Denisova Cave


Denisova Cave 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 originate from the cave, including artifacts dated to around 40,000 BP. A 32,000-year-old prehistoric species of horse has also been found in the cave.
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 by some as the most ancient needle known. Denisovans, Neanderthals and related hybrids may have inhabited the Denisova Cave for extended periods, but perhaps not at the same time. The attribution of the needle and certain other artifacts at the cave, whether to Homo sapiens or to the Denisova hominin, is uncertain.

Description

Located in Altai Krai, near the border with Altai Republic, both in Russia, the cave is near the village of Chorny Anui, and some south of Barnaul, the regional capital. The cave, which is approximately above the right bank of the Anuy River, has formed in upper Silurian limestone and contains a floor area of about. The cave is composed of three galleries. The central chamber, the Main Gallery, contains a floor of with side galleries, the East Gallery and the South Gallery. It has been described 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, and 39 species of small mammals, as well as remnants of reptiles, 50 bird species and other vertebrates. Pollen in the cave sediments is used for palaeoclimatological research.

History

In the 18th century, the cave was inhabited by an Old Believer hermit, Dyonisiy, and was named after him, while the indigenous Altay people call it Ayu-Tash. In the 1970s, Russian 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 Dyonisiy 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 chlorastrolite, and pendants. A 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."
Denisovans, Neanderthals and related hybrids, may have inhabited the Denisova Cave over thousands of years, but it is unclear whether they ever shared the cave.

Archaeogenetics

The average annual temperature of the cave remains at 0 °C, which has contributed to the preservation of archaic DNA among the remains discovered.

Denisova hominin

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, 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.

Neanderthal remains: the Altai Neanderthal

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. 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 years 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.

Denisova 11: a first-generation Neanderthal and Denisovan hybrid

The use of collagen peptide mass fingerprinting of ancient bone samples, so-called Zooarchaeology by Mass Spectrometry, for species identification allowed the sorting of 2,315 unidentified bone fragments from 2012 or 2014 excavation. 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, measuring in with a maximum length of and maximum width of. Further analysis showed the bone fragment to have Neanderthal mitochondrial DNA.
Whole genome sequencing and other characterization of Denisova 11 to 2.6-fold coverage showed this specimen belonged to a female at least thirteen years old at the time of death. Denisova 11 was found to be the hybrid progeny of a Neanderthal mother and a Denisovan father. Comparing the entire genome against all archaic hominin genomes on record, Denisova 11 shares the most genetic affinity with Denisova 3, indicating that her Denisovan father is more closely related to Denisova 3 than her mother was to any of the sequenced Neanderthals. Like Denisova 3, this father carries some
introgressed Neanderthal DNA from an admixture event far in the past, estimated at more than 300 generations earlier, and similar in sequence to the Altai Neanderthal genome. However, the mother of Denisova 11 was genetically closer to Neanderthal specimen Vindija 33.19 from Vindija Cave in Croatia and to other sequenced Neanderthal individuals than to the Altai Neanderthal. This suggests a migration or population turnover involving the Neanderthal populations of the region surrounding the Denisova cave.

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.

Ovodov horse

MtDNA has also been recovered from an equid 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 closest genetic affinity with zebras.

Fossils

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 2018, Denisova 11 was identified as a Neanderthal/Denisova hybrid, based on whole genome sequencing and comparisons.
During DNA sequencing, Denisova 2, Denisova 4 and Denisova 8 yielded low-coverage genomes, while Denisova 3 and the Altai Neanderthal yielded high-coverage genomes.
NameElementLayerLocationTypeAgeSexDiscoveryFirst public.ImageNotes
Denisova 2deciduous lower molar22.1Main GalleryDenisovan>100 ka♀1984
Denisova 3
or X Woman		finger phalanx11.2East GalleryDenisovan30–50 ka♀2008
Team of Michael Shunkov		Johannes Krause, et al.Cut in two, one piece partially destroyed to investigate the mtDNA.
Denisova 4upper molar11.1South GalleryDenisovan30–50 ka♂2000
Altai Neanderthal
or Denisova 5		proximal toe phalanx11.4East GalleryNeanderthal30–50 ka
♀2010M.B. Mednikova Molecular clock analysis of mtDNA suggested this specimen instead dates to ~120 ka.
Denisova 8upper molar11.4–12East GalleryDenisovan♂-
Denisova 11long bone fragment12East GalleryNeanderthal/Denisovan
hybrid		~90 ka♀2014Samantha Brown, et al.