This marks the second occasion researchers have successfully retrieved the complete genome of Denisovans, an ancient human lineage that inhabited Asia. The DNA was sourced from a tooth estimated to be 200,000 years old, discovered in a Siberian cave.

The genome indicates that there were at least three distinct groups of Denisovans, each with unique histories. It also suggests that early Denisovans intermixed with an unidentified ancient human group as well as a previously unknown Neanderthal population.

“This research is groundbreaking,” asserts David Reich from Harvard University.

“This study significantly broadened my perspective on the Denisovan ecosystem,” states Samantha Brown from the National Center for Human Evolution Research in Spain.

Denisovans were first described solely via their DNA. Finger bones retrieved from Denisova Cave in Siberia exhibited DNA distinct from both modern humans and Neanderthals found in western Eurasia. Genomic analysis indicates Denisovans mated with modern humans, with populations in Southeast Asia, including the Philippines and Papua New Guinea, carrying Denisovan DNA.

Since their initial discovery in 2010, researchers have found that: a small number of Denisovans also originated from East Asia. In June, a skull unearthed in Harbin, China, was confirmed as Denisovan through molecular evidence, providing the first insight into their physical appearance. However, despite DNA fragments being recovered from various specimens, only the original specimen yielded a high-quality genome.

Researchers led by Stéphane Pèregne from Germany’s Max Planck Institute for Evolutionary Anthropology has introduced an additional researcher. (Pèregne declined to comment as the study is pending peer review.)

In 2020, a team of researchers discovered a male Denisovan molar tooth and sequenced its entire genome from the preserved DNA.

The researchers estimated this individual lived around 205,000 years ago, judging by the number of genetic mutations and comparing them with other ancient human genomes. This timeframe aligns with findings that the deposits containing the teeth are dated between 170,000 to 200,000 years old. In contrast, the other high-quality genome belongs to Denisovans who lived between 55,000 and 75,000 years ago, revealing an earlier chapter in Denisovan history.

The researchers suggest that at least three distinct Denisovan populations likely existed, based on comparisons from various Denisovan cave sites. The oldest group comprised the individuals whose teeth were analyzed. Many millennia later, a second group supplanted this earlier population in Denisova Cave.

“Comprehending how early Denisovans were supplanted by subsequent groups underscores pivotal events in human history,” says Qiao Meifu from the Institute of Vertebrate Paleontology and Paleoanthropology in China.

A third group, absent from the cave, still interbred with modern humans as suggested by genetic testing. Thus, all Denisovan DNA present in modern humans derives from a Denisovan group about which little is known.

The new genome illuminates the fact that Denisovans mated repeatedly with Neanderthals, who resided in and around the Denisovan Cave. Notably, this genome also contained traces of Neanderthals who lived between 7,000 and 13,000 years prior to Denisovan individuals. These traces do not align with any known Neanderthal genomes, indicating that the Denisovans interbred with a Neanderthal group yet to be sequenced.

Moreover, it’s probable that Denisovans also mated with an as-yet unidentified ancient human group that evolved independently of both Denisovans and modern humans for hundreds of thousands of years. One possibility is Homo erectus, the earliest known human species to migrate out of Africa and inhabit regions as far as Java, Indonesia. However, no DNA has been retrieved to confirm this.”H. erectus, so certainty remains elusive.

“It’s endlessly fascinating to uncover these new populations,” Brown remarked.