Traces of long-buried Denisovan DNA are resurfacing in the genomes of modern humans—and they may still be working in our favor today
Traces of long-buried Denisovan DNA are resurfacing in the genomes of modern humans—and they may still be working to our advantage today.
The Denisovans were an extinct group of early humans, closely related to Neanderthals and modern humans, who lived mainly in Asia between about 300 and 30 years ago. We know them mainly from a very small number of fossils – mainly from Denisova Cave in Siberia – but their great importance stems from the ancient DNA extracted from some of the remains. Genetic comparisons have shown that modern humans who migrated through Asia and Oceania encountered and interbred with Denisovans, and that some populations still carry a small percentage of Denisovan DNA. In some cases, these genes appear to have provided an adaptive advantage, for example in coping with extreme environmental conditions or new pathogens, and have therefore been preserved and spread in certain populations over the generations.
Scientists have discovered a genetic variant passed down to us from extinct human relatives, which likely helped our ancestors survive as they spread into the Americas.
hybridization Ancient humans provided useful genetic “tools”
New research suggests that encounters between early modern humans and other archaic human groups provided genetic traits that helped our species adapt to unfamiliar environments as people migrated around the world.
The study, published in the journal Science, focuses on a gene called MUC19. This gene helps make proteins involved in saliva and the mucous layers that protect the digestive and respiratory systems. The team found that a version of this gene, which came from Denisovans — a lesser-known archaic human group — appears in many people in Latin America who have Native American ancestry. The same variant was also identified in DNA extracted from people who lived in the past at archaeological sites across North and South America.
Evidence suggests that this variant became common because it provided a significant survival advantage. Scientists still don't know exactly what that advantage was. However, since the gene's role is related to immune system processes, it is possible that it helped early populations cope with unfamiliar pathogens when they entered the Americas.
“From an evolutionary perspective, this finding shows how ancient hybridization can leave effects that we still see today,” said study author Emilia Huerta-Sánchez, a professor of ecology, evolution and organismal biology at Brown University. “And from a biological perspective, we identify a gene that appears to be adaptive, but its function has not yet been characterized. We hope this will lead to further research into what this gene actually does.”
Huerta-Sanchez conducted the research with Fernando Villanea, a former postdoctoral fellow at Brown who is now at the University of Colorado at Boulder; David Peede, an advanced graduate student at Brown; and colleagues from several international institutions.
What do we know about the Denisovans?
Scientists have limited information about Denisovans. They lived in various parts of Asia between 300 and 30 years ago. Existing fossils include a small collection of remains from Denisova Cave in Siberia, two jawbones from Tibet and Taiwan, and a nearly complete skull recently discovered in China.
One of the Siberian fossils contained ancient DNA. This allowed researchers to trace shared genetic traits between Denisovans and modern humans. Previous work by Huerta-Sanchez showed that people in Tibet, including the Sherpa tribe known for helping mountaineers climb Mount Everest, carry a Denisovan-derived version of the EPAS1 gene, which helps them adapt to high-altitude environments.
The Denisovan variant of the gene MUC19 In ancient and modern populations
In the new study, the researchers compared Denisovan genomic sequences with data from the 1,000 Genomes Project, which documents the world's human genetic diversity. The analysis showed that the Denisovan variant of the MUC19 gene appears at particularly high rates in Latin American people of Native American descent.
The team also examined DNA from 23 ancient people sampled from excavation sites in Alaska, California, Mexico and other locations across the Americas. The Denisovan-derived variant of MUC19 was also common in these ancient samples.
Several statistical approaches showed that this version of the gene became dominant in both ancient aborigines and their modern descendants due to strong natural selection. The gene is also found within an unusually long stretch of archaic DNA—another sign that natural selection played a major role. The researchers concluded that the gene likely passed from Denisovans to Neanderthals through introgression, and that Neanderthals then passed it on to early modern humans.
How did hybridization expand human genetic diversity?
Huerta-Sanchez noted that the findings highlight how interbreeding between different human groups provided useful genetic variations that shaped our evolutionary trajectory.
“Normally, genetic innovation occurs very slowly,” Huerta-Sanchez said. “But hybridization events like this were a way to suddenly introduce a lot of new variation.”
This influx of new variations could have been particularly important when early modern humans entered the Americas, perhaps improving immune responses in unfamiliar environments.
“Clearly something in this gene was useful to these populations, and maybe it still is useful — or will be useful in the future,” Huerta-Sanchez said.
She hopes that the growing recognition of the importance of MUC19 will encourage further research to understand how the genetic variants that alter proteins work, and whether they reveal new biological mechanisms.
More of the topic in Hayadan:
