It was a culture of exchange and integration that rose and fell with no clear answer as to why. But, new research done by a team of researchers from Tel Aviv University, the Israel Antiquities Authority and Harvard University may provide an answer to that mystery. That answer: migration.
According to the study, published in Nature Communications, waves of migration from Anatolia and the Zagros mountains – part of today’s Turkey and Iran – to the Levant helped develop the Chalcolithic culture that existed in Israel’s Upper Galilee region some 6,500 years ago.
It was a period of splendor, beautiful pottery, new and more developed tools for that age and the study is one of the largest ancient DNA studies ever conducted in Israel and for the first time sheds light on the origins of the Chalcolithic culture in the Levant – which includes today’s Israel, as well as other parts of the Middle East.

In 1995, Zvi Gal, Dina Shalem and Howard Smithline of the Israel Antiquities Authority began excavating the Peki’in Cave in northern Israel, which dates to the Chalcolithic Period in the Levant. The team unearthed dozens of burials in the natural stalactite cave that is 17 meters long and 5-8 meters wide.
The large number of unique ceramic ossuaries and the variety of burial offerings discovered in the cave suggest that it was once used as a mortuary center by the local Chalcolithic people, the researchers said. “The uniqueness of the cave is evident in the number of people buried in it – more than 600 – and the variety of ossuaries and jars and the outstanding motifs on them, including geometric and anthropomorphic designs,” explained Shalem, who is also a research associate at at Kinneret College’s Institute for Galilean Archaeology.
Shalem said that although some of the findings in the cave are typical to the region, “others suggest cultural exchange with remote regions.
“The study resolves a long debate about the origin of the unique culture of the Chalcolithic people. Did the cultural change in the region follow waves of migration; the infiltration of ideas due to trade relations and/or cultural exchange; or local invention? We now know that the answer is migration.”
The researchers subjected 22 of the skeletons excavated at Peki’in, dating to the Chalcolithic Period, to a whole genome analysis, meaning a full range of genetic testing.
“This study of 22 individuals is one of the largest ancient DNA studies carried out from a single archaeological site, and by far the largest ever reported in the Near East,” said Dr. Hila May.
Prof. David Reich of Harvard University said that the genetic analysis provided an answer to the central question they had set out to address, “It showed that the Peki’in people had substantial ancestry from northerners – similar to those living in Iran and Turkey – that was not present in earlier Levantine farmers.”
May added that several characteristics, such as genetic mutations, which contribute to blue eye color, were not seen in the DNA test results of earlier Levantine human remains.
“The chances for the success of such a study seemed slim, since most of the ancient DNA studies carried out in Israel have failed due to difficult climatic conditions in the region that destroy DNA,” she said.
However, due to several factors, which included cool conditions within the cave and the limestone crust that covered the bones, preserved human DNA was discovered in the bones of the buried people in Peki’in cave.
Éadaoin Harney of Harvard University, who led the statistical analysis for the study added that they also found the Peki’in population experienced an abrupt demographic change 6,000 years ago. “Indeed, these findings suggest that the rise and falls of the Chalcolithic culture are probably due to demographic changes in the region,” said May.
Written by Ilanit Chernick | Photo by Mariana Salzberger/Israel Antiquities Authority