Denisovan

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Denisova 4, a molar

The Denisovans or Denisova hominins (

archaic human that ranged across Asia during the Lower and Middle Paleolithic, and lived, based on current evidence, from 285 to 52 thousand years ago.[1] Denisovans are known from few physical remains; consequently, most of what is known about them comes from DNA
evidence. No formal species name has been established pending more complete fossil material.

The first identification of a Denisovan individual occurred in 2010, based on

.

Denisovans apparently interbred with modern humans, with a high percentage (roughly 5%) occurring in Melanesians, Aboriginal Australians, and Filipino 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.

Taxonomy

Denisovans may represent a new species of

Homo sapiens (modern humans), but there are too few fossils to erect a proper taxon. Proactively proposed species names for Denisovans are H. denisova[3] or H. altaiensis.[4]

Discovery

Denisovan is located in Asia
Denisova Cave
Denisova Cave
Baishiya Karst Cave
Baishiya Karst Cave
Tam Ngu Hao 2 Cave
Tam Ngu Hao 2 Cave
Locations of paleoarchaeological finds linked to Denisovans: Denisova Cave (blue) in the Altai Mountains of Siberia; Baishiya Karst Cave (yellow) on the Tibetan Plateau; and Tam Ngu Hao 2 Cave (grey) in northern Laos
The Denisova Cave, where the first reported Denisovans were found

canids.[5]

In 2008,

matrilineal mitochondrial DNA (mtDNA) extracted from the bone demonstrated it to belong to a novel ancient hominin, genetically distinct both from contemporary modern humans and from Neanderthals.[2]

In 2019, Greek archaeologist Katerina Douka and colleagues radiocarbon dated specimens from Denisova Cave, and estimated that Denisova 2 (the oldest specimen) lived 195,000–122,700 years ago.[7] Older Denisovan DNA collected from sediments in the East Chamber dates to 217,000 years ago. Based on artifacts also discovered in the cave, hominin occupation (most likely by Denisovans) began 287±41 or 203±14 ka. Neanderthals were also present 193±12 ka and 97±11 ka, possibly concurrently with Denisovans.[8]

Specimens

The fossils of five distinct Denisovan individuals from Denisova Cave have been identified through their ancient DNA (aDNA): Denisova 2, 3, 4, 8, and 11. An mtDNA-based phylogenetic analysis of these individuals suggests that Denisova 2 is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 were roughly contemporaneous.[9] During DNA sequencing, a low proportion of the Denisova 2, Denisova 4 and Denisova 8 genomes were found to have survived, but a high proportion of the Denisova 3 genome was intact.[9][10] 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.[11]

These specimens remained the only known examples of Denisovans until 2019, when a research group led by

Buddhist monk in the Baishiya Karst Cave on the Tibetan Plateau in China. Known as the Xiahe mandible, the fossil became part of the collection of Lanzhou University, where it remained unstudied until 2010.[12] It was determined by ancient protein analysis to contain collagen that by sequence was found to have close affiliation to that of the Denisovans from Denisova Cave, while uranium decay dating of the carbonate crust enshrouding the specimen indicated it was more than 160,000 years old.[13] The identity of this population was later confirmed through study of environmental DNA, which found Denisovan mtDNA in sediment layers ranging in date from 100,000 to 60,000 years before present, and perhaps more recent.[14]

In 2018, a team of Laotian, French, and American anthropologists, who had been excavating caves in the Laotian jungle of the

Annamite 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 of amelogenin (a protein on the Y 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.[15]

Some older findings may or may not belong to the Denisovan line, but Asia is not well mapped in regards to

Dali skull,[16] the Xujiayao hominin,[17] Maba Man, the Jinniushan hominin, and the Narmada Human.[18] The Xiahe mandible shows morphological similarities to some later East Asian fossils such as Penghu 1,[13][19] but also to Chinese H. erectus.[11] 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.[20]

