Denisovan

The Denisovans or Denisova hominins ( /dɪˈniːsəvə/ di-NEE-sə-və) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower and Middle Paleolithic (potentially surviving as late as 30,000–14,500 years ago in New Guinea). Denisovans are known from few remains, and, consequently, most of what is known about them comes from DNA evidence. Pending consensus on their taxonomic status, they have been referred to as Homo denisova, H. altaiensis, or H. sapiens denisova.

Denisova 4, a molar

The first Denisovan individual was identified in 2010 based on mitochondrial DNA (mtDNA) extracted from a juvenile female finger bone from the Siberian Denisova Cave. Nuclear DNA (nDNA) indicates close affinities with Neanderthals. The cave was also periodically inhabited by Neanderthals, but it is unclear whether they ever cohabited in the cave. Additional specimens from Denisova Cave were subsequently discovered, as was a single specimen from the Baishiya Karst Cave on the Tibetan Plateau in China. This indicates they lived in a wide variety of habitats, including forests, tundras, mountains, and jungles. DNA evidence suggests they had dark skin, eyes, and hair; and had a Neanderthal-like build and facial features, but had larger molars which are reminiscent of Middle Pleistocene to Late Pleistocene archaic humans and australopithecines.

Denisovans apparently interbred with modern humans, with about 3–5% of the DNA of Melanesians and Aboriginal Australians and around 6% in Papuans deriving from Denisovans. Denisovans may have interbred with modern humans in New Guinea as recently as 15,000 years ago. There is also evidence of interbreeding with the local 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. 4% of the Denisovan genome comes from an unknown archaic human species which diverged from modern humans over one million years ago.

Taxonomy

It is debated whether Denisovans represent a distinct species of Homo or are an archaic subspecies of H. sapiens. DNA analyses showing Denisovans as a sister taxon of Neanderthals also concerns the classification of the latter as H. neanderthalensis or H. s. neanderthalensis. Proposed species names for Denisovans are H. denisova[1] or H. altaiensis.[2]

Discovery
Denisova Cave
Baishiya Karst Cave
Locations of Denisova Cave in the Altai Mountains of Siberia and Baishiya Karst Cave on the Tibetan Plateau
The Denisova Cave, where the first reported Denisovans were found

Denisova Cave is in south-central Siberia, Russia in the Altai Mountains near the border with Kazakhstan, China and Mongolia. It is named after Denis (Dyonisiy), a Russian hermit who lived there in the 18th century. The cave was originally explored in the 1970s by Russian paleontologist Nikolai Ovodov, who was looking for remains of canids.[3]

In 2008, Michael Shunkov from the Russian Academy of Sciences and other Russian archaeologists from the Institute of Archaeology and Ethnology of Novosibirsk investigated the cave and found the finger bone of a juvenile female hominin originally dated to 50–30,000 years ago.[4][5] The estimate has changed to 76,200–51,600 years ago.[6] The specimen was originally named X-woman because matrilineal mitochondrial DNA (mtDNA) extracted from the bone demonstrated it to belong to a novel ancient hominin, genetically distinct from contemporary modern humans and Neanderthals.[4]

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.[6] 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.[7]

Specimens

The fossils of five distinct Denisovans from Denisova Cave have been identified through their Ancient DNA (aDNA): Denisova 2, Denisova 3, Denisova 4, Denisova 8, and Denisova 13. Denisova 11 was an F1 Denisovan-Neanderthal hybrid.[8] 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] Denisova 3 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 Fahu Chen, Dongju Zhang and Jean-Jacques Hublin described a partial mandible discovered in 1980 by a Buddhist monk in the Baishiya Karst Cave on the Tibetan Plateau in China. 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]

Some older findings may or may not belong to the Denisovan line, but Asia is not well mapped in regards to human evolution. Such findings include the Dali skull,[14] the Xujiayao hominin,[15] Maba Man, the Jinniushan hominin, and the Narmada hominin.[16] The Xiahe mandible shows morphological similarities to some later East Asian fossils such as Penghu 1,[13][17] but also to Chinese H. erectus.[11]

