TheDenisovans orDenisova hominins (/dəˈniːsəvə/də-NEE-sə-və) are anextinctspecies orsubspecies ofarchaic human that ranged across Asia during theLower andMiddle Paleolithic, and lived, based on current evidence, from 285 thousand to 25 thousand years ago.[1] Denisovans are known from few physical remains; consequently, most of what is known about them comes fromDNA evidence. No formal species name has been established pending more complete fossil material.
The first identification of a Denisovan individual occurred in 2010, based onmitochondrial DNA (mtDNA) extracted from ajuvenile female finger bone excavated from the SiberianDenisova Cave in theAltai Mountains in 2008.[2]Nuclear DNA indicates close affinities withNeanderthals. The cave was also periodically inhabited by Neanderthals, but it is unclear whether Neanderthals and Denisovans ever cohabited in the cave. Additional specimens from Denisova Cave were subsequently identified, as was a single specimen from theBaishiya Karst Cave on theTibetan Plateau, and Cobra Cave in theAnnamite Mountains of Laos. DNA evidence suggests they had dark skin, eyes, and hair, and had a Neanderthal-like build and facial features. However, they had largermolars which are reminiscent ofMiddle toLate Pleistocene archaic humans andaustralopithecines.
Denisovans apparentlyinterbred with modern humans, with a high percentage (roughly 5%) occurring inMelanesians,Aboriginal Australians, andFilipino Negritos. This distribution suggests that there were Denisovan populations across Asia. There is also evidence of interbreeding with the Altai Neanderthal population, with about 17% of the Denisovan genome from Denisova Cave deriving from them. A first-generation hybrid nicknamed "Denny" was discovered with a Denisovan father and a Neanderthal mother. Additionally, 4% of the Denisovan genome comes from an unknown archaic human species, which diverged from modern humans over one million years ago.
Denisovans may represent a new species ofHomo or an archaic subspecies ofHomo sapiens (modern humans), but there are too few fossils to erect a propertaxon. Proactively proposed species names for Denisovans areH. denisova[3] orH. altaiensis.[4]
In 2021, Chinese palaeoanthropologist Qiang Ji suggested his newly erected species,H. longi, may represent the Denisovans, based on the similarity between the type specimen's molar and that of the Xiahe mandible.[11] In 2024, paleoanthropologists Christopher Bae and Xiujie Wu designated theXujiayao fossils as theholotype of the speciesHomo juluensis, and suggested sinking Denisovans into this species. They recommended relegating the Dali Man and similar specimens toH. longi.[12]
In 2019, Greek archaeologistKaterina Douka and colleaguesradiocarbon dated specimens from Denisova Cave, and estimated that Denisova 2 (the oldest specimen) lived 195,000–122,700 years ago.[15] Older Denisovan DNA collected from sediments in the East Chamber dates to 217,000 years ago. Based onartifacts also discovered in the cave, hominin occupation (most likely by Denisovans) began 287±41 or 203±14ka. Neanderthals were also present 193±12 ka and 97±11 ka, possibly concurrently with Denisovans.[16]
The fossils of multiple distinct Denisovan individuals fromDenisova Cave have been identified through theirancient DNA (aDNA): Denisova 2, 3, 4, 8,11, 19, 20, 21 and 25.[17] An mtDNA-based phylogenetic analysis of these individuals suggested that Denisova 19, 20, and 21 are the oldest, followed by Denisova 2, then Denisova 8; while Denisova 3 and Denisova 4 were roughly contemporaneous.[18][17] In 2024, scientists announced the sequence of Denisova 25, which was in a layer dated to 200 ka.[19] During DNA sequencing, low proportions of the Denisova 2, Denisova 4 and Denisova 8 genomes were found to have survived, but high proportions of the Denisova 3 and Denisova 25 genomes were intact.[18][20][19] The Denisova 3 sample was cut into two, and the initial DNA sequencing of one fragment was later independently confirmed by sequencing the mtDNA from the second.[10] In 2022, a team from Germany, Austria, Russia and the UK found 3 Denisovans (Denisova 19, 20, 21) from layer 15 of the East Chamber, in Denisova Cave. It turns out that the mtDNA sequences of Denisova 19 and 21 are identical, indicating that they may belong to the same individual or be maternal relatives.The divergence date for the mtDNAs of the three new and the four previously published Denisovans is 229 ka (206 - 252 ka 95% Cl) during theInterglacial period MIS 7.[17]
