The importance of Denisova Cave to ancient genomics is difficult to overstate. The site has produced more high-quality ancient hominin genomes than any other location in the world, and the sequence of discoveries from the cave has transformed the understanding of archaic human population history.
The key factor is preservation. DNA degrades through chemical reactions that are accelerated by heat and moisture. Denisova Cave’s relatively cool, stable temperature—the cave maintains a temperature of about 0 degrees Celsius in some parts year-round—and the dry conditions in its deeper sediments have slowed degradation enough that DNA from individuals who died hundreds of thousands of years ago has survived in readable form.
The Denisova 3 finger bone, which produced the discovery genome published in 2010, yielded DNA of exceptional quality—good enough to generate a high-coverage genome that remains the most complete ancient hominin genome ever recovered, despite being approximately 50,000 to 80,000 years old. This quality was unprecedented and established Denisova Cave as a uniquely favorable site.
Subsequent sequencing from the cave has continued to yield important results. The Altai Neanderthal, whose toe bone was found in the cave, produced a high-coverage genome that showed Neanderthal populations had limited genetic diversity and experienced some inbreeding. Analysis of the Altai Neanderthal genome also revealed Denisovan ancestry in Neanderthal populations—the same signal of past interbreeding that the Denisova 11 study later confirmed through direct observation of an individual.
The cave’s sediments themselves have yielded ancient DNA independent of any identified bone. In 2017, researchers from the Max Planck Institute and the Russian Academy of Sciences published a paper in Science showing that they could extract and sequence ancient hominin DNA directly from cave sediment—without needing to find a bone or tooth. This technique, sedaDNA analysis, has the potential to identify the presence of specific hominin groups in a site even when no macroscopic remains are preserved.