Sex, disease, and extinction: what ancient DNA tells us about humans and Neanderthals

 In Science

Two new genetic analyses help explain the unexpected roles Neanderthals play in modern human life — influencing everything from hair color to mental health. The new research also adds to evidence that Neanderthals lived in small, isolated communities, while a third study suggests that early modern humans may have developed large social networks that facilitated the exchange of mates and ideas.

The findings help explain what exactly Neanderthal DNA is doing in many modern human genomes, and how it affects our health. Piecing together the sex lives of our human ancestors may also help us understand how and when these genes were exchanged. All together, the three studies — published in various journals last week — contribute key clues to the mystery of why humans survived to populate the globe, even as our close cousins, the Neanderthals, died out.

Modern humans, or Homo sapiens, and Neanderthals shared a common ancestor roughly half a million years ago. They then split and evolved in parallel: humans in Africa, and Neanderthals on the Eurasian continent. When humans finally ventured to Eurasia, they had sex with Neanderthals, swapping DNA around. Today, people who aren’t of African descent owe roughly 2 percent of their DNA to their Neanderthal ancestors. “The first question that anyone ever asks is ‘Well, what does it do?’” says Janet Kelso, a bioinformatician who studies genome evolution at the Max Planck Institute in Germany.

Previous studies have linked Neanderthal DNA to a big range of health conditions in modern-day people, including depression, nicotine addiction, and skin disorders. But it’s not all bad: understanding which stretches of Neanderthal DNA stuck around might also help scientists tease apart which traits might have helped ancient humans survive in Eurasia, like changes to skin and hair, or resistance to certain diseases.

There’s also another mystery to solve: Neanderthals went extinct about 40,000 years ago, while Homo sapiens did not. Why? There are a lot of theories, including that alliances between modern humans and dogs helped humans hunt food better, essentially starving Neanderthals out of Europe. Or, humans might have reproduced faster than Neanderthals, multiplying and edging them out. “It’s still one of those unsolved and really interesting questions,” says Martin Sikora, a geneticist at the University of Denmark. “Were we more successful because we had better technology, or was it just a consequence of pure numbers?”

To piece the story together, scientists are searching for more Neanderthal genomes locked in ancient bones, and for more Neanderthal DNA hiding in present-day genomes. The studies published last week have uncovered both.

A new ancient Neanderthal genome

The first study, published in Science, describes a bone fragment called Vindija 33.19, which was found in a Croatian cave of the same name in the 1980s. Now, researchers have finally been able to sequence the DNA locked inside, discovering it belonged to a female Neanderthal who lived 52,000 years ago. Researchers found that the Vindija Neanderthal was very similar genetically to another Neanderthal who died about 122,000 years ago in the Altai mountains of Siberia (dubbed the Altai Neanderthal).


Vindija Cave, Croatia.

Vindija Cave, Croatia.
Photo by J. Krause / Max Planck Institute of Evolutionary Anthropology

The fact that two Neanderthals separated by more than 3,700 miles and 70,000 years were so similar suggests that Neanderthal communities were tiny, with very little genetic diversity. “It’s quite amazing when you think about it,” says study author Kay Pruefer, at the Max Planck Institute. “They are really so closely related that you cannot find any two people on this planet that are this close.” That could support the theory that Neanderthals’ low genetic diversity may have contributed to their extinction.

Genetic diversity forms the basis for natural selection. If everyone in a population had the exact same versions of the same genes, then one plague or one hard winter could wipe everyone out. And then there’d be no survivors to pass on the genes that would give their offspring a chance to survive the next plague or harsh winter. Incest can also lead to genetic abnormalities: the Altai Neanderthal was the daughter of two half-siblings, and while the Vindija Neanderthal’s parents weren’t related, they were very, very genetically similar.

The newly sequenced Vindija genome is important for another reason: because Neanderthals and anatomically modern humans are thought to have interbred roughly 50,000 to 60,000 years ago, the Vindija genome is a closer match to the Neanderthal DNA still found in modern human genomes today. “That gives us more power, a greater ability to detect Neanderthal DNA that remains in modern humans,” says John (Tony) Capra, an evolutionary genomicist at Vanderbilt University, who was not involved in the research.


neanderthal-dorsal-bone-bence-viola

A Neanderthal toe bone discovered in the Denisova cave in Siberia’s Altai mountains.
Photo by Bence Viola

Thanks to the Vindija genome, the researchers tracked down Neanderthal DNA in genes that make certain modern-day humans more susceptible to rheumatoid arthritis, schizophrenia, and eating disorders. Neanderthal mutations also turned up in genes that influence how people respond to antipsychotic drugs, their levels of “bad” cholesterol and Vitamin D, and how much fat they pack around their middles.

