During its long migration, Sapiens mated with human species that have since disappeared. A clearly visible crossbreeding… in our genetic heritage.
Parietal painting:Upper Palaeolithic. A group of Homo sapiens draw a bison on the wall of a cave. Painting by Francisco Fonollosa.
This article is taken from n°204 of Indispensables de Sciences et Avenir, dated January/March 2021.
DNA does not lie. Hominids, or hominins, i.e. all members of the genus Homo and their Australopithecine cousins, did not evolve in isolation, each on its own branch of the species tree. Some got to know each other… and even warmed up.
And we are directly concerned! Because Neanderthal, or Homo neanderthalensis , is never very far from Sapiens… When the first fossil of this Homo disappeared about 30,000 years ago was discovered in 1856 in the Neander Valley, Germany, scientists of the time were so surprised at its resemblance to us that they renamed us. We have become Homo sapiens sapiens to make room for this Homo sapiens neanderthalensis , right next to us… in subspecies.
A proximity that had to be reinvented in 2010, when the Swedish geneticist Svante Pääbo, founder of the Max-Planck Institute for Evolutionary Anthropology in Leipzig, produced the first complete Neanderthal genome. And discovered that it was actually another human species. Neanderthal lost his sapiens , and we lowered our pride to keep only one. But this distancing in the classification hides other, more concrete comparisons. Sequencing the Neanderthal genome reveals that we "hybridized" with him, as geneticists coyly put it.
Mixed unions and the Y chromosome
This article is taken from n°204 of Indispensables de Sciences et Avenir, dated January/March 2021.
DNA does not lie. Hominids, or hominins, i.e. all members of the genus Homo and their Australopithecine cousins, did not evolve in isolation, each on its own branch of the species tree. Some got to know each other… and even warmed up.
And we are directly concerned! Because Neanderthal, or Homo neanderthalensis , is never very far from Sapiens… When the first fossil of this Homo disappeared about 30,000 years ago was discovered in 1856 in the Neander Valley, Germany, scientists of the time were so surprised at its resemblance to us that they renamed us. We have become Homo sapiens sapiens to make room for this Homo sapiens neanderthalensis , right next to us… in subspecies.
A proximity that had to be reinvented in 2010, when the Swedish geneticist Svante Pääbo, founder of the Max-Planck Institute for Evolutionary Anthropology in Leipzig, produced the first complete Neanderthal genome. And discovered that it was actually another human species. Neanderthal lost his sapiens , and we lowered our pride to keep only one. But this distancing in the classification hides other, more concrete comparisons. Sequencing the Neanderthal genome reveals that we "hybridized" with him, as geneticists coyly put it.
Mixed unions and the Y chromosome
We now know that when Sapiens came out of Africa about 60,000 years ago, he encountered this other human. Strong, with a broad face and eyes highlighted by an orbital bulge. Seduced? Perhaps… From this meeting, children were born. As adults, some stayed with the Sapiens; their Neanderthal DNA, transmitted to their descendants, was maintained over millennia in the genome of the species, even as Neanderthals eventually died out. If it was long believed that these mixed unions had produced only daughters - the hybridization of two species being more stable when the chromosomes are similar, like XX -, recent work suggests that males could be born from them.
To find out, paleogeneticians from the Max-Planck Institute had to reconstruct a Neanderthal Y chromosome from fragmentary sequences taken from three male Neanderthals and two men from Denisova, another human species close cousin of Neanderthals. Because this small piece of DNA is missing from the only three otherwise complete and high-resolution genomes available for Neanderthals. Fragile, the males?
"It is coincidental that the best preserved Neanderthals and Denisovans we have identified for previous studies were all female" , answers Janet Kelso, the archaic DNA specialist who led this study. The reconstructed chromosome is therefore the result of a very complex genetic puzzle. A feat… and a total surprise in terms of results:the Neanderthal Y chromosome was inherited from Sapiens! Our cousin would have acquired it during an overnight excursion by Sapiens out of Africa, 150,000 to 370,000 years ago. It is not known what became of those responsible for this donation. "We can assume that they were very few in number and became extinct" , says Janet Kelso. As for the advantage that this sapiens Y chromosome seems to have for Neanderthals, it remains to be discovered.
For our part, we have kept no trace of this hybridization, or very little. The sequences of archaic origin in our genome come from another encounter, which occurred between 60,000 and 40,000 years ago, just before Neanderthals disappeared. We thus carry in our genome between 1 and 4% of sequences inherited from Neanderthal. This dose of Neanderthalness, estimated in Europeans at 2 to 3%, is slightly higher in Asians. Several hypotheses attempt to explain this difference. Some researchers suggest that the Sapiens established in Asia may have cohabited more than once or longer with Neanderthals along the way. The Asians would therefore have benefited from a greater contribution of Neanderthal sequences. According to others, the ancestors of modern Asians would have gone through a crisis causing a drastic drop in the size of their group. The diversity of the population would have been temporarily impoverished, favoring the fixation of sequences. Finally, statistical models indicate that the Neanderthal heritage would have been diluted among European Sapiens. For this, we must imagine that the ancestors of the latter encountered another population of archaic Sapiens, which would have reduced the share of Neanderthal DNA. This archaic population, of which nothing is known but which allows demographic models to explain genomic data, is called "Basal Eurasian".
