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Neanderthal DNA Has Lingering Effects in Modern Humans

Computer-generated illustration of a DNA double helix.
Credit: Sangharsh Lohakare/Unsplash
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A study from a multi-institutional research team has found that Neanderthal DNA can actively influence some human traits, particularly those involved in immunity. The research, published in eLife, also suggests that modern human genes are winning out over Neanderthal ones over successive generations.

Neanderthal DNA in modern-day genomes

The genomes of some present-day humans can contain a surprising amount of Neanderthal DNA. People with ancestors who migrated out of Africa, particularly those of European ancestry, can have as much as 1–4% of their genome made up of Neanderthal DNA. These are likely remnants of interbreeding between ancient humans and Neanderthals some 50,000 years ago.

The introduction of Neanderthal DNA into the gene pool may have helped these ancient humans survive in the cold European climate as they encountered new environments in their migration out of Africa. For example, studies have shown that Neanderthal DNA can influence our nose shape or even our immune response to the flu.

However, the extent to which Neanderthal DNA contributes towards complex human traits has been difficult to explore due to the evolutionary history of different populations and the relatively small proportion of Neanderthal DNA in modern-day genomes.

The researchers in the current study investigated this in more detail using data from the UK Biobank, a vast database of genetic and trait information of almost 300,000 Britons of non-African ancestry.

47 traits identified

Over 235,000 genetic variants from the database were analyzed that were likely to have originated from Neanderthals. Of these, 4,303 variants were found to play a key role in influencing 47 distinct traits in modern humans. These include traits such as how fast someone can burn calories or natural immune resistance to certain diseases. Many identified traits have a significant influence on the immune system – however, the findings indicate that overall, modern human genes are winning out over successive generations.

Developing upon previous studies that could not entirely exclude modern human variants, the new study also utilized more precise statistical and computational methods to home in on variants they could attribute to Neanderthal DNA.

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“Interestingly, we found that several of the identified genes involved in modern human immune, metabolic and developmental systems might have influenced human evolution after the ancestors’ migration out of Africa,” said Dr. April (Xinzhu) Wei, an assistant professor of computational biology at Cornell University and co-lead author of the study. “We have made our custom software available for free download and use by anyone interested in further research.”

New evolutionary insights

Though limited by data almost exclusively from white individuals living in the UK, the novel computational techniques developed for this study lead to an increase in gleaning new evolutionary insights. For example, enabling the analysis of larger and more diverse databases to delve deeper into the influence of ancient genetics on humans today.

“For scientists studying human evolution interested in understanding how interbreeding with archaic humans tens of thousands of years ago still shapes the biology of many present-day humans, this study can fill in some of those blanks,” said Dr. Sriram Sankararaman, associate professor at the University of California, Los Angeles and the senior author of the study. “More broadly, our findings can also provide new insights for evolutionary biologists looking at how the echoes of these types of events may have both beneficial and detrimental consequences.”

Reference: Wei X, Robles CR, Pazokitoroudi A, et al. The lingering effects of Neanderthal introgression on human complex traits. eLife. 2023;12:e80757. doi: 10.7554/eLife.80757

This article is a rework of a press release issued by Cornell University. Material has been edited for length and content.