Of course, it’s too simplistic for people to attribute their cholesterol levels to their Neanderthal DNA. “Even though Neanderthal DNA influences these traits, the overall influence on any given person’s risk is really quite low,” Capra says. Still, Neanderthals have gone extinct, and this DNA was swapped tens of thousands of years ago — yet it still has a measurable effect on modern humans.

New traits linked to Neanderthal DNA

In the second study, published in the American Journal of Human Genetics, researchers compared the genome of the 122,000-year-old Altai Neanderthal to that of more than 100,000 present-day people. (The 100,000 people, part of the UK Biobank, also had to answer questions about their moods, personality, and food preferences.)

The researchers found that Neanderthal DNA was especially common in stretches of genes that contribute to hair color and skin tone. Some Neanderthal variations were associated with blonder, paler complexions, and others were with darker pigmentation. That could mean that Neanderthals themselves had different hair and skin colors. The one hair color Neanderthals almost certainly didn’t have (or had very rarely) was red hair, the researchers found — contrary to popular depictions of our extinct relatives. The Neanderthal DNA also influenced psychological and neurological traits — like being a night owl, reporting feelings of loneliness and depression, and smoking.

These results don’t mean that Neanderthal genetic mutations cause these traits in modern-day humans, or that the same genetic variations gave rise to the same traits in Neanderthals, says study author Janet Kelso, at the Max Planck Institute. For example, while mutations introduced by Neanderthal DNA might be linked with an increased likelihood that a person might smoke, it doesn’t mean that our extinct relatives had a cigarette habit.

Late Stone Age people avoided incest

Early modern humans weren’t just having sex with Neanderthals, of course. They were also banging each other. A third study published last week, also in Science, suggests that ancient humans lived in large, complex social networks that helped them swap genes and ideas.

Sikora, at the University of Denmark, analyzed the DNA of one man, two children, and a hollowed-out thigh bone, all buried at a late Stone Age site called Sunghir, in Russia, some 34,000 years ago. The man was buried by himself, but the children were buried together head-to-head, with the hollowed-out thigh bone placed next to their bodies.


Upper paleolithic Sunghir burial decorated with ivory beads.

Upper paleolithic Sunghir burial decorated with ivory beads.
Photo by José-Manuel Benito Álvarez

Sikora found that none of the individuals at the site were related and, what’s more, they were shockingly genetically diverse — far more so than the two Neanderthals analyzed in the other studies. “The two kids buried head-to-head in the same grave, you’d assume there was some sort of close relationship,” Sikora says. But their genes revealed they were, at most, second cousins.

The Sunghir burials gave Sikora a chance to test his hypothesis that early humans developed a form of social structure that allowed early modern humans to swap partners and genes. That, in turn, would have allowed them to be more genetically diverse, and possibly more successful. One of the children at the Sunghir site had clearly suffered some sort of developmental disorder: his thigh bones were bent and twisted, possibly the result of a genetic abnormality.

That seemed to suggest that, maybe, the kid’s parents were related, since incest often causes abnormalities. But when Sikora sequenced the bones’ DNA, he found that the four individuals were not remotely inbred. In fact, their genomes showed the same, or even more, genetic diversity than present-day populations of hunter-gatherers in Africa and Amazonia.

Sikora’s team calculated that about 300 people would need to be having sex with each other to produce so much genetic variation. That’s a much bigger population than these Stone Age people were probably traveling with, Sikora says. But it is possible that smaller groups were embedded in a larger social network where people had sex and exchanged ideas. This would have kept people from becoming as inbred as the Altai Neanderthal, or as genetically homogenous as the Vindija Neanderthal, which was the consequence of living in isolated groups.

The distribution of cultural artifacts and tools across Eurasia backs that up, says Erik Trinkaus, an anthropologist at Washington University, St. Louis who wrote a book on the Sunghir burials. “During this time period, people were covering huge distances. It’s not unusual to find materials 300 or 400 kilometers away from where they came from,” Trinkaus says.

Of course, we can’t generalize about all hunter-gatherers at the time from this one population in Sunghir, says Bastien Llamas, a research fellow specializing in ancient DNA at the University of Adelaide in Australia, in an email to The Verge. It’s possible that the adult and the thigh bone were separated from the children by generations, meaning that this cluster of burials isn’t a fair indicator of the community’s diversity. Still, the results suggest that hunter-gatherer groups 34,000 years ago had pretty similar social networks to us today: limited family relationships within a group, avoiding incest, and mating outside that group. “I find it amazing,” Llamas says.

The study, like the others published last week, are steps toward understanding the complex relationships that made us who were are today. “Understanding our past, especially our genetic past, is super useful for understanding our genetic present,” says Joshua Schraiber, a population geneticist at Temple University. “I think it’s important to understand and embrace the diversity of humans across the planet.”

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