendants of Japheth, exhibit the most Neanderthal DNA – refer articles: Homo neanderthalensis I, II & III. Thus the wife of Japheth, Adataneses, was likely not fully Neanderthal – possessing a mixture of Neanderthal and Homo sapiens mtDNA.

A 28,000-year-old ‘hybrid child’ confirms interbreeding between humans and Neanderthals, Jordan Joseph, 2025:

‘… found [were] a child’s bones 27 years ago in a shallow rock shelter in central Portugal. Researchers immediately noticed that the young skeleton [of a child] only around four years old, had traits belonging to modern humans and to Neanderthals… [indicating a] mixed heritage. The limb proportions were similar to those seen in Neanderthals, while the skull and jaw had features reminiscent of modern humans… suggesting these two groups once had children together.’

The Neanderthal carried 22 pairs of chromosomes (autosomes) and one pair of sex chromosomes (X and Y) just like Homo sapiens. 

Perhaps the merging of mtDNA from the two different, yet related humans has obscured the recessive like Neanderthal mtDNA, so that it is present but hidden?

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