Denisova Cave contained the only known examples of Denisovans until 2019, when a research group led byFahu Chen,Dongju Zhang, andJean-Jacques Hublin described a partial mandible discovered in 1980 by aBuddhist monk in theBaishiya Karst Cave on theTibetan Plateau in China. Known as the Xiahe mandible, the fossil became part of the collection ofLanzhou University, where it remained unstudied until 2010.[21] It was determined byancient protein analysis to containcollagen that by sequence was found to have close affiliation to that of the Denisovans from Denisova Cave, whileuranium decay dating of thecarbonate crust enshrouding the specimen indicated it was more than 160,000 years old.[8] The identity of this population was later confirmed through study ofenvironmental DNA, which found Denisovan mtDNA in sediment layers ranging in date from 100,000 to 60,000 years before present, and perhaps more recent.[22] A 2024 reanalysis identified a partial Denisovan rib fragment dating to between 48,000 and 32,000 BP.[23][24]
In 2018, a team of Laotian, French, and American anthropologists, who had been excavating caves in the Laotian jungle of theAnnamite Mountains since 2008, was directed by local children to the site Tam Ngu Hao 2 ("Cobra Cave") where they recovered a human tooth. The tooth (catalogue number TNH2-1) developmentally matches a 3.5 to 8.5 year old, and a lack ofamelogenin (a protein on theY chromosome) suggests it belonged to a girl, barring extreme degradation of the protein over a long period of time. Dental proteome analysis was inconclusive for this specimen, but the team found it anatomically comparable with the Xiahe mandible, and so tentatively categorized it as a Denisovan, although they could not rule out it being Neanderthal. The tooth probably dates to 164,000 to 131,000 years ago.[25]
Replica of the molar of Denisova. Part of the roots was destroyed to study the mtDNA. Their size and shape indicate it is neither neanderthal nor sapiens.
Sequencedmitochondrial DNA (mtDNA), preserved by the cool climate of the cave (average temperature is at freezing point), was extracted from Denisova 3 by a team of scientists led byJohannes Krause andSvante Pääbo from theMax Planck Institute for Evolutionary Anthropology inLeipzig, Germany. Denisova 3's mtDNA differs from that of modern humans by 385 bases (nucleotides) out of approximately 16,500, whereas the difference between modern humans andNeanderthals is around 202 bases. In comparison, the difference betweenchimpanzees and modern humans is approximately 1,462 mtDNA base pairs. This suggested that Denisovan mtDNA diverged from that of modern humans and Neanderthals about 1,313,500–779,300 years ago; whereas modern human and Neanderthal mtDNA diverged 618,000–321,200 years ago. Krause and colleagues then concluded that Denisovans were the descendants of an earlier migration ofH. erectus out of Africa, completely distinct from modern humans and Neanderthals.[2]
However, according to thenuclear DNA (nDNA) of Denisova 3—which had an unusual degree of DNA preservation with only low-level contamination—Denisovans and Neanderthals were more closely related to each other than they were to modern humans. Using the percent distance fromhuman–chimpanzee last common ancestor, Denisovans/Neanderthals split from modern humans about 804,000 years ago, and from each other 640,000 years ago.[26] Using a mutation rate of1×10−9 or0.5×10−9 perbase pair (bp) per year, the Neanderthal/Denisovan split occurred around either 236–190,000 or 473–381,000 years ago respectively.[29] Using1.1×10−8 per generation with a new generation every 29 years, the time is 744,000 years ago. Using5×10−10nucleotide site per year, it is 616,000 years ago. Using the latter dates, the split had likely already occurred by the time hominins spread out across Europe.[30]H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans.[31] Due to the strong divergence in dental anatomy, they may have split before characteristic Neanderthal dentition evolved about 300,000 years ago.[26]
The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic human population,[32] possibly arelictH. erectus orH. erectus-like population about 53,000 years ago.[29] Alternatively, divergent mtDNA could have also resulted from the persistence of an ancient mtDNA lineage which only went extinct in modern humans and Neanderthals throughgenetic drift.[26] Modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced.[33][34][35][36] The mtDNA sequence from the femur of a 400,000-year-oldH. heidelbergensis from theSima de los Huesos Cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to Denisovans,[37][38] and the authors posited that this mtDNA represents an archaic sequence which was subsequently lost in Neanderthals due to replacement by a modern-human-related sequence.[39]