Name Fossil elements Age Discovery Place Sex and age Publication Image GenBank accession
Denisova 3
(also known as X Woman)[21][11][2]
Distal
fifth finger
76.2–51.6 ka[7] 2008 Denisova cave (Russia) 13.5-year-old adolescent female 2010
Replica of part of the phalanx.
Replica of part of the phalanx.
NC013993
Denisova 4[21][16] Permanent upper 2nd or 3rd molar 84.1–55.2 ka[7] 2000 Denisova cave (Russia) Adult male 2010
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.
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.
FR695060
Denisova 8[10] Permanent upper 3rd molar 136.4–105.6 ka[7] 2010 Denisova cave (Russia) Adult male 2015 KT780370
Denisova 2[9]
Deciduous
2nd lower molar
194.4–122.7 ka[7] 1984 Denisova cave (Russia) Adolescent female 2017 KX663333
Xiahe mandible[13] Partial mandible > 160 ka 1980
Baishiya Cave
(China)
2019
Denisova 11
(also known as Denny, Denisovan x Neanderthal hybrid)
[22]
Arm or leg bone fragment 118.1–79.3 ka[7] 2012 Denisova cave (Russia) 13 year old adolescent female 2016

KU131206

Denisova 13[23] Parietal bone fragment Found in layer 22[23] which dates to ~285±39 ka[8] 2019 Denisova cave (Russia) pending
TNH2-1[15] Permanent lower left 1st or 2nd molar 164–131 ka 2018 Tam Ngu Hao 2 cave (Laos) 3.5 to 8.5 year old female 2022

Evolution

The evolution and geographic spread of Denisovans as compared with Neanderthals, Homo heidelbergensis and Homo erectus

chimpanzees 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 of H. erectus out of Africa, completely distinct from modern humans and Neanderthals.[2]

However, according to the

human–chimpanzee last common ancestor, Denisovans/Neanderthals split from modern humans about 804,000 years ago, and from each other 640,000 years ago.[21] Using a mutation rate of 1×10−9 or 0.5×10−9 per base pair (bp) per year, the Neanderthal/Denisovan split occurred around either 236–190,000 or 473–381,000 years ago respectively.[24] Using 1.1×10−8 per generation with a new generation every 29 years, the time is 744,000 years ago. Using 5×10−10 nucleotide 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.[25] H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans.[26] Due to the strong divergence in dental anatomy, they may have split before characteristic Neanderthal dentition evolved about 300,000 years ago.[21]

The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic human population,[27] possibly a relict H. erectus or H. erectus-like population about 53,000 years ago.[24] Alternatively, divergent mtDNA could have also resulted from the persistence of an ancient mtDNA lineage which only went extinct in modern humans and Neanderthals through genetic drift.[21] Modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced.[28][29][30][31] The mtDNA sequence from the femur of a 400,000-year-old H. heidelbergensis from the Sima de los Huesos Cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to Denisovans,[32][33] 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.[34]

Demographics

Denisovans appear to have crossed the Wallace Line.[18]

Denisovans are known to have lived in Siberia, Tibet, and Laos.[15] The Xiahe mandible is the earliest recorded human presence on the Tibetan Plateau.[13] Though their remains have been identified in only these three locations, traces of Denisovan DNA in modern humans suggest they ranged across East Asia,[35][36] and potentially western Eurasia.[37] 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; and Oceania and, to a lesser extent, across Asia. Using coalescent 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.[38]

Based on the high percentages of Denisovan DNA in modern Papuans and Australians, Denisovans may have crossed the Wallace Line into these regions (with little back-migration west), the second known human species to do so,[18] along with earlier Homo floresiensis. By this logic, they may have also entered the Philippines, living alongside H. luzonensis which, if this is the case, may represent the same or a closely related species.[39] These Denisovans may have needed to cross large bodies of water.[38] 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.[37]

Using exponential distribution analysis on haplotype lengths, Jacobs calculated introgression 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.[38]

The mtDNA from Denisova 4 bore a high similarity to that of Denisova 3, indicating that they belonged to the same population.[21] The genetic 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.[9]

