Mom is a Neanderthal, dad is a Denisovan
Yes, and that half-breed
Alexander Sokolov, XX2 century
What paleogeneticists have been saying for so long has happened. A hybrid of a Neanderthal and a Denisovan was found.
The location of Neanderthals, Denisovans and ancient Sapiens, aged 40 thousand years and earlier. Blue shows Neanderthals, yellow – Sapiens, red – Denisovans. Drawings from the article by Slon et al. The genome of the offspring of a Neanderthal mother and a Denisovan father, published in the journal Nature.
Neanderthals and mysterious Denisovans are groups of ancient people whose evolutionary paths diverged more than 400 thousand years ago. But it would be strange if these hominins did not contact at all, considering that the remains of both were found in the same Denisova cave in Altai. And indeed, in the genome of the first described Denisovian (the phalanx of the little finger "Denisov 3"), experts found a small Neanderthal admixture. And the fact that both Neanderthals and Denisovans interbred with our ancestors – ancient Sapiens, has long been no secret.
After the discovery of the Denisovans, scientists did not give up trying to find new bone remains belonging to this amazing population that lived somewhere in the east of Eurasia. The search had to be conducted by sorting through the bone cores, about which it is not even always clear whether they belonged to a person or an animal. But the hard work of scientists works wonders. Among 2000 fragments, a fragment of a human bone was found. The fact that it belonged to Homo was shown by an analysis of the composition of collagen, which revealed a specific human variant. At first, experts managed to isolate mitochondrial DNA from the remains, which turned out to be Neanderthal. They tried to date the bone with radiocarbon, but its age apparently went beyond the sensitivity of the method – that is, the find was clearly older than 50 thousand years. Judging by the thickness of the cortical layer of the bone, at the time of death its owner was at least 13 years old.
Then the scientists obtained a nuclear genome. Judging by the fact that sections of the X chromosome were found among DNA fragments as often as fragments of other chromosomes, the bone belonged to a woman (let me remind you that a man, unlike a woman, has only one X chromosome, and all other chromosomes in the nuclear genome have their own pair. If Denisova 11 were a man, sections of the X chromosome would come across geneticists 2 times less often). Experts also checked the presence of modern pollution – there were few of them, no more than 1.7%.
The most interesting thing began when scientists began to find out what kind of person Denisova 11 belonged to. To do this, the new genome was compared with the DNA of a Neanderthal from Denisova Cave (the so-called "Altai"), with the DNA of a Denisovan (Denisova 3) and with a modern African (pygmy mbuti). Suddenly, there were approximately equal matches with Neanderthal and Denisovan (38.6% of Neanderthal alleles and 42.3% of Denisovan). This meant that both fossil species made approximately the same contribution to the Denisov genome. 11 Geneticists also estimated heterozygosity (that is, the number of positions in which paired chromosomes contain different letters of the genetic alphabet). Denisov 11 had 4 times more such positions than Neanderthals and Denisovans. Such a picture should be obtained if the individual had combined chromosomes of Neanderthal and Denisov origin.
Did the parents of Denisov 11 belong to different types of people? Scientists did not rule out another option: perhaps there was a population of hominins of mixed Neanderthal-Denisovan origin in the Denisova Cave area, and a representative of such a group fell into the hands of scientists. But the number of heterozygous positions in which one variant was Neanderthal and the second was Denisovian, Denisov 11 turned out to be too large – more than 40%, that is, 2 times higher than it would be in the case of a mixed population. (For comparison, with a similar analysis of the genome of a Neanderthal from the Goye cave (Belgium), only 2.1% of such positions turned out).
After some additional checks, the geneticists were finally convinced that it was a hybrid of the first generation in front of them: mom is a Neanderthal (according to mtDNA), and dad is a Denisovan.
Using the molecular clock method, the authors of the study estimated the age of the find: approximately 90 thousand years.
The researchers did not stop there. In the hybrid genome, they found 5 large sites in which both paired chromosomes contained only Neanderthal alleles. This meant that the father of Denisov 11 was not a pure-blooded Denisovan, but with a Neanderthal admixture. The analysis showed that this admixture was "mixed" 300-600 generations before his birth, and from some Neanderthals not related to Denisov's mother 11. Confusing pedigree!
Since geneticists have at their disposal the complete genomes of two Neanderthals – from Denisova Cave and from Vindia (Croatia), the authors of the study decided to find out to whom these ancient people are closer to the mother of the individual Denisova 11. Unexpectedly, there were significantly more coincidences with Windia. Unexpectedly, because thousands of kilometers from Vindiya to Altai, and the remains of the Altai Neanderthal were found 1 meter from Denisov 11.
It turns out that the Neanderthal from Altai, who lived 90 thousand years ago, is a closer relative of the Neanderthal from Croatia, who lived 20 thousand years later than the Altai Neanderthal, who lived 30 thousand years earlier. This means that either Eastern Neanderthals migrated to Western Europe later than 90 thousand years ago, or Western Neanderthals migrated to Siberia before this date, displacing the locals. Which scenario is correct? It's hard to say yet, more Neanderthal genomes are needed.
Kinship and gene exchange between populations of Neanderthals and Denisovans, according to geneticists. Vertically – thousands of years.
What is the outcome? For the first time, direct evidence of the mixing of Neanderthals and Denisovans has been found. Moreover, the confusion is twofold: in the case of the parents of the woman Denisova 11 and in the case of her father's ancestors.
In total, it turns out that out of 6 individuals from Denisova Cave whose genomes were deciphered, two Neanderthal contributions were found. This means only one thing: the mixing of different types of people where their paths intersected occurred often. As Kelly Harris, a geneticist at the University of Washington in Seattle, notes, "I can count the number of Denisov bones found on the fingers of one hand. The fact that the hybrid has already been discovered shows that such offspring were commonplace." Scientists are wondering: how, in such a situation, did Neanderthals and Denisovans manage to preserve their genetic differences for thousands of years? Perhaps it's in different areas: the first lived in the West, the second – in the East. In addition, hybrids are often less viable than their parents. Maybe the wave of Sapiens migrants pouring out of Africa changed everything: our ancestors began to "recklessly" mix with aborigines throughout the area. Such mixing could lead to the complete dissolution of archaic groups among the more numerous Cro-Magnons.
There remains one more question, alas, not solved by means of paleogenetics: did it happen for love?
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