Some had dark skin and blue eyes.

Some had light skin and brown eyes.

And no one is sure what some others looked like.

But, according to a new study of ancient human genomes, three very different populations got together seven millennia ago and made modern Europeans.

“The surprising finding was that present-day Europeans trace their ancestry back to three and not just two ancestral groups as previously thought,” said study co-author Alan Cooper, the director of the Australian Centre for Ancient DNA, in a press release.

Until now, scientists couldn’t fully explain the gene pool of modern Europe. Clues from archaeological research and previous genetic comparisons suggested most Europeans descended from Middle Eastern farmers who migrated to Europe about 7,500 years ago and interbred with local hunter-gatherers.

“Ancient human genomes suggest three ancestral populations for present-day Europeans,” said the article, published Thursday in the journal Nature.

One of the groups, indigenous hunter-gatherers, had a “striking combination of dark skin and blue eyes that doesn’t exist anymore,” one the study’s lead authors, David Reich of Harvard Medical School, told the BBC.

Modern Europeans look more like the lighter-skinned Middle Eastern farmers that showed up some 7,000 years ago.

“There’s an evolutionary argument about this — that light skin in Europe is biologically advantageous for people who farm, because you need to make vitamin D,” Reich said. “Hunters and gatherers get vitamin D through their food — because animals have a lot of it. But once you’re farming, you don’t get a lot of it, and once you switch to agriculture, there’s strong natural selection to lighten your skin so that when it’s hit by sunlight you can synthesize vitamin D.”

Researchers sequenced nine ancient genomes: a 7,000-year-old farmer from Germany, an 8,000-year-old hunter-gatherer from Luxembourg and seven 8,000-year-old hunter-gatherers from Sweden. They compared these to the genomes of 2,345 modern Europeans.

They found, as suspected, much of Europe’s contemporary gene pool comes from the farmers and hunter-gatherers. The rest – up to 20 percent – come from a third, mysterious group called northern Eurasians who arrived sometime in the past 7,000 years. Traces of the group’s DNA were found last year in the body of a toddler buried 24,000 years ago in eastern Siberia.

These mysterious people are something of a missing link. The ancient north Eurasians “connect all modern Europeans and Native Americans,” Johannes Krause, a geneticist at the University of Tübingen and co-director of the Max Planck Institute for History and the Sciences in Germany, told Reuters.

The northern Eurasians were also related to the people who migrated more than 15,000 years ago across a frozen land bridge to the Americas – their DNA is genetically similar to Native Americans.

Carles Lalueza-Fox of the Institute of Evolutionary Biology in Barcelona, who was not involved with the research, told BBC News: “The interesting point is the idea that we can dissect these components in any modern European and explain diversity in modern Europeans as different proportions of these three populations.”

People living in different parts of Europe have different proportions of genes from the three groups. Scots and Estonians have more of the mysterious northern Eurasian group’s genes, while modern-day Sardinians have more in common with the ancient farmers that came from the Middle East. In fact, Sardinians could descend from a population of early farmers less affected by migrations in the rest of Europe because they were isolated on the Mediterranean island, Reich told the BBC.