New studies of ancient DNA are shifting scientists' ideas of how groups of people migrated across the globe and interacted with one another thousands of years ago. By comparing nine ancient genomes to those of modern humans, Howard Hughes Medical Institute (HHMI) scientists have shown that previously unrecognized groups contributed to the genetic mix now present in most modern-day Europeans.

"There are at least three major, highly differentiated populations that have contributed substantial amounts of ancestry to almost everybody that has European ancestry today," says David Reich, an HHMI investigator at Harvard Medical School.

Those include hunter-gatherers from western Europe, the early farmers who brought agriculture to Europe from the Near East, and a newly identified group of ancient north Eurasians who arrived in Europe sometime after the introduction of agriculture.

That means there were major movements of people into Europe later than previously thought. The team, led by Reich and Johannes Krause at the University of Tubingen in Germany, reported their findings in the September 18, 2014, issue of the journal Nature.

In the last five years, genetic evidence has demonstrated that migrants from the Near East brought agriculture with them to Europe when they arrived about 8,500 years ago. But the genomes of present-day Europeans show signs that they come from more than just the indigenous hunter-gatherers and these early farmers.

Two years ago, Reich's group uncovered genetic evidence that most present-day Europeans are a mixture of groups related to southern Europeans, Near Easterners, and a third group most closely related to Native Americans. "That was a crazy observation, but it's very strong statistically," Reich says.

"We argued that this is because of the contribution of an ancient north Eurasian population some of whose members contributed to the peopling of the Americas more than 15,000 years ago, and others of which later migrated to Europe."

To clarify that early history, Reich's team, including more than 100 collaborators worldwide, collected genetic data from nine ancient skeletons and 203 present-day populations living all over the world.

Collaborators isolated human DNA and sequenced the complete genomes from the bones of a 7,000-year old skeleton found in Germany and eight skeletons of hunter-gatherers who lived in Luxembourg and Sweden about 8,000 years ago. They compared those genomes to those of the 2,345 people in their contemporary populations.

That required developing new computational methods for genetic analysis. "Figuring out how these populations are related is extremely hard," Reich says.

"There's a lot that happened in Europe in the last 8,000 years, and this history acts like a veil, making it difficult to discern what happened at the beginning of this period. We had to find statistics that were able to tell us what happened deep in the past without getting confused by 8,000 years of intervening history, when massive and important events occurred."

"What we find is unambiguous evidence that people in Europe today have all three of these ancestries: early European farmers who brought agriculture to Europe, the indigenous hunter-gatherers who were in Europe prior to 8,000 years ago, and these ancient north Eurasians," Reich says.

Further analyses showed that describing present-day Europeans as a mixture of the three populations is a good fit for most, although not all, populations.

When the study began, the ancient north Eurasian population was a "ghost population" - identified based on genetic patterns without any ancient DNA. But in 2013, another group analyzed DNA from two skeletons found in Siberia, one from 24,000 years ago and one from 17,000 years ago, and found that it shared genetic similarities with Europeans and North Americans. The ghost, Reich says, had been found.

Although DNA from ancient north Eurasians is present in nearly all modern Europeans, Reich's team did not find it in their ancient hunter-gatherers or the ancient farmers. That means the north Eurasian line of ancestry was introduced into Europe after agriculture had been established, a scenario most archaeologists had thought unlikely.

"We have this amazing observation that only two ancestries are represented among the first farmers, from about 7,000 to 5,000 years ago. And then suddenly everybody today has ancient north Eurasian ancestry," Reich says.

"So there must have been a later movement of this ancestry into Europe."

Anthropologists have long thought that densely settled populations would be resistant to the arrival of new groups. "But this is hard evidence that exactly such a major migration occurred," Reich says.

"It's very important because it's a major contributor to Europeans today." The time of the ancient north Eurasians' arrival remains to be determined, but Reich says their later-than-expected movement into Europe might help explain the complex mix of languages that exists there today.

The team's data also reveals that the first farmers to reach Europe from the Near East had ancestors from a previously unidentified lineage, which Reich's group named the Basal Eurasians. Basal Eurasians were the first people to separate from the larger group of non-Africans, before other non-African groups diversified.

Reich says that attempts to identify the first group to split from the non-Africans had always been puzzling: genetic evidence indicates that this is likely to be Europeans or Near Easterners, even though some archaeological evidence has indicated that people were in New Guinea and Australia before they were Europe.

The new analysis shows that the Near Easterners who came into Europe 8,000 years ago brought with them a strand of ancestry that had separated before the ancestors of Australian aborigines separated from the indigenous people of Europe.

"That population must have been hanging out somewhere in the Near East for a very long time," Reich says. Now he would like to know how that population fits into the archaeological history of the region. Ancient DNA from Basal Europeans, if found, might lead to new revelations about early human history.