Denisova Cave is located in the Altai Mountains’ Bashelaksky Range in South-Central Siberia, Russia, near the borders with Kazakhstan, China, and Mongolia. It is named after Denis, a Russian hermit who lived there in the 18th century [8][9]. The cave consists of three main chambers - the Main Chamber, East Chamber, and South Chamber - each containing deposits with stratigraphic sequences ranging from the Middle Pleistocene to the Holocene [6][7]. 

The cave was first inspected for fossils in the 1970s by Russian paleontologist Nikolai Ovodov who was searching for canid remains [9]. In 2008, Russian researchers led by Michael Shunkov discovered a distal manual phalanx of the fifth digit of a female juvenile hominin in Denisova Cave. The phalanx was found in layer 11.2 of the East Chamber. When German researchers extracted and sequenced mitochondrial (mt) DNA from the fossil, it did not match that of either Neanderthals or modern humans. This discovery, known as Denisova 3 (51.6–76.2 ka) provided the first evidence of an unknown group of archaic humans named “Denisovans” [1][2][10][11]. Its high-coverage nuclear genome revealed that they diverged from a common ancestor with the Neanderthals between 440 and 390 thousand years ago [12].

The identification of Denisovan ancestry in indigenous peoples of Australia and Papua New Guinea and in East and Southeast Asians suggests that modern humans met and interbred with at least two distinct Denisovan populations [13][14]. This raises the possibility that Denisovans may have been widespread across continental Asia, island Southeast Asia, and near Oceania [10].

In addition to the traditional morphological identification of bones using diagnostic features, Zooarchaeology by Mass Spectrometry (ZooMS), a method of species identification by collagen peptide mass fingerprinting, was also used to identify hominin remains from thousands of archived unidentifiable bone fragments. At present, a total of 16 hominin remains have been identified: 4 Neanderthals, 7 Denisovans, a Neanderthal-Denisovan Hybrid, and 4 Homo sp. [4][11][10].

More Denisovans

Following Denisova 3, Six more Denisovan remains have been identified. Denisova 2 (122.7–194.4 ka) is a deciduous lower molar of an adolescent female from layer 22.1 of the Main Chamber [15]. Denisova 4 (55.2–84.1 ka) is an upper molar from a juvenile male discovered in layer 11.1 of the South Chamber [2]. Denisova 8 (105.6–136.4 ka) is also an upper molar found in the East Chamber but at the interface between layers 11.4 and 12 [16][11].

Denisova 2 was previously thought to be the oldest hominin identified in the Denisova Cave with an estimated age of  122.7–194.4 ka using a Bayesian approach incorporating optical, genetic, and stratigraphic data [11], or as early as 280 ka based solely on optical ages only [6]. However, Brown et al. [10] recently reported new finds from Layer 15, the oldest archaeological layer of the East Chamber, and estimated to date to 187.0–216.9 ka based on Bayesian modeling of existing optical ages [6]. This makes Denisova 19, Denisova 20, and Denisova 21 the oldest documented Denisovans based on mtDNA age estimates and the established chronology for layer 15 [10].

Neanderthals

Denisova 5 (90.9–130.0 ka) a proximal toe phalanx was discovered from layer 11.4 of the East Chamber, in 2010. DNA sequencing confirmed that it belonged to a Neanderthal woman, hence it was also referred to as the Altai Neanderthal [16][3]. Since the discovery of Denisova 5, three more neanderthal fossils have been identified in Denisova Cave. Denisova 9 (119.1–147.3 ka) and Denisova 17 (134.1–150.6 ka), are both from layer 12.3 of the East Chamber, while Denisova 15 (91.4–130.3 ka) came from the same layer as Denisova 5 [11][10].

Neanderthal-Denisovan Hybrid

Denisova 11 (79.3–118.1 ka) is yet another ground-breaking discovery from Denisova Cave. Denisova 11 is a fossil from a 13-year-old female found in layer 12.3 of the East Chamber [4]. Genome sequencing of Denisova 11 reveals that she is the first generation offspring of a Neanderthal mother and a Denisovan father. Her Denisovan father’s genome bears traces of Neanderthal ancestry and he also originates from a population related to Denisova 3, who in turn also carry small amounts of Neanderthal DNA. Her Neanderthal mother on the other hand came from a population that was more closely related to Neanderthals who lived later in Europe than to Denisova 5 [5].

Gene flow between Neanderthals and Denisovans provides additional indirect evidence of interbreeding. Denisova 2’s genome, for example, revealed that she had Neanderthal ancestry. Denisova 8 and Denisova 3 also show Neanderthal introgression from two different Neanderthal populations [17]. These findings suggest potential cohabitation and frequent interactions between the two hominin groups from >200 ka until their disappearance from the Altai around 50 ka [5][10].