By comparing ancient hunter-gatherers and early farmers to present day human genomes, the researchers from the University of Tübingen and Havard Medical School found the modern European gene pool was formed when three tribes mixed around 7,000 to 8,000 years ago.
Previous genetic studies on ancient hunter-gatherers and early farmers' remains have shown a massive migration of people to Europe coinciding with the spread of agriculture around 7,500 years ago.
The international team of researchers analyzed ancient human genomes from a 7,000-year-old early farmer found near Stuttgart, an 8,000-year-old hunter-gatherer in Luxembourg, and ancient hunter-gatherers in Sweden.
The team then compared the ancient genetic data to Europeans today.
To their surprise, they found that present-day Europeans trace their ancestry back to three and not just two ancestral groups.
The first group is indigenous hunter-gatherers, the second is farmers that migrated to Europe from the Near East around 7,500 years ago and the previously unknown third group is a population that spanned North Eurasia and genetically connects Europeans with Native Americans.
“We find a major surprise: Europeans are a mixture of three ancient populations, not two,” said David Reich from Harvard Medical School, one of the lead investigators of the study.
Johannes Krause from the University of Tübingen and director of the Max Planck Institute for History and Sciences said: "We are all the outcome of immigration. Europe has been a melting pot for the last 10,000 years."
Using present-day and ancient human data, the researchers were also able to calculate the proportion of the three groups' DNA in present-day European genomes. "Nearly all Europeans have ancestry from all three ancestral groups," said Iosif Lazaridis from Harvard Medical School.
"Differences between them are due to the relative proportions of ancestry. Northern Europeans have more hunter-gatherer ancestry - up to about fifty percent in Lithuanians - and southern Europeans have more farmer ancestry."
Hunter-gatherers were more likely to have blue eyes and darker skin, whereas the early farmers had lighter skin and brown eyes.
“We are only starting to understand the complex genetic relationship of our ancestors,” Krause added. “Only more genetic data from ancient human remains will allow us to disentangle our pre-historic past”.