And the Africans? According to the usual story, Sapiens came out of Africa around 60,000 years ago, just before encountering Neanderthals in the Near East. The latter never set foot in Africa, where groups of Sapiens therefore continued their history without frequenting him. However, according to a study conducted by Joshua Akey, of the American University of Princeton (New Jersey), all modern humans carry sequences inherited from Neanderthals, including Africans. It is a new method of analysis which has enabled the geneticist to open this breach in the dominant theory. He thus calculated that the genetic contribution of Neanderthals is on average 17 megabases in Africans, or 0.3% of their genome, when Europeans have 51 and Asians 55. Much more than previous estimates, which considered Africans as Homo sapiens devoid of any archaic interbreeding. As often with the history of humanity, "purity" is to be qualified... A group of Homo sapiens would therefore have returned to Africa after meeting Neanderthal. What happened then? In the absence of traces, science still does not know.
Following the coasts of the Indian Ocean
What we do know, however, is that another Hominid rubbed shoulders with Sapiens:Homo denisovensis . From this close cousin of Neanderthal - the two species diverged only about 350,000 years ago -, we know almost nothing. Some more or less putative fossils - including a tooth - in Asia, and a phalanx, discovered in the Denisova cave in Siberia, from which good quality DNA has been extracted and a complete genome sequenced.
READ. This cave in which Denisova Man and Neanderthal would have lived
Homo sapiens therefore also mixed with the Denisovans, a few millennia after its encounter with Neanderthals. "But since we don't have for Denisova that from the genome of a single individual, the estimate of the percentage of genes inherited from this archaic group remains imprecise" , emphasizes Céline Bon, paleogenetician at the Musée de l'Homme. This hybridization only concerns humans who went east, after their encounter with Neanderthals.
Among our contemporaries, we thus distinguish two groups holding these archaic sequences:Asians from the Far East (Chinese, Japanese, Vietnamese, etc.) and Melanesians. 2 to 3.7% of the genome of the latter comes from Denisova. "According to most settlement models, these populations now settled on islands in the Pacific Ocean moved along the coasts of the Indian Ocean. They could not therefore meet the Siberian Denisovans, but another group", says the researcher. There were therefore several groups of Denisovans at the time when our Sapiens ancestors were expanding their territory. Moreover, the Chinese, and Asians of the Far East in general, present Denisovan sequences from two distinct populations. It seems indeed that the populations of Neanderthal and Denisova were small, and quite isolated from each other. A situation that favors the maintenance of significant diversity between the groups. On the other hand, we find a great genetic continuity between the different Sapiens since their exit from Africa, which must result from constant exchanges between its populations. "But watch out! recalls Alicia Sanchez-Mazas, who heads the anthropology unit of the Department of Genetics and Evolution at the University of Geneva. We only have the DNA of very few archaic individuals." Understanding this archaic heritage also means looking at the sequences that we have preserved.
READ. The genome of the Ayta people would prove the late presence of Denisova in the Philippines
"The genes inherited from these exchanges were lost, expunged from our genome a long time ago , says Céline Bon. DNA of archaic origin that has persisted in the Sapiens genome mainly relates to regions outside the genes." Nevertheless, variants of Neanderthal or Denisovan origin have been associated with certain biological characteristics. "In particular, skin color has been linked to variants from Neanderthals, continues the researcher, without it being possible to determine whether they give a lighter or darker skin."
The modest influence of Neanderthals
"There has been a lot of talk about genes associated with immunity , completes Alicia Sanchez-Mazas. They are very dependent on the environment, the pathogens are not the same from one environment to another. However, after leaving Africa, Homo sapiens has faced significant climate change." It is therefore not surprising that he kept, from his encounters with hominids living in these conditions for a longer time, sequences which facilitated his adaptation to the environment.
On the other hand, for some genes, no alleles from archaic populations are found. "This is the case of the FoxP2 gene which participates in the development of language" , says Céline Bon, but also of genes expressed in the testicles. Hybrid children or descendants of hybrids who expressed certain alleles from Denisova or Neanderthal may have presented problems with cognitive development or fertility. At the population level, these alleles of archaic origin have completely disappeared.
Finally, advantageous genes in the past sometimes constitute a vulnerability today. Archaic sequences have been associated with many ailments:schizophrenia, depression, autism… And even freckles! But these data come from more or less reliable genetic association studies. Work carried out from the large DeCODE database, which contains the genome of thousands of Icelanders, has recently made it possible to qualify their responsibility. Only five complex traits, including variants related to shorter stature or accelerated blood clotting, seem truly attributable to sequences inherited from Neanderthals, and their influence is modest. But for infectious disease response, the impact can be far greater. A study published in September 2020 in Nature shows that one of the Neanderthal legacies is an increased risk of developing severe forms of Covid-19. Some encounters mark you forever.
By Agnes Vernet