Scientists use ancient DNA to reveal how natural selection shaped West Eurasians over 10,000 years

By analyzing the genetic material of thousands of ancient humans, researchers have mapped how natural selection influenced hundreds of physical and behavioral traits across West Eurasia over the past 10,000 years. The findings reveal that evolution continuously pushed specific genetic variations to become more or less common, affecting everything from blood type to disease risk. The study was published in Nature.

Evolution is driven by multiple forces, but one of the most recognizable is directional selection. This happens when a specific genetic mutation provides a survival or reproductive advantage, causing it to become increasingly common in a population. Conversely, a disadvantageous trait will be driven out of the population over successive generations.

Tracking this process in humans has proven highly difficult for geneticists. As human populations migrated, conquered, and mixed over thousands of years, the frequencies of certain genes shifted naturally. This natural, random fluctuation is known as genetic drift. It is hard for researchers to separate random genetic drift from genuine directional selection. For a long time, scientists could not easily tell if a gene became common because it was highly advantageous or simply because a migrating group of people happened to carry it.

A team of researchers led by Ali Akbari, a geneticist at Harvard Medical School, sought to solve this problem. They developed a new statistical method designed to track genetic changes over thousands of years and separate the effects of human migration from genuine evolutionary pressure.

The researchers gathered a massive dataset of genetic material from 15,836 ancient individuals who lived in West Eurasia. This geographic area includes Europe and neighboring parts of the Near East. The skeletal remains spanned a timeframe of 18,000 years. The team sequenced over 10,000 of these genomes for the first time, vastly expanding the available data for ancient human genetics.

Using their new statistical approach, the group examined nearly ten million distinct points in the human genome. They looked for consistent trends where a specific gene became steadily more or less common across different populations and eras. The immense sample size allowed them to spot subtle evolutionary nudges that earlier studies lacked the statistical power to definitively detect.

They found that directional selection has been incredibly common in West Eurasia over the past ten millennia. The team identified hundreds of specific genetic variants that were either favored or actively weeded out by evolutionary forces. Many of these genes are linked to the human immune system and the body’s response to changing diets.

Among the specific biology findings, the study tracked the rise of a gene associated with a high risk of celiac disease. This gene became much more common over the last 4,000 years. This suggests that the gene provided a strong, yet unknown, defense against certain pathogens, and this ancient defense outweighed the negative health effects of gluten sensitivity.

The researchers also noticed changing evolutionary preferences within the human blood group system. Over the past 6,000 years, blood type B became more common at the direct expense of blood type A. Because different blood types offer varying levels of resistance to different pathogens, this shift likely reflects the changing landscape of ancient infectious diseases.

Another discovery involved a genetic mutation that confers complete resistance to HIV infection. Previous theories suggested this mutation became common in Europe during the Middle Ages as a defense against the bubonic plague. The new study places the rise of this mutation much earlier, between 2,000 and 6,000 years ago, opening up new questions about which ancient pathogens actually drove its spread.

The data also showed that evolutionary pressures could completely reverse direction. A gene associated with a high risk of tuberculosis was actively selected for starting about 9,000 years ago, but then experienced strong negative selection starting 3,000 years ago. This suggests the diseases plaguing early populations changed dramatically as humans altered their living environments.

Physical appearance was also deeply shaped by these evolutionary pressures. The team found strong evidence for the selection of lighter skin tones. They also noted a steady decrease in a gene associated with straight hair and male pattern baldness over the last 7,000 years.

Some prior theories about human disease were challenged by the new data. For example, some scientists had hypothesized that the gene causing cystic fibrosis remained in the population because it provided resistance to ancient cholera outbreaks. Akbari and his colleagues found no evidence of directional selection for the cystic fibrosis gene during the historical timeframe that cholera was endemic to the region.

The researchers also evaluated polygenic traits. Most physical and behavioral characteristics are not controlled by a single mutation but are influenced by hundreds or thousands of different genes working together. Today, scientists can combine these genetic variants to predict the likelihood of a trait in living people. By tracking how these combinations of genes shifted in the past, the team found striking patterns.

Combinations of genes that today predict higher body fat, larger waist circumference, and a higher risk of type-2 diabetes were actively selected against as ancient people transitioned to farming lifestyles. This challenges the popular thrifty gene hypothesis, which proposed that early humans adapted to store fat to survive periods of famine. The genomic record suggests instead that extra weight became an evolutionary disadvantage in recent human history. Genetic combinations known today to increase the risk of schizophrenia and bipolar disorder were also driven down in frequency.

The most debated results involve behavioral and lifestyle traits. The team uncovered selection against genetic combinations associated with modern smoking behavior and overall health decline. Conversely, they observed positive selection for genetic combinations that today predict a faster modern walking pace, higher scores on intelligence tests, and more years of completed schooling.

Interpreting these complex behavioral traits requires high caution. The genetic predictors for traits like intelligence test scores and years of schooling were developed using data from modern, industrialized societies. It remains entirely unknown how these same genetic variations manifested in ancient, preliterate societies. A gene sequence associated with success in a modern classroom might have promoted a completely different advantageous behavior in an ancient agricultural community.

The researchers also note that evolutionary pressures did not remain constant across time. A gene that offered disease resistance in one millennium might have become useless or harmful in the next as entirely new pathogens emerged. The study assumes a constant rate of selection just to make the statistical analysis possible, which masks the reality of fluctuating environments.

Future research will likely apply these methods to other regions of the world to see if similar patterns exist globally. By examining longer timelines and different geographic areas, scientists hope to build a more complete picture of how human biology adapted to a rapidly changing world. The ability to pull detailed genetic maps from ancient bone allows researchers to watch human evolution happen in real time.

The study, “Ancient DNA reveals pervasive directional selection across West Eurasia,” was authored by Ali Akbari, Annabel Perry, Alison R. Barton, Mohammadreza Kariminejad, Steven Gazal, Zheng Li, Yating Zeng, Alissa Mittnik, Nick Patterson, Matthew Mah, Xiang Zhou, Alkes L. Price, Eric S. Lander, Ron Pinhasi, Nadin Rohland, Swapan Mallick, and David Reich.