Sex with Neanderthals was common for early Eurasian Homo sapiens, DNA says

Sex with Neanderthals was common for early Eurasian Homo sapiens, DNA says
Hajdinjak et al. 2020

DNA from the earliest Homo sapiens in Europe adds more detail to the story of our species’ expansion into Eurasia—and our complicated 5,000-year relationship with Neanderthals.

The earliest traces of our species in Eurasia are a lower molar and a few fragments of bone from Bacho Kiro Cave in Bulgaria, dating to between 46,000 and 42,000 years old. A recent paper describes DNA from those fossils, as well as a 42,000- to 37,000-year-old jawbone from the Oase site in Romania. The results suggest that the early waves of Homo sapiens in Eurasia included several genetically distinct groups, only some of which eventually passed their genes on to modern people. Most of those early Eurasians mingled with Neanderthals fairly often.

Paleolithic and ready to mingle

Neanderthals had lived in Europe and Asia for at least 350,000 years (and had a complicated population history of their own) when the first groups of Homo sapiens expanded northward from eastern Africa and the Levant. Today, many populations of modern humans still carry tiny fragments of Neanderthal DNA in our genomes as souvenirs from the mingling of two hominin species 45,000 years ago. But we still don’t know much about how often Neanderthals and Homo sapiens got together during the few millennia when they shared a continent.

When Max Planck Institute for Evolutionary Anthropology geneticist Mateja Hadjinjak and her colleagues sequenced DNA from the Homo sapiens bones at Bacho Kiro Cave in Bulgaria, one lower molar and a small scrap of bone were all that remained of a man who died at the site around 45,900 years ago. But that’s enough to get us genetic data these days. His genome contained fragments of the Neanderthal versions of some genes, which had been split up and rearranged in a way that suggested they’d been passed down through about six generations. In other words, one of his great-great-great-great grandparents was a Neanderthal.

Two other pieces of bone at Bacho Kiro Cave were the sole remains of two men who died around 45,000 to 42,000 years ago, and both of them had Neanderthal ancestors seven generations back. Meanwhile, at the Oase site in Romania, DNA from a man who died between 42,000 and 37,000 years ago revealed that one of his direct relatives—a parent or grandparent—was a Neanderthal.

That’s a rare glimpse of a specific, very human story: direct evidence that a Neanderthal and a Homo sapiens had sex and produced a child. A tooth from Denisova Cave in the Altai Mountains of Siberia tells a similar story about a Neanderthal, a Denisovan, and their daughter 90,000 years ago. Those moments are rare in a genetic and archaeological record, which usually only reveals big, sweeping populations trends.

While we don’t have direct evidence of individual relationships—whatever form they took, and whatever they meant to the people involved—the relationships themselves probably were anything but rare.

“It is striking that all four of the European individuals who overlapped in time with late Neanderthals and from whom genome-wide data have been retrieved had close Neanderthal relatives in their family histories,” wrote Hadjinjak and her colleagues in their paper. “This suggests that mixing between Neanderthals and the first modern humans that arrived into Europe was perhaps more common than is often assumed.”

Neanderthal deserts

If Neanderthals and Homo sapiens were really having sex—and offspring—that often, it may sound like modern people with European and Asian ancestry should be carrying around a lot more Neanderthal DNA. But on average, it’s only about two percent. But Hadjinjak’s study suggests that most Neanderthal genes got weeded out by the process of natural selection very quickly. Within just a few generations, the three men from Bacho Kiro Cave only had between 3.0 and 3.8 percent Neanderthal DNA.

In modern people, Neanderthal DNA is scattered throughout the genome, but Neanderthal versions of genes are more common in some parts of the genome than others. And in some areas, called “Neanderthal deserts,” there are no Neanderthal genes. When Hadjinjak and her colleagues examined the DNA from the three Bacho Kiro men and the one from Oase, they found that although a few Neanderthal alleles still lingered in those sections of the genome, the “Neanderthal deserts” were already starting to form. In other words, the Homo sapiens versions of certain genes offered such an evolutionary advantage that they had already out-competed the Neanderthal versions within just a few generations.

