A remarkable study has brought to light the most ancient human genome sequenced to date, belonging to a Denisovan male from 200,000 years ago. This significant find, presented by population geneticist Stéphane Peyrégne at the annual meeting of the Society for Molecular Biology and Evolution in Puerto Vallarta, Mexico, has profound implications for understanding our extinct cousins and their interactions with other archaic humans.
Discovery and Significance of the Denisovan Genome
The unveiling of the Denisovan genome, the oldest high-quality human genome yet, surpasses the previous record held by a 120,000-year-old Neanderthal. This new discovery stems from more than a decade of meticulous efforts to locate fossilized bones and sequence a second Denisovan genome. The first Denisovan genome was obtained from a girl's pinkie finger bone, dated between 60,000 to 80,000 years ago, found in Denisova Cave in the Altai Mountains of Siberia.
The Context of Denisova Cave
Denisova Cave, a cold and fossil-rich site, has yielded invaluable insights into the Denisovans. According to Peyrégne and his colleagues, the newly sequenced male originates from a distinct population of early Denisovans that interbred multiple times with a previously undetected Neanderthal group. Population geneticist Emilia Huerta-Sanchez of Brown University expressed excitement, noting that the discovery is more than just another ancient genome. It provides deeper insights into these elusive ancestors.
Insights from Genetic Analysis
Denisovans are primarily known from their DNA, with the first complete genome coming from a girl's pinkie finger bone. Subsequent discoveries have included bits of nuclear and mitochondrial DNA from fragmentary fossils—teeth, a toe bone—of seven additional individuals, all from Denisova Cave. Some Denisovan DNA has even been identified in modern humans, including Papuans and Han Chinese, indicating past interbreeding.
Excavations in Denisova Cave, led by archaeologist Maxim Kozlikin of the Russian Academy of Sciences (RAS), unearthed a molar in a deep layer dated to 200,000 years ago. The molar was sent to the Max Planck Institute, where evolutionary geneticists extracted enough DNA to provide 24-fold coverage of the genome, an exceptional quality for such ancient DNA.
Interbreeding and Migration Patterns
The DNA analysis revealed that the male Denisovan had inherited 5% of his genome from an ancient, previously unknown Neanderthal population. This male, labeled Denisova 25, came from a different population than the girl, known as Denisova 3, whose DNA is more closely related to Denisovan sequences found in living modern humans.
These findings suggest that the older male's population was eventually replaced in the cave by later Denisovans. The data also indicate that the male Denisovan's ancestors interbred multiple times with Neanderthals. Evidence from a Neanderthal fossil dated to about 120,000 years ago supports the idea that Neanderthals temporarily replaced Denisovans in the cave, but by 60,000 years ago, Denisovans had returned.
Denisovans, Neanderthals, and Modern Humans
The Altai region appears to have been a significant crossroads for various human species. DNA from a bone fragment of a female over 50,000 years old shows her mother was a Neanderthal and her father a Denisovan. Later, both Denisovan and Neanderthal DNA and fossils indicate that modern humans occupied the cave, and Denisovans and Neanderthals eventually disappeared.
Despite interbreeding, Denisovans and Neanderthals maintained distinct lineages. They diverged from a common ancestor at least 400,000 years ago, with Neanderthals settling in Europe and the Middle East, while Denisovans moved east into Asia. There, Denisovans evolved separately, acquiring roughly 300,000 genetic changes that differentiate them from Neanderthals.
Future Directions and Implications
During the question-and-answer session, an audience member inquired about the potential presence of DNA from an even older, unidentified human species, possibly Homo erectus, in the Denisovan genome. Peyrégne confirmed that if any such "superarchaic" ancestry exists, it would be shared between Denisova 3 and Denisova 25.
The Max Planck researchers plan to publish the new genome soon, offering further insights into this mysterious group. Population geneticist Priya Moorjani of the University of California, Berkeley, emphasized the significance of the discovery, noting that it provides a deeper understanding of Denisovans and their interactions with other human groups.
Conclusion
The sequencing of the 200,000-year-old Denisovan genome represents a significant milestone in the study of human evolution. This discovery not only provides valuable insights into the Denisovans' interactions with Neanderthals but also highlights the complexity of ancient human migrations and interbreeding. As researchers continue to explore and analyze these ancient genomes, our understanding of human history and evolution will undoubtedly expand, revealing the intricate tapestry of our ancestral past.