Denisova Cave in 2008
|Location||Soloneshensky District, Altai Krai|
|Altitude||700 m (2,297 ft)|
|Area||270 m2 (2,900 sq ft)|
|Periods||Paleolithic 30,000 to 48,000 years ago|
|Cultures||Denisovans, Neanderthals, Homo Sapiens Sapiens|
Denisova Cave (Russian: Дени́сова Пеще́ра, translit. Denisova peshchera, lit. 'the cave of Denis'; Altay: Аю-Таш, translit. Ayu Tash, lit. 'Bear Rock') is a cave in the Bashelaksky Range of the Altai mountains, Siberia, Russia. The cave is of great paleoarchaeological and paleontological interest. Bone fragments of the Denisova hominin, sometimes called the "X woman" (referring to the maternal descent of mitochondrial DNA) originate from the cave, including artifacts dated to around 40,000 BP.
The cave is located in a region thought to have been inhabited concurrently in the past by Neanderthals and modern humans. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known.
Located in Altai Krai, at the border of the Altai Republic, the cave is near the village of Chorny Anui (Чёрный Ануй), and some 150 km south of Barnaul, the regional capital. The cave, which is approximately 28 m (92 ft) above the right bank of the Anuy River (a left tributary of the Ob), has formed in upper Silurian limestone and contains a floor area of about 270 m2 (2,900 sq ft). The cave is composed of three galleries. The central chamber, the Main Gallery, contains a floor of 9 m (30 ft) x 11 m (36 ft) with side galleries, the East Gallery and the South Gallery. It has been described as both as a karst cave and as a sandstone cave.
Cave sediments are rich with remnants of animals, including extinct ones. Remains of 27 species of large and medium-sized mammals have been found, (such as cave hyena, cave lion, etc.) and 39 species of small mammals, as well as remnants of reptiles, 50 bird species and other vertebrates. Pollen in the cave sediments are used for palaeoclimatological research.
In the 18th century, the cave was inhabited by a hermit, Dionisij (Denis), and was named after him, while the indigenous Altay people call it Ayu-Tash (Bear Rock). In the 1970s, Soviet scientists discovered paleoarcheological remains in the cave that led to further explorations. So far, 22 strata have been identified, with archeological artifacts that cover the time from Dionisij back to about 125,000–180,000 years ago. The dating of the strata was accomplished by the use of thermoluminescence dating of sediments, or, in some cases, radiocarbon dating on charcoal.
Among the archeological artifacts are Mousterian- and Levallois-style tools attributed to Neanderthals. Beside tools, researchers found decorative objects of bone, mammoth tusk, animal teeth, ostrich egg shell, fragments of a stone bracelet made of drilled, worked, and polished dark green chloritolite, and pendants. A 7 cm (2.8 in) sewing needle made from bird bone, estimated to be around 50,000 years-old, was found in Denisova Cave. The cave also contains stone tools and bone artifacts made by modern humans, and Pääbo commented: "The one place where we are sure all three human forms have lived at one time or another is here in Denisova Cave."
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.
Scientists from the Institute of Archaeology and Ethnology of 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", apparently an extinct hominin species or subspecies. Further analysis revealed the Denisovans were related to the Neanderthals and interbred with the ancestors of modern Melanesians.
The Altai Neanderthal
In 2011, 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. The first high-coverage genome of Neanderthals was taken from this toe bone.
This Neanderthal is referred to as the Altai Neanderthal. The Altai Neanderthal is estimated to be around 120,000-year-old. Other Neanderthals for which nuclear DNA has been recovered are all genetically closer to each other than to the Altai Neanderthal. Modern humans and Ust'-Ishim man share more alleles with all other Neanderthals than with the Altai Neanderthal, which shows that the introgression event from Neanderthals into humans likely took place after the split of the lineage of the Altai Neanderthal from that of other Neanderthals.
In 2015, researchers applied a new technique via species identification by collagen peptide mass fingerprinting, Zooarchaeology by Mass Spectrometry (ZooMS), to sort through 2,315 unidentified bone fragments retrieved from a 2014 excavation. They found that one sample, DC1227, 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 human. DC1227 was a bone fragment weighing 1.68 g (0.059 oz), measuring in with a maximum length of 24.7 mm (0.97 in) and maximum width of 8.39 mm (0.330 in). mtDNA analysis revealed that the owner of the bone fragment was a Neanderthal.
DNA from soil
In 2017, researchers successfully sequenced DNA from soil samples taken from Denisova Cave. They were able to identify Neanderthal and Denisovan mtDNA from several samples, as well as the DNA of several animals. The researchers identified Neanderthal mtDNA from soil samples taken from layer 15 from the Main Gallery, a layer associated with Paleolithic artifacts where no Neanderthal fossil has ever been found. The researchers also identified Neanderthal and Denisovan mtDNA taken from layers 14 and 15, respectively, from the East Gallery, at layers lower than any previous fossil finds, layers where no hominin fossil has ever been found.
In 2017, researchers successfully recovered mtDNA from an equiid fossil, dating to around 32,000 years ago, taken from Denisova Cave. The equiid fossil is described by its authors as coming from Equus ovodovi (Ovodov horse), an extinct species first described in 2010 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 closest genetic affinity for zebras.
So far, the fossils of six distinct individuals from Denisova Cave have been identified through their DNA. Four of the individuals, Denisova 2, Denisova 3, Denisova 4 and Denisova 8 are classified as Denisovans. Denisova 2 and Denisova 3 are young girls, while Denisova 4 and Denisova 8 are adult males. mtDNA analysis of the Denisovan individuals suggests that Denisova 2 is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 are roughly contemporaneous.
One of the individuals, the Altai Neanderthal, is a Neanderthal woman. Before its DNA was sequenced, the Altai Neanderthal had been given the provisional name of Denisova 5. In 2016, Denisova 11 was identified as a Neanderthal based on mtDNA evidence.
or X Woman 
|finger phalanx||11.2||East Gallery||Homo sp.||30–50 ka||♀||2008
Team of Michael Shunkov
|Johannes Krause, et al.||Destroyed to investigate the mtDNA.|
|Denisova 4||upper molar||11.1||South Gallery||Homo sp.||30–50 ka||♂||2000|
|Altai Neanderthal ||proximal toe phalanx||11.4||East Gallery||H. neandertalensis||30–50 ka||♀||2010||M.B. Mednikova (2011)|||
|Denisova 8||upper molar||11.4–12||East Gallery||Homo sp.||♂|
|Denisova 11 ||bone fragment from sample DC1227||12||East Gallery||H. neandertalensis||>50 ka||2014||Samantha Brown, et al. (2016)|
|Denisova 2 ||deciduous lower molar||22.1||Main Gallery||Homo sp.||>100 ka||♀||1984|
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- Picture of the actually molar of Denisova.
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- Pedal phalanx, actually fossil.