Earlier this summer, a team of scientists led by Leipzig researcher Svante Pääbo identified a man who, living 40,000 years ago in what is now Romania, had a recent Neanderthal ancestor. Examining the DNA extracted from the man’s fossilized bones, the researchers discovered that he had a Neanderthal in his family tree only four to six generations back. In other words, the man had a great- or great-great-grandparent who was something that, only a few years ago, many scientists were skeptical actually existed: a human/Neanderthal hybrid. Actually getting our hands on the DNA of an individual who was so closely related to one is a stunning development. This latest find is part of a series of remarkable and very recent discoveries that are prompting a major re-consideration of our ideas about who the Neanderthals were, and how modern humans came to be.

It's hard to overstate how rapidly our scientific understanding of the relationship between humans and Neanderthals has changed. As recently as 2009, scientists could reasonably claim that "incontrovertible evidence for or against Neanderthal and modern human admixture has yet to be identified." At the time, studies of actual ancient Neanderthal DNA were starting to trickle in, but, despite the evidence that humans and Neanderthals had inhabited the same regions of the world for thousands of years, the genetic data offered no evidence that humans and Neanderthals had interbred. It wasn’t even clear whether humans and Neanderthals could actually produce fertile offspring if they tried, or whether they were too genetically distant. In a 2004 analysis, researchers looked at the available DNA evidence and concluded that "evidence in favor of no, or very little, interbreeding between Neanderthals and modern humans is much stronger than previously realized." The picture was much the same two years later, when researchers took advantage of a new technology that let researchers obtain substantially more genetic material from ancient bones and published a much more extensive study of Neanderthal DNA. Despite having more data, there was no sign that Neanderthals and humans produced viable offspring—the researchers estimated that "the Neanderthal contribution to modern genetic diversity is zero," though they acknowledged that this conclusion could change with new evidence.

"Modern humans were part of what one could term a 'hominin metapopulation'—that is, a web of different hominin populations, including Neanderthals, Denisovans and other groups, who were linked by limited, but intermittent or even persistent, gene flow."

That evidence began to appear in 2010, when the first draft of a full Neanderthal genome was published. The new genomic data wasn't conclusive, but it did show that, though all humans today are descendants of the original modern humans who evolved in Africa, there were surprising genetic similarities between Neanderthals and contemporary non-Africans. This seemed to suggest that Neanderthals mixed with an early population of non-African humans, perhaps living in the Middle East, who would later settle the Eurasian continent, carrying Neanderthal genes with them. Following this study, definitive evidence for human/Neanderthal interbreeding quickly emerged as higher-quality Neanderthal DNA data rolled in. Two studies last year reported that Neanderthals and another type of extinct, archaic humans, called Denisovans, left genetic traces in nearly all modern humans—particularly Europeans and Asians, but also Native Americans (through their descent from ancient East Asians—Neanderthals did not live in the Western Hemisphere), and even, to a lesser degree, Africans. As Svante Pääbo, whose lab pioneered the technology to recover ancient DNA, recently wrote, "modern humans were part of what one could term a 'hominin metapopulation'—that is, a web of different hominin populations, including Neanderthals, Denisovans and other groups, who were linked by limited, but intermittent or even persistent, gene flow."

What was debatable in 2009 is now unquestionable: Neanderthals contributed to our gene pool. The important scientific issues have now shifted. With the existence of human/Neanderthal offspring established, researchers now want to understand what role those offspring played in our evolutionary history. Which populations of Neanderthals and humans interbred, and when? Because Neanderthal DNA is found primarily in non-Africans, researchers initially believed that a single, main "pulse" of Neanderthal gene flow into modern humans occurred before those humans settled the Eurasian continent, probably in the Middle East between 50,000 to 80,000 years ago. But the DNA of the ancient European man with the recent Neanderthal ancestor shows that human/Neanderthal interbreeding also happened at other times and places.

Two studies published earlier this year also suggest that human/Neanderthal admixture was not limited to one place and time. Working independently, Benjamin Vernot and Joshua Akey at the University of Washington, and Bernard Kim and Kirk Lohmueller at the University of California–Los Angeles, ran simulations of different demographic models and compared those models against DNA data from hundreds of contemporary Asians and Europeans. Their results showed that there were likely at least two major pulses of Neanderthal gene flow into modern humans, one into the common ancestors of all Europeans and Asians, and a subsequent pulse into Asians. As Vernot and Akey wrote, "The history of admixture between modern humans and Neanderthals is most likely more complex than previously thought."

Another important question that scientists are now asking is this: How does our Neanderthal genetic heritage affect our biology? The modern humans who left Africa and first colonized Europe and Asia were entering new environments, with new climates, new food sources, and new diseases. Archaic humans, on the other hand, had inhabited and adapted to those environments for hundreds of thousands of years. As modern humans encountered Neanderthals, they had an opportunity to get a little genetic help, by an evolutionary process called "adaptive introgression." Adaptive introgression means that the hybrid children of modern and archaic humans, as well as their descendants, could have inherited some genes from their Neanderthal parents that helped them survive better in European and Asian environments. Researchers are only just beginning to examine this possibility, but they have already found some good candidates for adaptive, introgressed genes, including an archaic version of a gene that may have helped Tibetans adapt to life at high altitudes, and other genes that affect freckling, skin pigmentation, immunity, and metabolism.

Findings like this are forcing us to re-define what it means to be a biologically modern human. For more than a century, we've compared ourselves with Neanderthals in order to make ourselves feel special. Our archaic cousins dwindled to extinction while we went on to dominate the world. What do we have that they didn't? It’s a question that has spawned a lot of controversy among anthropologists, but few certain answers; and now the rapid developments in Neanderthal DNA analysis make it clear that the solution won't be as simple as we thought. The surprising results in genetics are also mirrored by new archeological findings, which show that Neanderthals probably behaved in ways that were once thought to be exclusive to us. These discoveries make it more difficult to use Neanderthals as yardsticks for measuring the evolutionary progress of modern humans. Our revised view of Neanderthals is, however, a sign of our scientific progress, as we begin to understand how we became the species we are today.

Inside the Lab explores the promise and hype of genetics research and advancements in medicine.