Neanderthal genes make about 1–4% of the genomes of contemporary humans whose ancestors left Africa, but how much they still influence human features is unknown.

Cornell University led a multi-institutional collaboration that developed computational genetic techniques to study the genetic effects of 50,000-year-old interbreeding between non-African people and Neanderthals. (The study only applies to descendants of Africans who arrived before Neanderthals went out, namely Europeans.)

In an eLife study, researchers found that some Neanderthal genes impact current human features, particularly the immune system. The study reveals that current human genes prevail throughout time.

“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 co-lead author April (Xinzhu) Wei, an assistant professor of computational biology in the College of Arts and Sciences. “Our custom software is free to download and use for research.”

Previous research could not totally eliminate current human variant genes.

The researchers examined more than 235,000 genetic variations believed to have come from Neanderthals in a massive UK Biobank dataset of over 300,000 Brits of non-African descent. They found that 4,303 of those DNA changes affect 47 genetic features in modern people, such as calorie burning speed and illness resistance.

The current study used more precise statistical approaches to isolate Neanderthal gene variations from modern human variants.

The study used a dataset of almost exclusively white UK residents, but the team’s new computational methods could help uncover archaic humans’ genetic influences on modern humans from other large databases.

“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 senior investigator Sriram Sankararaman, an associate professor at UC Los Angeles.
“More broadly, our findings can also provide new insights for evolutionary biologists looking at how echoes of these types of events may have both beneficial and detrimental consequences,” he added.