Digging Deep: Genetics gives a closer look into origins of the world’s first farmers

The Neolithic (~10000 BCE), human hory witnessed a watershed: a transition from a nomadic lifestyle involving hunting-and-gathering to settled agriculture. The region where this took place – stretching all the way from Egypt in the East to Iraq in the West – is known as the ‘Fertile Crescent.’ This shift paved the way for humans to colonise every habitable continent on earth. Slowly, these farming communities would make their way across geographical corridors to Europe and Asia and, in another two to three thousand years, nearly all parts of the Old World would have been introduced to agriculture.
But, who were these first farmers? A study published in Cell this week, led a team of genetics from Switzerland and Germany, tries to answer that question tapping into ancient genomes taken from archaeological remains found in Neolithic Europe and South-West Asia. In particular, the archaeological remains consed of 15 Neolithic individuals (13 farmers, two hunter-gatherers) from as far as Luxembourg in the West and Iran in the East. This was supplemented previously ten (six farmers, four hunter gatherer) published genomes.
Previous ancient DNA studies have largely maintained that European early farmers and European hunter gatherers were genetically dinct, at least in the early stages of agriculture, and mixed only later on. According to these studies, farmers that inhabited continental Europe ~9 kya (thousand years ago) came from the Aegean basin (primarily Greece and North Turkey). The DNA of these early Aegean farmers bore significant similarity with those of Central Anatolia (present-day Turkey) and South Levant (essentially present day Jordan, Israel, Lebanon).

Previous studies have also noted a genetic similarity between Epipalaeolithic (a transitionary period between Palaeolithic and Mesolithic, ~20-10 kya) and Neolithic people in Turkey, suggesting little to no gene flow in terms of migrations, etc.Best of Express PremiumPremiumPremiumPremiumPremium
Speaking on the connect between Aegean farmers and those from central Anatolia, Daniel Wegmann, one of the corresponding authors of the study told , “the theory of a common origin appears to be the most likely. But of course other theories might also be plausible. We currently lack a high quality genome from the Southern Levant and could not test these hypotheses to the degree we would like to.”
Marchi et al.’s (2022) work has resulted in four main findings. For ease of interpretation, it identifies three metapopulations: Western, Central and Eastern. The Western metapopulation gave rise to the cluster of European hunter gatherers, which are genetically different from modern Europeans. The Central metapopulation gave rise to the cluster of western (from Europe and present-day Turkey) early farmers. Eastern metapopulation gave rise to the cluster consing of early farmers of Iran and the hunter-gatherers of Caucasus.

The study found that European hunter gatherers had a much lower genetic diversity due to a population bottleneck imposed at the time of the Last Glacial Maximum (LGM). LGM was a period between 26-20 kya when ice sheets were at their greatest extent. After the genetic bottleneck imposed the Last Glacial Maxima, the European hunter gatherers split into two subgroups ~23 kya. This is a departure from earlier studies that maintained the low genetic diversity among European hunter gatherers was a consequence of small population size.
Instead, Marchi et al. (2022) find that the effective population size (i e roughly speaking, the number of individuals in a population that contributes to the genetic composition of the next generation through reproduction) was actually higher among European hunter gatherers than in contemporary early farmers.
The other major finding of the group was that the Western and Eastern metapopulations had diverged from each other at around 25.6 kya, long before the Neolithic. The Central and Eastern metapopulations had diverged around 13.6 kya. However, this date is still far later than what had been arrived at earlier. Previous studies had maintained that the ancestors of European hunter-gatherers and those of Iranian early farmers at 46-77 kya. This, Marchi et al. (2022) argue, is due to the possibility of population bottlenecks having been overlooked.

Later, populations from North Turkey and North Greece diverged ~9.1-9.3 kya, around the same time as the Aegean peninsula was being colonised early neolithic farmers. Both the Turkish and the Aegean populations show different levels of recent gene flow from the western metapopulations, suggesting that their interactions with contemporary hunter gatherers were not entirely uniform.
While at LGM, the Eastern and Western metapopulations diverged because they were stranded in pockets not covered ice sheets, they were able to spread beyond these refugia after these ice sheets receded. The period from ~14-12 kya is known as an ‘interstadial,’ when temperatures were relatively warmer compared to the periods before and after. Around 14.2 kya, the central hunter-gatherer metapopulations came in contact with populations ancestral to both the hunter-gatherers in Caucasus and early farmers in western Europe. Based on the information we have on the glacial extent, the study argues that these ‘admixtures’ likely took place in Southeast Turkey and Northern Levant.
It is, however, difficult to identify when and where exactly central Turkish and Aegean early farmer populations differentiated because not only did the ancestors of western early farmers expand further West but there were multiple ‘admixture events’ as well during the interstadial. It could be that they were part of the same ‘expansion wave,’ for the early farmers in the Aegean Peninsula and Central Turkey share similar genetic signatures. It could also be that Turkish and Aegean populations had already mixed before the transition to agriculture, or that hunter-gatherer populations from the Fertile Crescent had moved into the area.
The study, overall, challenges the current idea that all early farmers in Europe owe their cultural and biological origins to the first farmers in Fertile Crescent. The picture is, in fact, far more complex, with western early farmers experiencing multiple ‘admixture’ events with European hunter gatherers and farming populations in southwest Asia. In a press release issued the University of Bern, Laurent Excoffer, one of the corresponding authors, clarifies that ‘spatial and temporal gaps remain, and this does not imply the end of studies on the evolution of humans in this area’.
The author is a research fellow at the Indian Institute of Science (IISc), Bengaluru, and a freelance science communicator. He tweets at @critvik