Denisovans are known to have lived in Siberia, Tibet, and Laos.[25] The Xiahe mandible is the earliest recorded human presence on the Tibetan Plateau.[8] Though their remains have been identified in only these three locations, traces of Denisovan DNA in modern humans suggest they ranged acrossEast Asia,[40][41] and potentially western Eurasia.[42] In 2019,geneticist Guy Jacobs and colleagues identified three distinct populations of Denisovans responsible for the introgression into modern populations now native to, respectively: Siberia and East Asia; New Guinea and nearby islands; andOceania and, to a lesser extent, across Asia. Usingcoalescent modeling, the Denisova Cave Denisovans split from the second population about 283,000 years ago; and from the third population about 363,000 years ago. This indicates that there was considerable reproductive isolation between Denisovan populations.[43] In a 2024 study, scientist Danat Yermakovich, of theUniversity of Tartu, discovered that people living at different elevations in Papua New Guinea have differences in Denisovan DNA; with people living in the highlands having variants for early brain development and those living in the lowlands having variants for the immune system.[44]
Based on the high percentages of Denisovan DNA in modern Papuans and Australians, Denisovans may have crossed theWallace Line into these regions (with little back-migration west), the second known human species to do so,[7] along with earlierHomo floresiensis. By this logic, they may have also entered the Philippines, living alongsideH. luzonensis which, if this is the case, may represent the same or a closely related species.[45] These Denisovans may have needed to cross large bodies of water.[43] Alternately, high Denisovan DNA admixture in modern Papuan populations may simply represent higher mixing among the original ancestors of Papuans prior to crossing the Wallace line.
Icelanders also have an anomalously high Denisovan heritage, which could have stemmed from a Denisovan population far west of the Altai Mountains. Genetic data suggests Neanderthals were frequently making long crossings between Europe and the Altai Mountains especially towards the date of their extinction.[42]
Usingexponential distribution analysis onhaplotype lengths, Jacobs calculatedintrogression into modern humans occurred about 29,900 years ago with the Denisovan population ancestral to New Guineans; and 45,700 years ago with the population ancestral to both New Guineans and Oceanians. Such a late date for the New Guinean group could indicate Denisovan survival as late as 14,500 years ago, which would make them the latest surviving archaic human species. A third wave appears to have introgressed into East Asia, but there is not enough DNA evidence to pinpoint a solid timeframe.[43]
The mtDNA from Denisova 4 bore a high similarity to that of Denisova 3, indicating that they belonged to the same population.[26] Thegenetic diversity among the Denisovans from Denisova Cave is on the lower range of what is seen in modern humans, and is comparable to that of Neanderthals. However, it is possible that the inhabitants of Denisova Cave were more or less reproductively isolated from other Denisovans, and that, across their entire range, Denisovan genetic diversity may have been much higher.[18]
Denisova Cave, over time of habitation, continually swung from a fairly warm and moderately humid pine and birch forest to tundra or forest-tundra landscape.[16] Conversely, Baishiya Karst Cave is situated at a high elevation, an area characterized by low temperature, low oxygen, and poor resource availability. Colonization of high-altitude regions, due to such harsh conditions, was previously assumed to have only been accomplished by modern humans.[8] Denisovans seem to have also inhabited the jungles of Southeast Asia.[41] The Tam Ngu Hao 2 site might have been a closed forest environment.[25]
