Before farming began to spread across Europe some 8500 years ago, the continent’s occupants were hunter-gatherers. They were unable to digest starch and milk, according to a new ancient DNA study of a nearly 8000-year-old human skeleton from Spain. But these original occupants did already possess immune defenses against some of the diseases that would later become the scourge of civilization, and they apparently had dark skin. The findings are helping researchers understand what genetic and biological changes humans went through as they made the transition from hunting and gathering to farming.

The rise of farming about 10,000 years ago was one of the most dramatic events in human history. Europe’s farmers came originally from the Middle East and migrated west via Greece and Bulgaria. For decades, the only way scientists could study these events was by extrapolating back from the genetics of modern-day Europeans, a rough guide at best to what had happened in the past. But over the past several years, ever more sophisticated techniques for extracting and sequencing DNA from ancient skeletons have opened the window on to the genetics of ancient hunter-gatherers and farmers alike, allowing researchers to not only trace their movements and interactions but also how the rise of farming changed their biology.

In June 2012, for example, a team led by geneticist Carles Lalueza-Fox of the University of Barcelona in Spain reported a complete DNA sequence from the mitochondria—the energy plant of living cells—of a hunter-gatherer skeleton discovered in 2006 at the La Braña-Arintero cave site in northwest Spain. The skeleton was one of two found in the cave, accompanied by ornaments made of the teeth of red deer, which this population apparently hunted along with other animals. This southern European genome showed striking similarities with that of a number of other hunter-gatherers in northern and Eastern Europe and suggested that early nomadic hunter-gatherers were a far more cohesive group—both genetically and culturally—than researchers had realized. The findings, some researchers pointed out, could help explain why prehistoric hunter-gatherers were able to coexist with early farmers for several thousand years before fading from the scene.

For the new research, published online today in Nature, Lalueza-Fox teamed up with ancient DNA ace Eske Willerslev of the University of Copenhagen and other scientists to completely sequence the nuclear DNA of the same La Braña skeleton. Although the new genome is a preliminary rough draft, a comparison of key genes involved in skin and eye color, diet, and the immune system with those of both early farmers and modern Europeans provides a tantalizing new picture of the changes that took place in European populations as farming took over.

One surprise is that the La Braña man had dark skin and blue eyes, a combination rarely seen in modern Europeans. Although today’s southern Europeans tend to be somewhat darker than their northern counterparts, they are still relatively light-skinned compared with Africans, an adaptation often linked to the need to absorb more sunlight and so produce adequate amounts of vitamin D. That this feature of the La Braña skeleton might have been widely shared and not just a one-off is also suggested by recent findings, as yet unpublished but posted online in preliminary form, that other European hunter-gatherers also had dark skin and blue eyes.

Lalueza-Fox suggests that prehistoric hunter-gatherers got most of their vitamin D from eating lots of meat and that natural selection did not lead to the evolution of light skin until the advent of farming and diets based more on carbohydrates. Thus meat, fish, and eggs, which make up a much higher proportion of diets today than they did for early farmers, are a major source of vitamin D in modern populations, but early farmers would have been much more reliant on sunlight to help produce vitamin D in their skin. “It seems possible that latitude is not the key factor in skin depigmentation, but diet,” he says.

Another feature of the La Braña genome is more consistent with current thinking about how farming changed human biology, however. The genes involved in breaking down lactose (the key sugar in milk products) and starch (the key nutrient in domesticated plants) were in an “ancestral” form, the team reports, meaning that hunter-gatherers were not good at digesting these foods, which later became essential to farming societies.

But the La Braña man did have some talents thought to have originated only with farming societies: His immune system was apparently capable of fighting off a number of diseases, such as tuberculosis, pneumonia, and malaria (which was endemic in southern Europe until modern times), which researchers had assumed were passed to humans from animals once cattle, sheep, and other species were domesticated. Out of 40 genes involved in immunity that the team looked at, 24 (60%) were similar to those of modern Europeans. “It appears that the first line of defense against pathogens was already there,” says Wolfgang Haak, an ancient DNA researcher at the University of Adelaide in Australia. One possible explanation, Lalueza-Fox adds, is that “epidemics affecting early farmers in the [Middle East] spread to continental Europe before they went themselves.”

Finally, the La Braña genome provides new evidence, Lalueza-Fox and Willerslev say, for the initial hypothesis that European hunter-gatherers were a widespread, genetically and culturally cohesive population long before farmers arrived, rather than a collection of isolated nomadic bands. Thus the new genome bears significant affinities with that of a 24,000-year-old child found at the Siberian site of Mal’ta, the sequence of which was reported by Willerslev late last year. This suggests, Willerslev says, that there might have been “substantial gene flow between east and west” leading to more homogenous populations than previously suspected.

Pontus Skoglund, a geneticist at Uppsala University in Sweden, says that this conclusion is supported by his own work on the ancient DNA of Scandinavian hunter-gatherers, who, although from the far north, show genetic affinities not only with the southern La Braña individual but also with the eastern Mal’ta child. “It is quite clear that we are looking at a big genetic watershed” during the transition from hunting and gathering to farming, Skoglund says, in which both genes and biology changed markedly. The farmers from across Europe “look the same” and the hunter-gatherers also “look the same, the opposite of what we would expect from geography alone.”