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A new analysis of ancient genomes is deepening scientists’ understanding of the Neanderthal DNA carried by human populations in Europe and Asia — genetic traces that may have medical relevance today.
The finding, published Wednesday in the journal Science Advances, tracks the genetic legacy of the archaic relatives of our species, Homo sapiens, with more precision, thanks to a critical mass of invaluable data, according to the researchers.
Most humans alive today can trace a very small percentage of their DNA to Neanderthals — a result of prehistoric sexual encounters between our ancestors and the now-extinct Stone Age hominins before the latter disappeared around 40,000 years ago.
However, Neanderthal DNA is slightly more abundant in the genomes of East Asian populations.
This discrepancy has long perplexed scientists because Neanderthal remains have been found extensively across Europe and the Middle East but not further east of the Altai Mountains in Central Asia.
“So what’s puzzling is that an area where we’ve never found any Neanderthal remains, there’s more Neanderthal DNA,” said study coauthor Mathias Currat, a senior lecturer of genetics and evolution at the University of Geneva.
On average, Neanderthal DNA accounts for about 2% of the genetic makeup of people in Eurasia, while in East Asia the proportion can be as high as 4%, Currat said.
Currat and his colleagues at the University of Geneva came up with an explanation for this inconsistency by analyzing the distribution of the DNA inherited from Neanderthals in the genomes of humans over the past 40,000 years.
“We are beginning to have enough data to describe more and more precisely the percentage of DNA of Neanderthal origin in the genome of Sapiens at certain periods of prehistory,” Currat explained.
The researchers found that, over time, the distribution of Neanderthal DNA didn’t always look as it does now.
Diluting the genome
The study team mined information from a database of more than 4,000 ancient genomes from across Europe and Asia collected by a team led by Dr. David Reich, professor of genetics and human evolutionary biology at Harvard Medical School in Boston.
The genomes of Stone Age Homo sapiens who lived as hunter-gatherers in Europe after Neanderthals’ extinction contained a slightly higher proportion of Neanderthal DNA than those who lived in Asia for samples older than 20,000 years, the researchers found.
The study team thereby concluded that the current pattern of a higher percentage of Neanderthal ancestry in Asian populations compared with those in Europe must have developed at a later stage, mostly likely during the Neolithic transition when farming began to replace hunting and gathering as a way of life some 10,000 to 5,000 years ago.
At this point in time, the first farmers from Anatolia, in what’s now western Turkey and the Aegean, began to mix with the existing hunter-gatherers in Western and Northern Europe. This resulted in a lower proportion of Neanderthal DNA observed in European genomes during this period.
“The thing was that they had less Neanderthal ancestry so they diluted the (Neanderthal ancestry) in European populations,” Currat said.
He said it was less clear how this transition unfolded in Asia because of a relative lack of information. The study included 1,517 samples from Europe versus 1,108 from Asia — an area more than four times as large.
Tony Capra, an associate professor of epidemiology and biostatistics in the Bakar Computational Health Sciences Institute at the University of California, San Francisco, said the paper was “an example of a very exciting and promising strategy for integrating analysis of ancient human DNA from different geographic locations with modern genomes to connect the dots of evolution through time and space.” He wasn’t involved in the research.
Some of the genetic traces left by encounters with Neanderthals could make a difference in modern humans’ health. For example, Neanderthal DNA may play a small role in swaying the course of Covid-19 infection, according to a September 2020 study.