Little is known of the precise anatomical features of the Denisovans since the only physical remains discovered so far are a finger bone, four teeth,long bone fragments, a partial jawbone,[21][25] aparietal bone skull fragment,[28] and a rib bone.[23] The finger bone is within the modern human range of variation for women,[10] which is in contrast to the large, robust molars which are more similar to those of Middle to Late Pleistocene archaic humans. The third molar is outside the range of anyHomo species exceptH. habilis andH. rudolfensis, and is more like those ofaustralopithecines. The second molar is larger than those of modern humans and Neanderthals, and is more similar to those ofH. erectus andH. habilis.[26] Like Neanderthals, the mandible had a gap behind the molars, and the front teeth were flattened; but Denisovans lacked a high mandibular body, and themandibular symphysis at the midline of the jaw was more receding.[8][9] The parietal is reminiscent of that ofH. erectus.[46]
A facial reconstruction has been generated by comparingmethylation at individual genetic loci associated with facial structure.[47] This analysis suggested that Denisovans, much like Neanderthals, had a long, broad, and projecting face; large nose; sloping forehead; protruding jaw; elongated and flattened skull; and wide chest and hips. The Denisovantooth row was longer than that of Neanderthals and anatomically modern humans.[48]
Middle-to-Late Pleistocene East Asian archaic human skullcaps typically share features with Neanderthals. The skullcaps from Xuchang feature prominent brow ridges like Neanderthals, though the nuchal and angular tori near the base of the skull are either reduced or absent, and the back of the skull is rounded off like inearly modern humans. Xuchang 1 had a large brain volume of approximately 1800 cc, on the high end for Neanderthals and early modern humans, and well beyond the present-day human average.[49]
The Denisovan genome from Denisova Cave has variants of genes which, in modern humans, are associated with dark skin, brown hair, and brown eyes.[50] The Denisovan genome also contains a variant region around theEPAS1 gene that inTibetans assists with adaptation to low oxygen levels at high elevation,[51][8] and in a region containing theWARS2 andTBX15 loci which affect body-fat distribution in theInuit.[52] In Papuans, introgressed Neanderthal alleles are highest in frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissue.[53]
Some ornaments (above) and animal bones and stone tools (below) found in Denisova Cave. Note, ornaments may have been crafted by modern humans
EarlyMiddle Paleolithic stone tools from Denisova Cave includedcores,scrapers,denticulate tools, and notched tools, deposited about 287±41 thousand years ago in the Main Chamber of the cave; and about 269±97 thousand years ago in the South Chamber; up to 170±19 thousand and 187±14 thousand years ago in the Main and East Chambers, respectively.[16]
Middle Paleolithic assemblages were dominated by flat, discoidal, and Levallois cores, and there were some isolated sub-prismatic cores. There were predominantly side scrapers (a scraper with only the sides used to scrape), but also notched-denticulate tools, end-scrapers (a scraper with only the ends used to scrape),burins,chisel-like tools, and truncated flakes. These dated to 156±15 thousand years ago in the Main Chamber, 58±6 thousand years ago in the East Chamber, and 136±26–47±8 thousand years ago in the South Chamber.[16]
EarlyUpper Paleolithic artefacts date to 44±5 thousand years ago in the Main Chamber, 63±6 thousand years ago in the East Chamber, and 47±8 thousand years ago in the South Chamber, though some layers of the East Chamber seem to have been disturbed. There wasblade production and Levallois production, but scrapers were again predominant. A well-developed, Upper Paleolithic stone bladelet technology distinct from the previous scrapers began accumulating in the Main Chamber around 36±4 thousand years ago.[16]
In the Upper Paleolithic layers, there were also severalbone tools and ornaments: amarble ring, an ivory ring, an ivory pendant, ared deer tooth pendant, anelk tooth pendant, achloritolite bracelet, and a bone needle. However, Denisovans are only confirmed to have inhabited the cave until 55 ka; the dating of Upper Paleolithic artefacts overlaps with modern human migration into Siberia (though there are no occurrences in the Altai region); and the DNA of the only specimen in the cave dating to the time interval (Denisova 14) is too degraded to confirm species identity, so the attribution of these artefacts is unclear.[54][16]
