Earliest Modern Humans in Europe Had Neanderthals in the Family

Archaeologists identify one of the first women to reach Europe. Her line died out, but three other early humans, in Bulgaria, appear to have descendants today

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Reconstruction of Neanderthal and child. Museum for Prehistory in Eyzies-de-Taya
Reconstruction of Neanderthal and child.Credit: AFP

Modern humanity began to evolve in Africa at least 300,000 years ago and began to exit the continent for Eurasia at least 200,000 years ago. The earliest Homo sapiens migrants out of Africa went extinct. All non-Africans descend from modern human migrants around 50,000 years ago – from some of them, that is.

Now two new genetic studies have identified three early humans in Bulgaria, whose descendants seem to live on, and a woman in the Czech Republic, as among the first to leave Africa in the Great Exit – but her line apparently went extinct.

All had Neanderthals in the family tree, and reveal our amatory secret: not only admixture, but a lot of it.

One new study describes three people who lived in Bulgaria between 45,930 and 42,580 years ago, in Bacho Kiro Cave. They are, write Mateja Hajdinjak and colleagues in Nature Ecology & Evolution, among the earliest modern humans whose remains have been recovered in Europe so far.

The other new study analyzed the genome of a woman whose skull was found in Zlaty kun, the Czech Republic, report Kay Prüfer and colleagues, in Nature. Dating her skull proved unusually difficult, but based on the length of her Neanderthal sequences (recombination will inevitably break up long Neanderthal segments into shorter segments over time) and other indicators, she seems to have been among the earliest sapiens migrants to Europe. That would make her over 45,000 years old.

The three found in Bacho Kiro may have descendants in present-day east and central Asia and the Americas; a later Bacho Kiro person from about 35,000 years ago, analyzed separately, may have descendants in western Europe. A separate study of modern remains in China from 40,000 years ago found it also contributed to the ancestry of the ancient and present-day East Asian population.

Excavations at Bacho Kiro Cave, BulgariaCredit: Zeljko Rezek / MPI-EVA Leipzig
The skull of the woman from Zlaty kun, who may have been one of the earliest modern humans in Europe.Credit: Marek Janta / TM studio

But separate research on early modern humans who also lived over 40,000 years ago in Romania and Siberia indicates their lines died out too, like the Czech woman.

So, some modern humans migrated from Africa to Europe and died out; some didn’t – this makes sense. The data indicates continuity to some degree between some early arrivers in Europe and today’s populations. This makes sense too. But what are those whispers from the Neanderthals?

Granny was a Neanderthal

The evidence that Homo sapiens interfaced with Neanderthals seems incontrovertible by now. Questions that remain are where and when – the how, we will probably never know, and that’s probably just as well.

As for how often, the answer seems to have been “very.”

The land that is today Israel was one arena where Neanderthals and Homo sapiens tangoed. Homo sapiens reached Israel at least 200,000 years ago, as we know from a jaw found in Misliya Cave in northern Israel. (Some contest its identification as sapiens; that’s how it is in physical anthropology.)

Entrance to Bacho Kiro caveCredit: Nikolay Zahariev / MPI-EVA Leipz

But then sapiens disappeared from these parts about 100,000 years ago, for reasons unknown. And then Neanderthals appeared in the Levant, migrating south from Europe, about 70,000 years ago, and survived in Israel until 50,000 years ago – which is roughly when modern humans reappeared on the scene.

What happened next is murky, but clearly we mixed. Remains of hybrid sapiens-Neanderthals have been found in Israel. Neanderthals living in the West Bank even seem to have been using technology thought to have been the exclusive fief of Homo sapiens. Then, as we said, 50,000 years ago the local Neanderthals vanished: possibly out-competed by the incoming sapiens, or for any of the other myriad reasons touted for the demise of the Neanderthals. (They held on in Iraq rather longer.)

All in the family

So what have we? Modern humans in Israel and the Levant who mixed with Neanderthals about 50,000 years ago and some of the hybridized descendants migrated to Europe. There in Europe they encountered more Neanderthals and mated with them there too.

Between 3 to 3.8 percent of the genome of the three individuals found in Bulgaria was Neanderthal in origin, Hajdinjak and the team write. The distribution of Neanderthal DNA in their genomes indicates they may have had Neanderthal ancestors as recently as six or fewer generations back.

Oase1, the modern human found in Romania, had even more recent Neanderthal ancestry: he or she had somewhere between 6 to 9 percent Neanderthal DNA.

The Zlaty kun lady had around 3.2 percent Neanderthal DNA – but the intriguing thing is that her unbroken Neanderthal sequences were longer than those observed in the 45,000-year-old Siberian known as Ust-Ishim, suggesting she was older than him. And that is why the team suspects she was among the earliest population to leave Africa and reach Europe in the expansion out of Africa that succeeded (i.e., that didn’t go extinct, though her line evidently did).

By the way, the analysis of prehistoric DNA is technically difficult and extremely painstaking. Weeding out “alien” signals, including from bacteria and the like, the molecular archaeologists deduced that at some point an attempt had been made to preserve the Zlaty kun skull using glue derived from cows.

Second lower molar of a modern human found in Bacho Kiro Cave who had a Neanderthal ancestor less than 6 generations agoCredit: Rosen Spasov / MPI-EVA Leipzig

The bottom line is that modern humans and Neanderthals coexisted in the Levant and Europe for thousands of years, and that when we encountered Neanderthals, things got intimate.

But the noisy genetic messages arising from the modern humans indicates another thing, too – that theories of successive population replacements in Europe hold water.

It seems that today’s Europeans stemmed from a deeply divergent out-of-Africa lineage and that the Zlaty kun woman preceded the split of European and Asian sapiens populations – as did the gentlemen in prehistoric Siberia and Romania, Prüfer and the team write.

So they wondered if the Zlaty kun woman could have been related to the Siberian man – members of the same population. Nope. Ust-Ishim turned out to share ancestry with later Eurasians, which she didn’t; and that in turn implied that the Zlaty kun woman lived in a people who split earlier from the people who gave rise to Ust-Ishim and Eurasian populations.

We were a messy lot. “In conclusion, the Bacho Kiro Cave genomes show that several distinct modern human populations existed during the early Upper Palaeolithic in Eurasia,” write Hajdinjak and her team. The lines Oase1 and Ust-Ishim died out, it seems; the earlier Bulgarian cave people did not – in Asia and eastern Europe – but their signal is not found in western Europe. The later Bulgarian cave people do seem to have gone on in western Europe. And at the end of the day, all the early Europeans had “close Neanderthal relatives in the family.”

All this lends even more credence to yet another separate paper, which argues that Neanderthals and Homo sapiens had similar auditory and speech capacities. We could, possibly, speak to one another, though chances are we didn’t understand each other any better than humans understand each other today – one glance at Reddit shows as much. But the language of love may have been universal.