Study Reveals Ancient DNA Evolutions

About 4,000 years ago, as early civilizations like the Minoans in Crete and the Neo-Sumerian Empire in Mesopotamia were emerging, human biology was also undergoing significant changes.

A recent study published in Nature has made an exciting discovery: the prevalence of two DNA variants associated with celiac disease has surged in certain populations across Europe and the Middle East.

This research, which identified numerous additional DNA variants, provides new insights into how natural selection has influenced human biology over the past 10,000 years. Natural selection, as you may know, happens when specific gene versions linked to traits, whether disease susceptibility or physical characteristics like red hair or blood types, give their carriers a better chance at survival and reproduction.

Conducted by a team from Harvard University, the researchers examined and compared DNA sequences from around 22,000 individuals. This included 10,000 ancient genomes that had never been analyzed before, as well as 6,000 that were previously published, alongside 6,000 modern genomes.

Historically, only a limited number of genetic variations driven by natural selection had been documented.

“It’s remarkable to actually observe evolution in progress, rather than just analyzing the remnants it leaves behind in modern genetic patterns,” David Reich, a geneticist from Harvard and lead author of the study, shared in a video interview.

Advancements in Ancient DNA Research

Reich explained that the extraction of ancient DNA has just become feasible in recent years. It required some time to gather enough data for a focused study on human evolution.

“The methods for retrieving ancient DNA from remains became available around 2010. I think it’s safe to say it has greatly changed how we view the past,” he noted.

Reich is no stranger to researching human history across various groups and archaeological sites and has focused on populations in Israel and the Jewish community.

The Nature study, which covered genomes from places like Iceland, Spain, Russia, Iran, and Israel, took a unique direction by focusing on human biology rather than human history.

“Many early researchers believed the most intriguing aspect of ancient DNA would be understanding how our biology has evolved, but studying human history just requires a few samples from each group,” he clarified. “To grasp evolution, we needed many more samples, which the field simply didn’t have until now.”

To facilitate these studies, Reich’s lab and others have been working on “industrializing the production of ancient DNA” over the last decade.

“We used robots for DNA extraction, cleaning, and sequencing. Also, we applied various computational methods to ensure that the data produced was high-quality and consistently analyzed,” he described.

Collaboration played a crucial role, with about 270 archaeologists providing samples for this invaluable research. “These archaeologists might not have been focused on biological changes, but recognized the potential value of the data,” Reich remarked.

Overall, the new research has significantly boosted the amount of data available in the ancient DNA field, particularly for West Eurasia.

Reich mentioned that they worked with reliably dated samples, primarily using radiocarbon dating and established timelines based on soil layers.

Isolating Natural Selection’s Impact

A significant challenge addressed in this study was the need to isolate genetic changes caused solely by natural selection. As Reich explained, “The history across Europe and the Middle East is complex, with migrations and group mixtures being common. Many apparent changes could simply be the result of population movement. We needed a way to identify the specific adaptations.”

The researchers employed a statistical model comparing each genome to the others and examining their genetic relationships.

“Typically, human genomes are very similar. Lining them up reveals that 99.9% of the DNA letters are the same,” Reich elaborated. “Among the 3 billion letters in a genome, the differences might seem massive, but they often represent a very small fraction of the total.”

They analyzed around 10 million variations across the studied genomes to see if time played a role in predicting these changes.

Reich noted that prior research identified about 20 significant genetic positions that changed over time. Now, this study has revealed nearly 500 positions with clear signs of adaptation, and likely many more if one lowers the certainty threshold.

Among these findings is the substantial increase in frequencies of the two DNA variants tied to celiac disease.

“You might assume that as populations began consuming wheat, these variants would have decreased in prevalence, but instead, they became more common,” he reflected. “Why that’s the case remains uncertain—possibly these variants also conferred protection against other illnesses.”

They also found variations linked to tuberculosis risk, with one particular variant showing a significant increase in frequency between 6,000 and 2,000 years ago, followed by a selection against it in later years.

“It seems likely that as tuberculosis spread, carrying that variant became detrimental, while beforehand, it may have offered protection against a different disease,” Reich speculated.

The study examined variants associated with conditions like multiple sclerosis, hemochromatosis, and traits such as blood types and skin tone, even publishing an open database for researchers to explore genomic locations and variants.

When asked about insights specific to ancient Jewish DNA, Reich noted that the study lacked sufficient Jewish samples, explaining that Jewish DNA is usually identifiable due to historical isolation. However, due to burial practices, chances of finding Jewish remains among non-Jewish contexts are low.

While the study hasn’t compared specific regions or groups within West Eurasia yet, Reich emphasized that this will likely be a focus for future research. The current study serves as merely a starting point, showcasing the potential for its findings to advance studies in medical and biological fields as well as archaeology.

“We haven’t systematically examined how Near Eastern populations differ from European ones, but that’s an intriguing direction to explore,” he said.

Increasing the genomic sample size is expected to facilitate even more discoveries.

He mentioned aspirations to conduct similar studies in other parts of the world: “What if we studied ancient DNA in East Asia or Native American populations? Would the results be similar or different?”

Reich noted that research on animal DNA could also enhance our understanding of their evolution, which is another avenue they are keen on pursuing.