The inhabitants of Baishiya Karst Cave seem to have been extensively processinggoat antelopes, cows, deer, horses, andwoolly rhinoceros. They were also butchering large carnivores (cave hyena, dog, and big cat),marmots,hare, andeagles. They may have also used these animals'long bones to make bone tools, and additionally there are stone artefacts in each layer excavated.[23]
In 1998, five child hand- and footprint impressions were discovered in atravertineunit near the Quesanghot springs in Tibet; in 2021, they were dated to 226 to 169 thousand years ago using uranium decay dating. This is the oldest evidence of human occupation of the Tibetan Plateau, and since the Xiahe mandible is the oldest human fossil from the region (though younger than the Quesang impressions), these may have been made by Denisovan children. The impressions were printed onto a small panel of space, and there is little overlap between all the prints, so they seem to have been taking care to make new imprints in unused space. If considered art, they are the oldest known examples ofrock art. Similar hand stencils and impressions do not appear again in the archeological record until roughly 40,000 years ago.[55]
The footprints comprise four right impressions and one left superimposed on one of the rights. They were probably left by two individuals. The tracks of the individual who superimposed their left onto their right may have scrunched up their toes and wiggled them in the mud, or dug their finger into the toe prints. The footprints average 192.3 mm (7.57 in) long, which roughly equates to a 7 or 8 year old child by modern human growth rates. There are two sets of handprints (from a left and right hand), which may have been created by an older child unless one of the former two individuals had long fingers. The handprints average 161.1 mm (6.34 in), which roughly equates with a 12 year old modern human child, and the middle finger length agrees with a 17 year old modern human. One of the handprints shows an impression of the forearm, and the individual was wiggling their thumb through the mud.[55]
Analyses of the modern human genomes indicate past interbreeding with at least two groups of archaic humans, Neanderthals[56] and Denisovans,[26][57] and that such interbreeding events occurred on multiple occasions. Comparisons of the Denisovan, Neanderthal, and modern human genomes have revealed evidence of a complex web of interbreeding among these lineages.[56]
As much as 17% of the Denisovan genome from Denisova Cave represents DNA from the local Neanderthal population.[56] Denisova 11 was anF1 (first generation) Denisovan/Neanderthal hybrid; the fact that such an individual was found may indicate interbreeding was a common occurrence here.[58] The Denisovan genome shares more derived alleles with the Altai Neanderthal genome from Siberia than with theVindija Cave Neanderthal genome from Croatia or theMezmaiskaya cave Neanderthal genome from the Caucasus, suggesting that the gene flow came from a population that was more closely related to the local Altai Neanderthals.[59] However, Denny's Denisovan father had the typical Altai Neanderthalintrogression, while her Neanderthal mother represented a population more closely related to Vindija Neanderthals.[60] Denisova 25, dated to 200ka, is estimated to have inherited 5% of his genome from a previously unknown population of Neanderthals, and came from a different population of Denisovans than the younger samples.[19]
About 4% of the Denisovan genome derives from an unidentified archaic hominin,[56] perhaps the source of the anomalous ancient mtDNA, indicating this species diverged from Neanderthals and humans over a million years ago. The only identifiedHomo species ofLate Pleistocene Asia areH. erectus andH. heidelbergensis,[59][61] though in 2021, specimens allocated to the latter species were reclassified asH. longi andH. daliensis.[62]
Before splitting from Neanderthals, their ancestors ("Neandersovans") migrating into Europe apparently interbred with an unidentified "superarchaic" human species who were already present there; these superarchaics were the descendants of a very early migration out of Africa around 1.9 mya.[63]
