Neanderthals Had Sex with Everybody, and Other Findings from a New DNA Sequence

A new analysis of Neanderthal genomes has found that not only did Neanderthals interbreed with early humans, they also interbred with at least two other early human relatives, and possibly many more.

The findings are the result of a seven-year project to completely sequence a Neanderthal genome. The group produced a draft genome sequence in 2010, but the one released Wednesday is “of a quality at least as high as that of genomes sequenced from present-day people,” according to the Max Planck Society, the group that funded the research.

The genome was sequenced from DNA taken from a 50,000-year-old toe bone found in 2010 by a team of Russian archaeologists in southern Siberia. According to the paper, published in Nature, modern humans share between 1.5 and 2.1 percent of our DNA with Neanderthals, and share another 3-6 percent of our DNA with Denisovans, an early hominin species that interbred with both Neanderthals and modern humans. Researchers also found evidence for interbreeding between Neanderthals and unknown early hominins.

One early hypothesis from the team is that the "unknown hominin" could be Homo erectus, a group that originated in Africa 1.8 million years ago. But researchers aren't sure exactly how Homo erectus genes would have ended up in Siberia. Despite findings that suggest interbreeding, they say that, ultimately, gene flow between Neanderthals and other hominin species remained very low, for various reasons.

“We present evidence for three to five cases of interbreeding among four distinct hominin populations,” the paper says. “Clearly the real population history is likely to have been even more complex … our analyses show that that hominin groups met and had offspring on many occasions in the Late Pleistocene, but that the extent of gene flow between the groups was generally low.”

Though we’ve known for several years that Neanderthals and humans interbred, and that humans have bits of neanderthal DNA, researchers working on this paper still aren’t sure how often humans and Neanderthals met and interbred.

“We don’t know if interbreeding took place once, where a group of Neanderthals got mixed in with modern humans and it didn’t happen again, or whether groups lived side by side, and there was interbreeding over a prolonged period,” Montgomery Slatkin, a University of California, Berkeley graduate student who worked on the paper said. “The history of humans and hominins during this period was very complicated.”

The paper is clear about one thing, however: Though Neanderthals at least occasionally interbred with other early hominins, the individual analyzed in the study was definitely the result of inbreeding.

“We performed simulations of several inbreeding scenarios and discovered that the parents of this Neanderthal individual were either half siblings who had a mother in common, double first cousins, an uncle and a niece, an aunt and a nephew, a grandfather and a granddaughter, or a grandmother and a grandson,” Slatkin said.

This is the most thorough DNA sequencing of a Neanderthal, and the team has set up a catalog for researchers to compare human, Neanderthal, Denisovan, and modern ape genomes. Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology, says that it’s a catalog “of the genetic features that sets all modern humans apart from all other organisms, living or extinct.”

“I believe that in it hide some of the things that made the enormous expansion of human populations and human culture and technology in the last 100,000 years possible,” he said.