How Multiple Denisovan Populations Shaped Modern Human Genes

New research reveals distinct Denisovan populations that interbred with early humans, adapting to diverse environments and impacting human evolution.

One of the most intriguing chapters in human evolution is the story of the Denisovans, a mysterious, now-extinct hominin group that left a significant genetic footprint in the DNA of modern humans. Initially discovered through a single finger bone in Siberia’s Denisova Cave, Denisovans are now known to have had a far-reaching impact on the genetic makeup of modern humans, particularly in populations across Asia and Oceania. Recent research¹ has unveiled that multiple Denisovan populations existed, each uniquely adapted to their environments and contributing beneficial genes to various human populations through several distinct interbreeding events.

Overview of the distinct Denisovan populations that introgressed into modern humans.

Denisovans: An Unfolding Mystery in Human Evolution

Denisovans, an enigmatic branch of the human family tree, were first identified through a groundbreaking genome analysis of a finger bone fragment found in Siberia’s Denisova Cave. The analysis revealed that Denisovans diverged from Neanderthals around 400,000 years ago, although the two groups share a common ancestry. Unlike Neanderthals, whose fossils are relatively numerous, Denisovan remains are limited to a few skeletal fragments, making the study of this hominin group a challenging pursuit.

Dr. Linda Ongaro, a researcher at Trinity College Dublin, noted the significance of the Denisovan discovery:

“This was one of the most exciting discoveries in human evolution in the last decade.”

Despite the limited fossil evidence, advances in genetic analysis have enabled researchers to trace Denisovan contributions to modern human DNA.

Multiple Denisovan Populations Interbred with Early Humans

While Denisovans and Neanderthals share a common lineage, genetic evidence indicates that Denisovans diverged into at least two distinct populations, each of which contributed genetic material to early humans. Research led by Dr. Ongaro and her colleague, Professor Emilia Huerta-Sanchez of Trinity College Dublin and Brown University, has identified at least three separate instances of interbreeding between Denisovans and early humans. Each interbreeding event left different Denisovan genetic markers, suggesting interactions with distinct Denisovan populations. Dr. Ongaro explained,

“By leveraging the surviving Denisovan segments in modern human genomes, scientists have uncovered evidence of at least three past events whereby genes from distinct Denisovan populations made their way into the genetic signatures of modern humans.”

This complex intermingling with Denisovan populations indicates that early humans and Denisovans had a long, overlapping history.

A Wide Geographic Range and Environmental Adaptations

Evidence points to Denisovans inhabiting a vast geographic area, from the cold climates of Siberia to the high altitudes of the Tibetan Plateau and possibly even extending into Southeast Asia and Oceania. These environmental ranges likely contributed to Denisovans developing unique adaptations, some of which were passed to modern humans through interbreeding. The Altai Denisovan population from Siberia, the first Denisovan group to be identified, is genetically distinct from another Denisovan population discovered in the Baishiya Karst Cave on the Tibetan Plateau.

Dr. Ongaro and Professor Huerta-Sanchez’s research also sheds light on how Denisovan genes may have helped human populations adapt to different environments. Ongaro noted,

“Among these is a genetic locus that confers a tolerance to hypoxia, or low oxygen conditions, which is seen in Tibetan populations.”

Additional Denisovan genes are associated with heightened immune response and lipid metabolism, the latter aiding in cold adaptation, which benefits Inuit populations in Arctic conditions.

Denisovan Genes and Modern Human Adaptations

The Denisovan legacy within modern human genomes goes beyond merely interbreeding events—it directly influences traits essential for survival in extreme environments. For instance, the genetic adaptation to hypoxia found in Tibetan populations allows people to live at high altitudes with lower oxygen levels. This Denisovan gene confers a significant survival advantage, especially in the thin air of mountainous regions. Similarly, the genes that influence lipid metabolism in cold environments enable certain Arctic populations to generate heat through their body’s metabolic processes, demonstrating a Denisovan impact on human adaptability. oted Dr. Ongaro noted,

“This shows the extent to which Denisovans may have contributed to our genetic resilience and adaptability in various climates.”

Such findings underscore the Denisovan legacy as one that extends across continents, influencing human biology in profound ways.

The Denisovan Impact on Human Evolution

The Denisovan genetic contributions reflect a broader pattern of ancient human interbreeding that likely played a crucial role in shaping early human populations. Dr. Ongaro’s team proposes that these Denisovan-human interactions were not isolated events but part of a complex network of interbreeding among archaic humans, including Neanderthals, Denisovans, and early Homo sapiens. Dr. Ongaro explained,

“It’s a common misconception that humans evolved suddenly and neatly from one common ancestor. The more we learn, the more we realize interbreeding with different hominins occurred and helped shape the people we are today.”

This idea challenges the previously held view of a linear evolutionary pathway, highlighting instead the diversity and interconnectedness among early hominin groups.

Future Directions in Denisovan Research

The limited fossil record of Denisovans has prompted researchers to focus on their genetic legacy to fill in the gaps. Yet, many questions remain unanswered. Dr. Ongaro’s team has identified areas for further research, including more extensive genetic studies of understudied populations that may carry yet-undiscovered traces of Denisovan ancestry.

In addition, Dr. Ongaro emphasized the importance of integrating genetic findings with archaeological evidence:

“Integrating more genetic data with archaeological information—if we can find more Denisovan fossils—would certainly fill in a few more gaps.”

The search for additional Denisovan remains, particularly outside the known Siberian and Tibetan sites, could provide valuable insight into the extent of Denisovan influence on early humans.

Conclusion: Tracing the Denisovan Legacy

The story of the Denisovans, an extinct group of ancient humans, is a reminder of the complexity of human evolution. As scientists continue to unravel the Denisovan genetic contributions to modern humans, a clearer picture emerges of how this mysterious hominin group influenced human adaptability across diverse environments. The discoveries at Denisova and Baishiya Karst Caves, coupled with the genetic evidence of multiple interbreeding events, suggest that Denisovans left a lasting legacy that still shapes human populations today.

This research, published in Nature Genetics, continues to reshape our understanding of human evolution. The Denisovan impact, while hidden within the genetic code, reveals an evolutionary story rich with interbreeding, migration, and environmental adaptation—elements that underscore the shared and interconnected history of humanity.

1. Ongaro, L., & Huerta-Sanchez, E. (2024). A history of multiple Denisovan introgression events in modern humans. Nature Genetics, 1–11. https://doi.org/10.1038/s41588-024-01960-y