What does it mean to be part Neanderthal? We’ve known since 2010 that if you have any non-African ancestry you probably carry Neanderthal DNA. Since this groundbreaking finding, new research on ancient DNA is showing that this wasn’t a fluke. Growing evidence of widespread interbreeding between ancient human populations is forcing scientists to rethink how our genetic identity was formed.
Last month, Svante Pääbo and his colleagues at the Max Plank Institute in Leipzig published the highest quality Neanderthal genome sequence yet, from a 50,000-year-old toe bone found in a Siberian cave. This new genome reveals surprisingly intimate details about the life of the Neanderthal woman to whom the bone belonged. Her genome sequence shows that the maternal and paternal copies of her DNA are extremely similar, a clear sign that her parents were very close relatives. The level of inbreeding detected in the Neanderthal woman’s genome is consistent with a few different scenarios: her parents were an uncle and niece, a grandparent and grandchild, half siblings who shared a mother, or double first cousins. The scientists found evidence that the widespread inbreeding among these Siberian Neanderthals was higher than in any contemporary human population. This suggests that these Neanderthals lived as small, isolated families on a vast, empty landscape. The genetic data also show that the extinction of Neanderthals was likely a foregone conclusion by 60,000 years ago, before modern humans appeared in Europe. Neanderthal genetic diversity, an important sign of a population’s health was “among the lowest measured for any organism” on the planet today. Their genes tell the story of a doomed species.
Now it’s clear that humans, both modern and archaic, hooked up wherever they encountered each other.
And yet this image of an isolated, declining species is misleading. More Neanderthal DNA is present on the planet today than ever before. In their 2010 study, Pääbo and his colleagues first reported that non-Africans typically have one to four percent Neanderthal DNA in their genomes. In a recent paper titled “Resurrecting Surviving Neanderthal Lineages From Modern Human Genomes,” Benjamin Vernot and Joshua Akey, a pair of University of Washington researchers, report that one-fifth of the entire Neanderthal genome can still be found in living humans. While any one non-African individual today carries only a small percentage of Neanderthal DNA, different individuals carry different bits of the Neanderthal genome. In aggregate, Vernot and Akey argue, there is so much Neanderthal DNA in living humans that it is possible to study the genetics of Neanderthals without being limited to DNA extracted from fossils.
Vernot and Akey’s most striking finding is that sex with Neanderthals was helpful to the descendants of the early modern humans who moved into Europe and Asia. Between 60,000 and 40,000 years ago, these modern humans were migrating out of Africa and encountering populations of archaic humans in new environments—Neanderthals in Europe, and another recently discovered group, called Denisovans, in Asia. The researchers found that 70 percent of Europeans have the non-African, Neanderthal version of a gene that contributes to skin pigmentation and integrity. The same is true of East Asians, but with a different skin-related gene. A research group led by David Reich at Harvard University independently reached a similar conclusion. By the time modern humans arrived in Europe and Asia, the Neanderthals and Denisovans had already been there for hundreds of thousands of years. These older, archaic humans were better adapted to the local environment than the newcomers, and interbreeding with the locals appears to have helped modern humans adapt.
SCIENTISTS KNOW THAT HYBRIDIZATION between two populations or species can be a source of evolutionary innovation, but just five years ago, the idea that humans interbred with Neanderthals frequently enough to leave a mark on our genetics was highly controversial. Now it’s clear that humans, both modern and archaic, hooked up wherever they encountered each other. Pääbo’s team showed that, not only was there interbreeding between modern humans and archaic populations, but Neanderthals and Denisovans mixed with each other, and Denisovans appeared to have mixed with an even older, as yet unidentified population of archaic humans.
Other genetic studies tell us that the same story has played out over and over again. Long after the Neanderthals were gone and only modern humans were left, Europe was populated by older groups of hunter-gatherers, and new groups of farming tribes that had migrated from the Near East. Researchers had previously believed that the farmers largely replaced the hunter-gatherer groups, but new ancient DNA studies are uncovering extensive interbreeding here as well. Harvard’s David Reich and Johannes Krause, at the University of Tübingen, led a research team that sequenced the genomes of nine 8,000-year-old European remains. They found that Europeans today carry plenty of hunter-gatherer DNA, meaning that the early farmers didn’t simply replace the older population; they assimilated them.
These ancient DNA studies are the genetic equivalent of the Dead Sea Scrolls, offering scientists a direct look at a portion of our deep past that seemed irretrievable. It is now clear that our genetic identities are a complex mosaic of the ancient and modern. It’s a striking change from what we believed just a few years ago. We didn’t emerge from our African Eden fully formed and ready to conquer the archaic humans who populated Europe and Asia. Sometimes we made love and not war, and we’re better off for it.
