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May 4, 2020
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Neanderthals and Icelanders

Neanderthal heritage in our genomes is already being studied years - since, thanks to the efforts of paleogenetics, we know that in each of us there is a little bit of Neanderthal. About 2% of Neanderthal DNA is found in every person outside of Africa. And recently, a noticeable Neanderthal trace was found among Africans. Let's not forget about Denisovans - their genetic variants were found in the inhabitants of Oceania and East Asia.

In numerous studies, experts specify the size of the Neanderthal contribution, try to find out the amount of " waves of confusion ”between our ancestors and other types of hominins. And, of course, the most interesting: which of our genes are affected and how the archaic heritage is manifested in the work of the organism of modern man.

Once again, it must be said that the percentage of DNA of Neanderthal origin among the inhabitants of Eurasia is approximately the same, but in different individuals this impurity affects different parts of the genome. So, from DNA of many modern people, you can try to collect a noticeable piece of the Neanderthal genome, or even not one.

Once again, the authors of a new article in Nature undertook similar work, using more 26) of thousands of fully read genomes of the inhabitants of Iceland.

One of the difficulties is in the fact that so far only 3 complete genomes of ancient hominins are known to scientists - 2 Neanderthals (from Vindia in Croatia and from Denisova Cave in Altai) and one Denisovskaya (again from Denisova Cave). In the article, this trinity is indicated by the abbreviation DAV (Denisova - Altai - Vindia). Obviously, these specific individuals did not interbreed with our ancestors, but some others that differed from them - therefore, some of the archaic variants in modern genomes remain elusive.

The authors of the new study used sophisticated statistical methods to “catch” Icelanders fragments of DNA of archaic origin. Such fragments, according to scientists, should contain a large number of derivative genetic variants (different from chimpanzee variants) that are absent in the indigenous population of Africa. For comparison, we used the genomes 261 of Africans from the project "651 genomes. ”

As you can see, in this study, Africans are still considered as“ pure sapiens ”, which were not affected by mixing with Neanderthals. As we now know, this is still not quite so.

As a result, scientists found approximately 14 million fragments of DNA are probably of archaic origin. Next, this set was filtered, giving preference to those fragments on which DAV (genetic variants found in Neanderthals or Denisovans), or alleles linked to them (that is, often found next to DAV) are located.
With the most rigorous selection, the total accumulated 55 of thousands of unique fragments, covering about 1 Gigabyte, that is, more than 27% of the human genome. And these are just Icelanders. With a similar search in other human populations, there is clearly still more.

I repeat that this terrifying volume is collected “by guts” 26 thousand genomes. Each specific person carries in his genome on average 56 fragment, or 33 Megabytes of archaic origin.

It is important that archaic fragments covering the same sections of DNA were found in the genomes of different people , but at the same time very different from each other. This suggests that the confusion clearly occurred many times. Researchers have counted at least six different ancient haplotypes captured in the genomes of Icelanders.

And which of the famous ancient genomes is this legacy most similar to? Scientists got 38% of matches with the Neanderthal from Vindia, 13)% - with Altai Neanderthal and 3% - with Denisovan. In addition, 13% of archaic fragments are immediately similar to at least two ancient genomes, and % does not look like anything.

In previous studies, it was already shown that Neanderthals, who left a mark on the European genomes, are related to Vindia. But the presence of the Icelanders Denisov's options was a surprise. How to explain this? Echoes of the common ancestor of the Denisovans and Neanderthals? Or did someone similar to the Denisovites mingle with the Neanderthals, and after that they crossed themselves with the ancestors of the Europeans? Another intriguing scenario - the ancestors of the Europeans still met in immemorial times with someone deniso-like. Which version is true is still unclear, but the authors admit that some hominins related to the Denisovites could live in Eurasia much west of Altai. We know that Neanderthals were very mobile, why not the Denisovans to migrate.

The researchers went further and decided to compare the features of the mutational process of sapiens and Neanderthals, comparing archaic and “native” DNA fragments of each individual. It turned out that the rate of accumulation of mutations in the two species is approximately the same. But the ratio of the types of mutations is different (for example, Neanderthals have more substitutions of C for G and less - T for C). It is known that the frequency of such mutations in a modern person is significantly affected by the age of the parents. Judging by the observed picture, Neanderthal mothers were on average older and fathers younger than Sapiens.
Finally, scientists began to assess the influence of Neanderthal heritage: how archaic options manifest in the appearance and work of the body of Icelanders? Such studies have already been carried out: they took some kind of human population and looked for correlations between Neanderthal genetic variants and some peculiarities. Suppose there is a gene that affects hair color, and an archaic fragment of the genome is located just close to it. Is there a certain Neanderthal allele in this fragment more often in redheads? Or the burning brunettes? If such a connection was found - perhaps this is it, Neanderthal influence?
The catch is that correlation does not mean a causal relationship. And suddenly, next to the archaic option is some completely non-archaic, and the reason is it?

That's what the researchers did. At first they began to look for associations among Icelanders between 56 the human trait and archaic genetic variants. The result is a list of 500 independent associations between the genotype and phenotype. Cool! However, further analysis gave a sad result: in most cases, near (at a distance of up to 2 Megabases) with the archaic allele, there was a non-archaic allele (in conjunction with it), which was associated with the same sign significantly more strongly. After strict filtering, out of hundreds of options, there are only 5 left. Probably only these Neanderthal alleles really affect something in the human body. What for?

Here is a list of these symptoms:

- a reduced level of prostate-specific antigen that is associated with a reduced risk of prostate cancer,

- a reduced concentration of hemoglobin,
- a lower average corpuscular hemoglobin,
- short stature,
- increased prothrombin time.

But what about the color of the skin and hair? Type 2 diabetes, Crohn's disease, and even smoking addiction? Well, the authors of the publication took 14 signs, the Neanderthal influence by which was revealed in previous studies and checked them according to a new technique. For from the list, the associations were not significant, and for 12 again non-archaic options were found - a more likely reason for the association. Only three remained: two associations with growth and one with pulse rate, and the effect on these characteristics is very moderate. Everything.

Discussion

The resulting archaic fragments came from many archaic individuals belonging to a population close to Vindia. However, the noticeable part is closer to the Denisovites, which cannot be explained by incomplete divergence of lines. Rather, it requires Denisov's admixture — either directly to people, or to Neanderthals who later interbreed with people — shortly after leaving Africa, since a signal was found in all non-African populations. Perhaps there was a Denisov-like population west of Altai. This is consistent with evidence of active Neanderthal migrations at the end of their history.

The coincidence of the mutation rate of Neander and sapiens suggests that a decrease in the human mutation level is unlikely to happen between 500 and 38 thousand years ago. However, the difference in the types of mutations indicates a difference in the length of generations of men and women between species.

Perhaps the influence of Neanderthal variants was higher in the past.

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