A 2011 study found that Denisovan DNA is present at a comparatively high level inPapuans,Aboriginal Australians,Near Oceanians,Polynesians,Fijians, EasternIndonesians, andAeta (from the Philippines); but not inEast Asians, western Indonesians,Jahai people (from Malaysia), orOnge (from theAndaman Islands). This may suggest that Denisovan introgression occurred within the Pacific region rather than on the Asian mainland, and that ancestors of the latter groups were not present in Southeast Asia at the time.[41][64] In theMelanesian genome, about 4–6%[26] or 1.9–3.4% derives from Denisovan introgression.[65] Prior to 2021, New Guineans and Australian Aborigines were reported to have the most introgressed DNA,[7] but Australians have less than New Guineans.[66] A 2021 study discovered 30 to 40% more Denisovan ancestry inAeta people in the Philippines than inPapuans, estimated as about 5% of the genome. The Aeta Magbukon in Luzon have the highest known proportion of Denisovan ancestry of any population in the world.[45] In Papuans, less Denisovan ancestry is seen in theX chromosome thanautosomes, and some autosomes (such aschromosome 11) also have less Denisovan ancestry, which could indicatehybrid incompatibility. The former observation could also be explained by less female Denisovan introgression into modern humans, or more female modern human immigrants who diluted Denisovan X chromosome ancestry.[50]
In contrast, 0.2% derives from Denisovan ancestry in mainland Asians andNative Americans.[67]South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians.[68] The discovery of the 40,000-year-old Chinese modern humanTianyuan Man lacking Denisovan DNA significantly different from the levels in modern-day East Asians discounts the hypothesis that immigrating modern humans simply diluted Denisovan ancestry whereas Melanesians lived in reproductive isolation.[69][7] A 2018 study of Han Chinese,Japanese, andDai genomes showed that modern East Asians have DNA from two different Denisovan populations: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from Denisova Cave. This could indicate two separate introgression events involving two different Denisovan populations. In South Asian genomes, DNA only came from the same single Denisovan introgression seen in Papuans.[68] A 2019 study found a third wave of Denisovans which introgressed into East Asians. Introgression, also, may not have immediately occurred when modern humans immigrated into the region.[43]
The timing of introgression into Oceanian populations likely occurred after Eurasians and Oceanians split roughly 58,000 years ago, and before Papuan and Aboriginal Australians split from each other roughly 37,000 years ago. Given the present day distribution of Denisovan DNA, this may have taken place in Wallacea, though the discovery of a 7,200 year oldToalean girl (closely related to Papuans and Aboriginal Australians) from Sulawesi carrying Denisovan DNA makes Sundaland another potential candidate. Other early Sunda hunter gatherers so far sequenced carry very little Denisovan DNA, which either means the introgression event did not take place in Sundaland, or Denisovan ancestry was diluted with gene flow from the mainland AsianHòabìnhian culture and subsequentNeolithic cultures.[70]
In other regions of the world, archaic introgression into humans stems from a group of Neanderthals related to those which inhabitedVindija Cave, Croatia, as opposed to archaics related to Siberian Neanderthals and Denisovans. However, about 3.3% of the archaic DNA in the modern Icelandic genome descends from the Denisovans, and such a high percentage could indicate a western Eurasian population of Denisovans which introgressed into either Vindija-related Neanderthals or immigrating modern humans.[42]
A haplotype of EPAS1 in modern Tibetans, which allows them to live at high elevations in a low-oxygen environment, likely came from Denisovans.[51][8] Genes related tophospholipid transporters (which are involved infat metabolism) and totrace amine-associated receptors (involved in smelling) are more active in people with more Denisovan ancestry.[71] Denisovan genes may have conferred a degree of immunity against the G614 mutation ofSARS-CoV-2.[72] Denisovan introgressions may have influenced the immune system of present-day Papuans and potentially favoured "variants to immune-related phenotypes" and "adaptation to the local environment".[73]
In December 2023, scientists reported thatgenes inherited bymodern humans fromNeanderthals and Denisovans may biologically influence the daily routine of modern humans.[74]
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^abcViola, B. T.; Gunz, P.; Neubauer, S. (2019)."A parietal fragment from Denisova cave".88th Annual Meeting of the American Association of Physical Anthropologists.Archived from the original on 26 September 2019. Retrieved18 January 2020.