Name Fossil elements Age Discovery Place Sex and age Publication Image GenBank accession
Denisova 3
(aka X Woman)[18][11][4]		Fifth distal finger phalanx76.2–51.6 ka[6]2008Denisova cave (Russia)13.5 year adolescent female2010
Replica of part of the phalanx.
NC013993
Denisova 4[18][14]Permanent upper 2nd or 3rd molar84.1–55.2 ka[6]2000Denisova cave (Russia)Adult male2010
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 molar136.4–105.6 ka[6]2010Denisova cave (Russia)Adult male2015KT780370
Denisova 2[9] Deciduous 2nd lower molar 194.4–122.7 ka[6]1984Denisova cave (Russia)Adolescent female2017KX663333
Xiahe mandible[13] Partial mandible > 160 ka1980Baishiya Cave (China)2019
Denisova 11
(aka Denny, Denisovan x Neanderthal hybrid)
[19]		 Arm or leg bone fragment 118.1–79.3 ka[6]2012Denisova cave (Russia)13 year old adolescent female2016

KU131206

Denisova 13[20] Parietal bone fragment Found in layer 22[20] which dates to ~285±39 ka[7]2019Denisova cave (Russia)pending

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

Sequenced mitochondrial 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 by Johannes Krause and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, 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 and Neanderthals is around 202 bases. In comparison, the difference between 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 618–321,200 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.[4]

However, according to nuclear DNA (nDNA)—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 from human–chimpanzee last common ancestor, Denisovans/Neanderthals split from modern humans about 804,000 years ago, and from each other 640,000 years ago.[18] Using a mutation rate of 1x10−9 or 0.5x10−9 per base pair (bp) per year, the Neanderthal/Denisovan split occurred around either 236–190,000 or 473–381,000 years ago respectively.[21] Using 1.1x10−8 per generation with a new generation every 29 years, the time is 744,000 years ago. Using 5x10−10 nucleotide site per year, it is 644,000 years ago. Using the latter dates, the split had likely already occurred by the time hominins spread out across Europe.[22] H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans.[23] Due to the strong divergence in dental anatomy, they may have split before characteristic Neanderthal dentition evolved about 300,000 years ago.[18]

The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic human population,[24] possibly a relict H. erectus or H. erectus-like population about 53,000 years ago.[21] 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.[18] Modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced.[25][26][27][28] 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,[29][30] 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.[31]

Demographics
Denisovans appear to have crossed the Wallace Line.[16]

Though their remains have been identified in only two locations, traces of Denisovan DNA in modern humans suggest they ranged across East Asia.[32][33] In 2019, geneticist Guy Jacobs identified three distinct populations of Denisovans in, respectively, Siberia and East Asia, New Guinea and nearby islands, and Oceania and to a lesser extent across Asia. 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 marked reproductive separation between Denisovan populations.[34] Based on the modern distribution of Denisovan DNA, Denisovans may have crossed the Wallace Line into Wallacea and also Sahul (New Guinea and Australia), with little back-migration to west of the line.[16] These Denisovans may have needed to cross large bodies of water.[34]

Using exponential distribution analysis on haplotype lengths, Jacobs calculated introgression into modern humans occurred about 29,900 years ago with the second population; and 45,700 years ago in the third population. Such a late date for the second population could indicate survival as late as 14,500 years ago, which would make them the latest surviving archaic human species. New Guineans have introgression from these two latter populations. A third wave appears to have introgressed into East Asia, but there is not enough DNA evidence to pinpoint a solid timeframe.[34]

The mtDNA from Denisova 4 bore a high similarity to that of Denisova 3, indicating that they belonged to the same population.[18] 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 inhabitance, continually swung from a fairly warm and moderately humid pine and birch forest to a tundra or forest–tundra landscape.[7] 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.[33]

Anatomy

Little is known of the precise anatomical features of the Denisovans since the only physical remains discovered so far are a finger bone, three teeth, long bone fragments, a partial jawbone,[12] and a parietal bone skull fragment.[20] 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 of 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.[18] 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][17]

A facial reconstruction has been generated by comparing methylation at individual genetic loci associated with facial structure.[35] This analysis suggested that Denisovans, much like Neanderthals, had a long, broad, and projecting face; larger nose; sloping forehead; protruding jaw; elongated and flattened skull; and wide chest and hips. However, the Denisovan tooth row was longer than that of Neanderthals and anatomically modern humans.[36]