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.[8] 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.[13] Denisovans seem to have also inhabited the jungles of Southeast Asia.[36] The Tam Ngu Hao 2 site might have been a closed forest environment.[15]

Anatomy

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,[12][15] and a parietal bone skull fragment.[23] The finger bone is within the modern human range of variation for women,[11] 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 any Homo species except H. habilis and H. rudolfensis, and is more like those of australopithecines. The second molar is larger than those of modern humans and Neanderthals, and is more similar to those of H. erectus and H. habilis.[21] Like Neanderthals, the mandible had a gap behind the molars, and the front teeth were flattened; but Denisovans lacked a high mandibular body, and the mandibular symphysis at the midline of the jaw was more receding.[13][19] The parietal is reminiscent of that of H. erectus.[40]

A facial reconstruction has been generated by comparing methylation at individual genetic loci associated with facial structure.[41] 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 Denisovan tooth row was longer than that of Neanderthals and anatomically modern humans.[42]

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 in early 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.[43]

The Denisovan genome from Denisova Cave has variants of genes which, in modern humans, are associated with dark skin, brown hair, and brown eyes.

Tibetans assists with adaptation to low oxygen levels at high elevation,[45][13] and in a region containing the WARS2 and TBX15 loci which affect body-fat distribution in the Inuit.[46] 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.[47]

Culture

Denisova Cave

Some ornaments (above) and animal bones and stone tools (below) found in Denisova Cave. Note, ornaments may have been crafted by modern humans

Early Middle Paleolithic stone tools from Denisova Cave were characterized by discoidal (disk-like) cores and Kombewa cores, but Levallois cores and flakes were also present. There were 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.[8]

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.[8]

Early Upper 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 was blade 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.[8]

In the Upper Paleolithic layers, there were also several bone tools and ornaments: a marble ring, an ivory ring, an ivory pendant, a red deer tooth pendant, an elk tooth pendant, a chloritolite 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.[48][8]

Tibet

In 1998, five child hand- and footprint impressions were discovered in a travertine unit near the Quesang hot 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 given the Xiahe mandible is the oldest human fossil from the region (albeit, 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 of rock art. Similar hand stencils and impressions do not appear again in the archeological record until roughly 40,000 years ago.[49]

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.[49]

Interbreeding

Analyses of the modern human genomes indicate past interbreeding with at least two groups of archaic humans, Neanderthals[50] and Denisovans,[21][51] 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.[50]

Archaic humans

As much as 17% of the Denisovan genome from Denisova Cave represents DNA from the local Neanderthal population.[50] Denisova 11 was an F1 (first generation) Denisovan/Neanderthal hybrid; the fact that such an individual was found may indicate interbreeding was a common occurrence here.[52] The Denisovan genome shares more derived alleles with the Altai Neanderthal genome from Siberia than with the Vindija Cave Neanderthal genome from Croatia or the Mezmaiskaya 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.[53] However, Denny's Denisovan father had the typical Altai Neanderthal introgression, while her Neanderthal mother represented a population more closely related to Vindija Neanderthals.[54]

About 4% of the Denisovan genome derives from an unidentified archaic hominin,

H. daliensis.[56]

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.[57]

Modern humans

A 2011 study found that Denisovan DNA is prevalent in

autosomes, and some autosomes (such as chromosome 11) also have less Denisovan ancestry, which could indicate hybrid 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.[44]

In contrast, 0.2% derives from Denisovan ancestry in mainland Asians and

Tianyuan 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.[63][18] A 2018 study of Han Chinese, Japanese, and Dai 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.[62] 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.[38]

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 old

Hòabìnhian culture and subsequent Neolithic cultures.[64]

In other regions of the world, archaic introgression into humans stems from a group of Neanderthals related to those which inhabited Vindija 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.[37]

Denisovan genes may have helped early modern humans migrating out of Africa to acclimatize[

SARS-CoV-2.[67] 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".[68]

In December 2023, scientists reported that

modern humans from Neanderthals and Denisovans may biologically influence the daily routine of modern humans.[69]

See also

References

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Further reading

External links