From Cavemen to COVID: The Surprising Power of Archaic DNA and how ancient hominins continue to shape us

Ever wondered why some individuals catch allergic reactions frequently, sense pain differently, or even well acclimatized to high altitudes?

Before we get into details a quick intro to Neanderthals (Homo neanderthalensis) and Denisovans are extinct species or subspecies of archaic humans who lived during the Pleistocene epoch. Both are closely related to modern humans (Homo sapiens) and share a common ancestor with us.

I think now you could guess what could be hiding in the DNA from long-extinct human relatives Neanderthals and Denisovans. Although these archaic humans were wiped out tens of thousands of years ago, their genetic imprints are still a legacy among us, impacting everything from immunity to metabolism.

An interesting study by UC Berkeley and Max Planck Institute in 2024 has rewritten the timeline of human-Neanderthal interbreeding. It seems that the intermixing wasn't an isolated incident it occurred repeatedly over a 7,000-year period, between around 50,500 and 43,500 years ago. Over this time, modern humans and ancient Neanderthals swapped genes that still exist in non-African populations, who retain 1–2% Neanderthal DNA today.

The effects of this genetic inheritance on our health are enormous. A recent report has associated Neanderthal DNA with chronic smoking habit, mental health, baldness, sun sensitivity, and even pregnancy complications. These genes could benefited human populations in the past such as providing strengthened immune reactions against novel pathogens in Europe and Asia . But are now detrimental to us with the rapid evolving human landscape.

The research also pointed to areas of the contemporary human genome that contain no Neanderthal DNA, so-called "Neanderthal deserts." They probably formed relatively quickly following interbreeding and indicate that some Neanderthal gene forms were harmful or even fatal for modern humans. In contrast, other Neanderthal genes survived and could have been advantageous, influencing traits such as immune defence, skin coloration, and metabolism. For example, a Neanderthal-inherited immune gene variant has been linked to defensive effects against the coronavirus that caused COVID-19.

One of the populations with extremely rich records of these ancient interactions is South Asians. A new paper that came out in PNAS mentions that Indian genomes are the most diverse for Neanderthal and Denisovan genetic sequences. It is likely that this diversity is due to India being an important migration and mixing area for early humans. Yet another report points out that these ancient genes could influence disease susceptibility, impacting public health regionally from respiratory diseases to autoimmune conditions.

The Denisovans, while more slippery in the fossil record, left major genetic legacies as well. Tibetans and some of Oceania inherit Denisovan variants that aid high-altitude adaptation, like the EPAS1 gene, which controls blood oxygen levels. Denisovan genes associated with other effects are believed to influence fat metabolism, the immune system, and even brain formation although several of these links are ongoing research as researchers untangle ancient DNA with the help of present-day AI and bioinformatics technologies.

With new genome mapping technology and deep learning tools speeding up ancient DNA research, we’re close to discovering more on how these archaic genes can impact our mental health, circadian rhythms, pain sensitivity, and even drug responses. With evolving personalized medicine, your Neanderthal (or Denisovan) DNA might not just be an astonishing fact it can even determine your course of treatment in a hospital.

"Though Neanderthals and Denisovans vanished long ago, their legacy still walks among us in our genes, our strength, our immunity, and even how we adapt to the world around us. They may be history, but they’ve never truly left us. Evolution didn’t end it lives on in you."

References

1. Sanders, R. (2024, December 12). A new timeline for Neanderthal interbreeding with modern humans - Berkeley News. Berkeley News. https://news.berkeley.edu/2024/12/12/a-new-timeline-for-neanderthal-interbreeding-with-modern-humans/

2. Cooke, E. (2024, May 17). 10 unexpected ways Neanderthal DNA affects our health. livescience.com. https://www.livescience.com/health/genetics/10-unexpected-ways-neanderthal-dna-affects-our-health

3. Yermakovich, D., André, M., Brucato, N., Kariwiga, J., Leavesley, M., Pankratov, V., Mondal, M., Ricaut, F., & Dannemann, M. (2024). Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations. Proceedings of the National Academy of Sciences, 121(26). https://doi.org/10.1073/pnas.2405889121

4. Rohini Krishnamurthy, & Rohini Krishnamurthy. (2024, April 20). ‘Indians have largest variety of Neanderthal, Denisovan genes.’ Down to Earth. https://www.downtoearth.org.in/science-technology/-indians-have-largest-variety-of-neanderthal-denisovan-genes--95571

5. Whelan, S., PhD. (2023b, June 8). Neanderthal DNA has lingering effects in modern humans. Genomics Research From Technology Networks. https://www.technologynetworks.com/genomics/news/neanderthal-dna-has-lingering-effects-in-modern-humans-374462

6. Ungar, L., & Burakoff, M. (2023, September 27). We carry DNA from extinct cousins like Neanderthals. Science is now revealing their genetic legacy | AP News. AP News. https://apnews.com/article/neanderthals-denisovans-genetics-dna-disease-e49cb7d939cfe5d583e7ed0af8751784