The stock of modern Europeans, thought to arise from ancient hunter-gatherers and late-arriving Near Eastern farmers, also bears the mark of a mysterious third ancestral population, representing a large yet previously unknown migration into the region thousands of years ago.

Researchers from Harvard and the University of Tübingen in Germany said this week that the third line originated in northern Eurasia and left its signal in the DNA of nearly all modern Europeans.

The new ancestral band appears to have had a broad geographic reach, also leaving a genetic signature halfway around the world, in the DNA of modern Native Americans. In addition to the light it casts on European ancestry, the findings provide a piece to a genetic puzzle that emerged in 2012 when work on Native American DNA showed unexpected connections to modern Europeans.

The research was conducted by an international consortium led by scientists from the Harvard Medical School lab of Genetics Professor David Reich, who spearheaded the comparative DNA analysis, and Professor Johannes Krause at the University of Tübingen, who did the work of extracting the ancient DNA. It was published today in the journal Nature.

Reich said the research provides evidence that the prevailing view among archaeologists that there were no major influxes of new peoples into Europe after the advent of agriculture is wrong.

“Our evidence that Europeans today harbor ancestry that wasn’t present in the first farmers is important as it shows directly that there was a major movement of people into Europe after the advent of agriculture,” Reich said. “This motivates further ancient DNA work to try and figure out what archaeological cultures were responsible for bringing this ancestry.”

To conduct their analysis, researchers compared the DNA of 2,345 modern Europeans to that of a 7,000-year-old farmer from Germany and eight 8,000-year-old hunter-gatherers from Luxembourg and Sweden. Among other findings, researchers detected about 2 percent ancestry from Neanderthals in the ancients, about the level expected from prior research, Reich said. The research also included examining genetic sequences from more recent remains, including those of Otzi, “The Iceman,” a mummified 5,000-year-old man discovered in the Italian Alps in 1991.

Until January, the mysterious third genetic line constituted a “ghost population,” whose existence was theorized by geneticists to explain the link between Europeans and Native Americans, but of whom no archaeological evidence had been found. Then another group of archaeologists and geneticists published a paper on 24,000-year-old remains excavated in Siberia whose genetic signature matched what researchers expected from their European and Native American work.

With one “ghost population” found, Iosif Lazaridis, a postdoctoral fellow in Reich’s lab and the paper’s first author, is proposing another. In addition to the European findings, Lazaridis said the work also indicates the existence of a new “basal Eurasian” population, one that split from modern humans as they emerged from Africa, predating other early divergences, such as those that led to Australian aborigines, New Guineans, and other eastern peoples.

The research is just the latest illumination of human origins to come out of Reich’s lab. His past work has touched on everything from the relationship between humans and their closest animal relative, the chimpanzee, to ties between humans and Neanderthals and connections among an array of human populations.

Lazaridis said he believes the new work provides the “big picture” of European genetic heritage, with much of the variation among European peoples explained by different proportions of farmers and hunter-gatherers. Northern Europeans, for example, have more hunter-gatherer ancestry — up to 50 percent, in Lithuanians — while Southern Europeans have proportionally more farmer ancestry.

The new line, which researchers refer to as Ancient North Eurasians, is present in nearly all European populations, but makes up a smaller part of their genetic makeup, a maximum of 20 percent, and is relatively evenly spread in the population.

The Ancient North Eurasian line was not present in either the 8,000-year-old hunter-gatherers or the 7,000-year-old farmer, so researchers believe it represents a migration into Europe sometime after those individuals lived but before recorded history in the region.

“These Ancient North Eurasians must have spread into Europe at a later time, and so encountered early farmer- or hunter-gatherer-type populations and mixed with them,” Lazaridis said. “It’s definitely, chronologically, the last thing that arrived in most of Europe.”

Lazaridis said the period of approximately 4,500 years ago appears likely for the influx, because that is when new types of mitochondrial DNA appear in the genetic record. Reich added that there are hints from other disciplines, including linguistics, that point to migrations during that time span.

“The big question is to study Europeans from later periods to try and pinpoint some space and time where these Ancient North Eurasians make their first appearance,” Lazaridis said.