The Denisovan genome from Denisova Cave has variants of genes which, in modern humans, are associated with dark skin, brown hair, and brown eyes.[37] The Denisovan genome also contains a variant region around the EPAS1 gene that in Tibetans assists with adaptation to low oxygen levels at high elevation,[38][13] and in a region containing the WARS2 and TBX15 loci which affect body-fat distribution in the Inuit.[39] 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.[40]

Artifacts
Some ornaments (above) and animal bones and stone tools (below) found in Denisova Cave

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 kya in the Main Chamber of the cave; and about 269±97 kya years ago in the South Chamber; up to 170±19 kya and 187±14 kya in the Main and East Chambers, respectively.[7]

Middle 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 kya in the Main Chamber, 58±6 kya in the East Chamber, and 136±26–47±8 kya in the South Chamber.[7]

Early Upper Paleolithic artifacts date to 44±5 kya in the Main Chamber, 63±6 kya in the East Chamber, and 47±8 kya 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 kya.[7]

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 artifacts 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 a species identity, so the attribution of these artifacts is unclear.[41][7]

Interbreeding
See also: Interbreeding between archaic and modern humans

Analyses of modern humans genomes show past interbreeding with at least two groups of archaic humans, Neanderthals[42] and Denisovans,[18][43] and that such interbreeding events occurred on multiple occasions. Comparisons of the Denisovan, Neanderthal, and modern human genomes has revealed evidence for a complex web of interbreeding among these lineages.[42]

Archaic humans

As much as 17% of the Denisovan genome from Denisova Cave represents DNA from the local Neanderthal population.[42] 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 Altai Neanderthal.[44] However, Denny's Denisovan father had the typical Altai Neanderthal introgression, while her Neanderthal mother represented a population more closely related to Vindija Neanderthals than to those of Altai.[45]

About 4% of the Denisovan genome derives from an unidentified archaic hominin,[42] perhaps the source of the anomalous ancient mtDNA, indicating this species diverged from Neanderthals and humans over a million years ago. The only identified Homo species of Late Pleistocene Asia are H. erectus and H. heidelbergensis.[44][46] It is unclear if Denisovan populations which introgressed into modern humans had this archaic hominin ancestry.[34]

Before splitting from Neanderthals, their ancestors ("Neandersovans") migrating out of Africa 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.[47]

Modern humans
Modern human migration out of Africa showing approximate dates

A 2011 study found that Denisovan DNA is prevalent in Australian Aborigines, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwans (from the Philippines); but not in East Asians, western Indonesians, Jahai people (from Malaysia), or Onge (from the Andaman Islands). This means that Denisovan introgression occurred within Southeast Asia rather than on the Asian mainland, and that ancestors of East Asians and Indonesians were not present in Southeast Asia at the time, which in turn means that eastern Asia was settled by modern humans in two distinct migrations.[33] Around 0.2% Denisovan ancestry are found in mainland Asians and Native Americans,[48] whereas, in the Melanesian genome, it is 4–6%[18] or 1.9–3.4%.[49] New Guineans and Australian Aborigines have the most introgressed DNA,[16] but Aborigines have less than New Guineans.[50]

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. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans.[51] 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.[34]

The discovery of the 40,000 year old Chinese modern human 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.[52][16] In Papuans, less Denisovan ancestry is seen in the X chromosome than 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.[37]

Denisovan genes may have helped early modern humans migrating out of Africa to acclimatize. Although not present in the sequenced Denisovan genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles (involved in the immune system's natural killer cell receptors) has led to the suggestion that it introgressed from Denisovans into modern humans in West Asia. In a 2011 study, half of the HLA alleles of modern Eurasians were shown to represent archaic HLA haplotypes, and were inferred to be of Denisovan or Neanderthal origin.[53] A haplotype of EPAS1, likely introgressed into Tibetans from Denisovans, allows them to live at high elevations in a low-oxygen environment.[38][13] Genes related to phospholipid transporters (which are involved in fat metabolism) and to trace amine-associated receptors (involved in smelling) are more active in people with more Denisovan ancestry.[54]

See also
  • Timeline of human evolution – Chronological outline of major events in the development of the human species
  • Red Deer Cave people – Extinct archaic humans from 12,500 BCE in southwest China
  • Homo luzonensis – Archaic human from Luzon, Philippines
  • Homo naledi – Small-brained South African archaic human
  • Homo floresiensis – Archaic human from Flores, Indonesia

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