When agriculture was introduced into Europe some 8,500 years ago, early farmers quickly adapted to new diets and pathogens. Now, researchers analyzing DNA from hundreds of West Eurasians who lived several millennia ago reveal how genomes were changed by the transition from hunting and gathering to farming. The findings, published in Nature this week, demonstrate how ancient DNA allows us to observe natural selection on humans directly.
Researchers can study the way we adapted genetically to past events both indirectly and directly. Indirect evidence of adaptations can be detected in patterns of genetic variation in modern genomes today, but these patterns are difficult to date and interpret. The direct way of studying these patterns would be ancient DNA, and until recently, large sample sizes were required to detect selection. But now, better DNA extraction techniques and ever-growing datasets make it possible to conduct a genome-wide scan for selection.
A large international team of researchers led by the Harvard Medical School, University of Adelaide, and University College Dublin sequenced DNA from 230 people who lived in Europe, Turkey, and Siberia between 300 B.C.E. and 6500 B.C.E. Earlier this year, an analysis of 101 ancient Eurasian genomes helped explain the prevalence of traits like skin color and lactose intolerance. Among the new ancient individuals sampled for this study were 26 Neolithic farmers from Anatolia, or modern-day Turkey. Their DNA was extracted from the pyramid-shaped petrous bone (pictured above); this skull bone houses the internal auditory organs, and it’s rich in DNA. Turns out, those 26 Neolithic farmers from the eastern Mediterranean were members of the population that gave rise to Europe’s first farmers.
The team identified 12 positions on the genome where natural selection – specifically related to the introduction and expansion of farming in northern latitudes – appears to have occurred. These DNA regions are associated with diet, immunity, height, and light skin pigmentation.
The transition to farming, for example, favored genes for metabolizing fats, circulating vitamin D levels, and the ability to digest lactose as adults. Two variants appear on genes that have been linked to higher risk of celiac disease; these may have been important in adapting to an agricultural diet, which can result in the deficiency of an amino acid called ergothioneine. As for immunity-related genes, selection favored resistance against tuberculosis, leprosy, and other mycobacterial infections.
Additionally, the team detected two independent signals for height: a selection for reduced height on the Iberian Peninsula relative to both Anatolian and central European samples, followed by a signal for increased height in the Eurasian steppe populations around Russia. These suggest that the modern south–north gradient in height across Europe is due to both increased steppe ancestry in northern populations as well as selection for decreased height in southern Europe.
“It’s a great mystery how present-day populations got to be the way we are today, both in terms of how our ancestors moved around and intermingled and how populations developed the adaptations that help us survive a bit better in the different environments in which we live,” Harvard’s David Reich said in a statement. “Now that ancient DNA is available at the genome-wide scale and in large sample sizes, we have an extraordinary new instrument for studying these questions.”