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Demographic Modeling of Ancient Genomes Indicates First Farmers Arose From Mixing of Populations

NEW YORK — The world's first farmers likely did not arise in one population in the Fertile Crescent but through a mixing of groups, a new study of ancient genomes has found.

Farming is thought to have emerged about 13,000 years ago in Southwest Asia and the Middle East before spreading across Turkey and Greece and into Western Europe. But the exact genetic origins of those early farmers have been unclear.

To find out more, an international team of researchers sequenced the genomes of 15 ancient individuals who lived across Southwest Asia, the Middle East, and Europe during the early Holocene and compared them to a number of previously analyzed genomes from other ancient individuals. As they reported in Cell on Thursday, the researchers fed this data into demographic models of how hunter-gatherers and early farming populations changed over time.

"I see the study as the first attempt at demonstrating demographic modeling based on ancient DNA," senior author Laurent Excoffier from the University of Bern said in a statement.

The researchers first analyzed the neutral portions of the genomes from 25 ancient individuals to cluster them into three overarching populations: European hunter-gatherers, Western early farmers, and a cluster consisting of an early Iranian farmer and a Mesolithic hunter-gatherer from the Caucasus.

Using these three clusters, the researchers then generated a number of models to describe how the populations could have differentiated. These models assumed that these individuals descended from three larger meta-populations they dubbed Western, Central, and Eastern. By slowly adding in data from additional ancient individuals to the models, the researchers homed in on a potential demographic history.

Overall, they noted that the population ancestral to all their sampled individuals was genetically closely related to Iranian early farmers and hunter-gatherers from the Caucasus, but then split, with the ancestors of European hunter-gatherers moving into Europe and others remaining in Southwest Asia.

The model further indicates that European hunter-gatherers themselves split into two subgroups by about 23,000 years ago, after experiencing an extreme population bottleneck during the Last Glacial Maximum. That bottleneck was likely responsible for the low level of genetic diversity in the group.

"This is a new finding, and it leads to a different interpretation of how these hunter-gatherer populations were structured socially," Excoffier said. "What it implies to us is that they were perhaps more connected between different groups."

The researchers further found that the ancestors of Western early farmers shared a common ancestor with hunter-gatherers from the Caucasus but that they also shared a common ancestor with the European hunter-gatherers who had undergone a strong population bottleneck. These first farmers of Anatolia and Europe further underwent additional genetic drift as they expanded westward.

This modeling, they noted, indicates that there was not a single cultural or genetic origin of all farmers.

The researchers' findings further underscore the effect of climate and changes in temperature on human populations. Prior to the Last Glacial Maximum, more than 27,000 years ago, human populations in the region were not very structured. But they split during the Last Glacial Maximum — as populations retreated to glacial refugia — into two Western and one Eastern populations. Admixture events then occurred during the Bølling Interstadial period, followed by separation during the Older Dryas about 13,800 years ago. Then during the Allerød, about 12,900 years ago, the ancestors of early farmers expanded and underwent admixture events, which then led to the Neolithic expansion.

The researchers plan to next analyze additional ancient genomes from different eras and locations.