In fact, a younger bone fragment from Bacho Kiro dating to around 35,000 years ago came from a person who had just 1.9 percent Neanderthal DNA, similar to the levels seen in most modern non-African people. However, Hadjinjak and her colleagues acknowledged that “additional individuals with recent Neanderthal ancestry will be needed to fully resolve this question.”

A complicated relationship history

Before this pair of recent studies, we had DNA from just three individuals older than 45,000 years. Now we have DNA from seven, and that drastically improves our view. Still, as always in archaeology, the more data we get, the more questions we can ask.

And there are some questions we may never be able to answer. When Homo sapiens and Neanderthals had offspring, were those pairings the result of illicit relationships, intergroup marriages, or something more violent? It’s hard to imagine what kind of archaeological evidence could provide those details, and the genetic evidence records only the bare biological facts. But because people have always been people, the answer is likely “all of the above, at different times and places.”

Another recent study supports the suggestion that the story wasn’t the same everywhere. DNA from the bones of a 45,000-year-old member of our species, from the Ust’Ishim site in Siberia, suggested that this person’s most recent Neanderthal ancestor was 80 to 95 generations back in the family tree.

And when anthropologist Kay Prüfer, also of the Max Planck Institute, sequenced the DNA of a woman who died at Zlatý kůň in the Czech Republic, her mitochondrial DNA (DNA outside the cell nucleus that is passed directly from mother to child) suggested that she was about 43,000 years old. And based on the length of the segments of Neanderthal DNA in her nuclear genome, her last Neanderthal ancestor lived about 64 to 80 generations before she did. This could mean that interactions varied as different groups of humans and Neanderthals moved around and potentially interacted in different ways.

Who’s related to who?

The DNA from both recent studies sheds some light on how those different groups moved around and how some of them are related to groups of modern people in central and eastern Asia. Both Hadjinjak and her colleagues and Prüfer and her colleagues compared DNA from their specimens to genomes from other ancient and modern people, looking to see how many alleles they shared in common and using computer modeling to see how they might be related.

In Prüfer and her colleagues’ study, the woman from Zlatý kůň belonged to a group of people who apparently didn’t contribute much to the ancestry of later Eurasian people. And DNA from Oase 1, the son of a Neanderthal and a Homo sapiens, suggested that his population also hadn’t “contributed detectably to later populations.” In other words, he was part of a lineage that had died out.

On the other hand, the earliest known Homo sapiens remains in Europe, at Bacho Kiro Cave, belonged to a group that shared noticeably more alleles with modern people in eastern and central Asia than with the people now living in Bulgaria (or anywhere else in Europe or western Asia). The Bacho Kiro population also seems to have been related to another group, which included the ancestors of a 40,000-year-old person unearthed at Tiayuan, in China.

That “provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia,” as Hadjinjak and her colleagues put it, but it’s also clear that several of the first Homo sapiens groups to reach Europe eventually faded away without leaving much of a genetic mark.

The tooth and bone fragments at Bacho Kiro Cave were found buried in a layer of sediment that also contained the remains of a culture known to archaeologists as the Initial Upper Paleolithic. Based on a common style of making stone tools, Initial Upper Paleolithic, or IUP, artifacts have turned up at sites from central and eastern Europe all the way to Mongolia, and it’s possible that some may be waiting to be discovered even further east.

Archaeologists are still debating whether the IUP spans such a wide area because one group of people managed to spread that far or because ideas spread between groups. But both archaeological and genetic evidence now suggest connections between the first Homo sapiens to gain a foothold in Europe and those who lived in Asia just a few thousand years later.

Nature, 2021 DOI: 10.1038/s41586-021-03335-3  (About DOIs).