The average annual temperature of the cave remains at 0 °C (32 °F), which has contributed to the preservation of archaic DNA among the remains discovered.
Denisova hominin Scientists from the Russian Academy of Sciences' Institute of Archaeology and Ethnography in
Novosibirsk have investigated the cave. Among the artifacts which had been left about 30,000 to 48,000 years ago (strata 9–11), bones were identified. One of these bones was a piece of
phalanx of a child found in layer 11.2 of the East Gallery. The fossil element was analyzed by
Svante Pääbo and coworkers from the
Max Planck Institute for Evolutionary Anthropology in
Leipzig; its
mitochondrial DNA revealed a structure that differs from known human patterns and has been ascribed to "Denisova hominin". Pääbo and his co-workers first intended to classify the Denisovans as a separate species but changed their minds prior to publication of the results. Further analysis revealed the Denisovans were related to the Neanderthals and interbred with the ancestors of modern
Melanesians.
Neanderthal remains: the Altai Neanderthal distribution. In 2010, a toe bone was discovered in the cave, in layer 11.4 of the East Gallery, and therefore contemporary with the Denisovan finger bone. Preliminary characterization of the bone's mitochondrial DNA suggested it belonged to a Neanderthal, not a Denisovan. Later analysis confirmed the toe bone as coming from a Neanderthal.
Denisova 11: a first-generation Neanderthal and Denisovan hybrid The use of collagen
peptide mass fingerprinting of ancient bone samples, called
Zooarchaeology by Mass Spectrometry (ZooMS), for species identification allowed the sorting of 2,315 unidentified bone fragments from 2012 One sample, DC1227 (
Denisova 11), taken from layer 12 of the East Gallery, carried human traits. This was the first time that this technique was used to successfully identify the presence of an extinct hominid.
DNA from soil Sequencing of DNA from soil samples taken from Denisova Cave showed the presence of Neanderthal and Denisovan mtDNA from several samples, as well as the DNA of several animals. Neanderthal mtDNA was present in soil samples from layer 15 of the Main Gallery, a layer associated with Paleolithic artifacts where no Neanderthal fossils have been found. Neanderthal and Denisovan mtDNA were present in samples from layers 14 and 15, respectively, from the East Gallery, lower than any previous fossil finds.
Equus ovodovi MtDNA has also been recovered from an
equine fossil, dating to around 32,000 years ago, taken from Denisova Cave. The equid fossil was identified as coming from
Equus ovodovi an extinct species first described based on a 40,000 year old fossil taken from Proskuryakova Cave in
Khakassia, Russia. The mtDNA of the Denisova sample shows close affinity for that taken from Proskuryakova Cave. DNA analysis places
Equus ovodovi as a
phylogenetically basal group for
non-caballine horses, with closer genetic affinities with
zebras and
asses.
Ancient North Eurasian woman File:ANE deer tooth pendant from Denisova Cave.jpg|thumb|upright|Deer tooth pendant of an ANE woman, from Denisova Cave, dated circa 24,700 years BP. == Fossils ==