A high-quality genome sequence obtained from a female Neanderthal toe bone reveals that the individual’s parents were close relatives and that such inbreeding was prevalent among her recent ancestors, according to a paper published today (December 18) in Nature. But the sequence also reveals that interbreeding occurred between Neanderthals and other hominin groups, including early modern humans.

“Did humans evolve like a constantly branching tree? A lot of people think so,” said Milford Wolpoff, a professor of anthropology at the University of Michigan, who was not involved in the study. “But there’s also been this thread of thought, by some people like me, that humans evolved more like a network, where there are different populations and they split and sometimes they come back together and they mate.” The new toe bone sequence data, he said, is “really important because it’s giving us good evidence that there’s been constant interbreeding between different human groups all through prehistory.”

The toe bone was found in a cave in Denisova, Siberia, where the conditions for DNA preservation are near-perfect. “The cave year-round has an average temperature of zero degrees Celsius and that’s probably helping to contribute to the preservation,” explained John Hawks, a professor of anthropology at the University of Wisconsin, who also did not participate in the study.

Indeed, the toe bone and its DNA were so well preserved that it was possible to obtain sequence data that “is on the same level, as far as quality goes, as many other modern human genomes,” said Kay Prüfer, an evolutionary geneticist from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the study. “For every position in the genome we have on average 50 fragments covering it, which is amazing,” he said. Just how amazing? Previously sequenced Neanderthal genomes have average coverages of 0.5 to 1.3.

Also amazing, was the fact that the toe bone was Neanderthal at all. Previous bone and tooth samples found in the cave had yielded high-quality DNA sequences identified as belonging to a new and different group of hominins called the Denisovans, who were named after the location. “We were expecting that it [the toe] would be another Denisovan,” said Prüfer, “but, to our surprise, it wasn’t.”