Denisovan

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Denisova 4, a molar

The Denisovans or Denisova hominins ( /dɪˈnsəvə/ di-NEE-sə-və) are an extinct species or subspecies of archaic human in the genus Homo without an agreed taxonomic name. Pending consensus on its taxonomic status, it has been referred to as Homo denisova, Homo altaiensis, or Homo sapiens denisova.

In 2010, the discovery of a juvenile female finger bone from the Siberian Denisova Cave was announced. The cave was also periodically inhabited by modern humans and Neanderthals, but it is unclear whether they ever cohabited in the cave. Mitochondrial DNA (mtDNA) extracted from the finger bone revealed her to have been a distinct species, and nuclear DNA (nDNA) indicates close affinities with Neanderthals. Several additional specimens from the Denisova Cave were subsequently discovered, as was a single specimen from the Baishiya Karst Cave on the Tibetan Plateau in China.

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. It also indicates Denisovans once spanned across East Asia. 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. 4% of the Denisovan genome comes from an unknown archaic human species. while an unexpected degree of mtDNA divergence among Denisovans was detected. A first generation hybrid nicknamed "Denny" was discovered with a Denisovan father and a Neanderthal mother.

Taxonomy[edit]

It is debated whether Denisovans represent a distinct species of Homo or are an archaic subspecies of H. sapiens.[1] 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[2] or H. altaiensis.[3]

Discovery[edit]

Denisovan is located in Asia
Denisova Cave
Denisova Cave
Baishiya Karst 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.[4]

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.[5][6] The estimate has changed to 76.2–51.6 ka.[7] 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.[5]

In 2019, Greek archaeologist Katerina Douka and colleagues radiocarbon dated specimens from Denisova Cave, and estimated that Denisova 2 (the oldest specimen) lived 122,700–195,000 years ago.[7] Older Denisovan DNA collected from sediments in the East Chamber dates to 217 ka. Based on artefacts 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[edit]

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.[9][10] 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.[11] 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.[12][11] 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.[13]

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.[14] 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.[15]

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 and a number of more fragmentary remains from Asia,[16] such as the 370–260,000 year old Xujiayao hominin.[17] The Xiahe mandible shows morphological similarities to some later East Asian fossils such as Penghu 1,[15][18] but also to Chinese H. erectus.[13]

Name Species Age Discovery Place Sex and age Publication Image Conservation GenBank accession
Denisova 3
(aka X Woman)
(fifth distal finger phalanx)[19][13][5]
Homo sp. 76.2–51.6 ka[7] 2008 Denisova cave (Russia) 13.5 year adolescent female 2010
Replica of part of the phalanx.
Cut in two parts in 2010, proximal base sent to Max Planck Institute where it was partially destroyed for genomic analysis, distal part to UC Berkeley.[13] NC013993
Denisova 4 (permanent upper 2nd or 3rd molar)[19][16] Homo sp. 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.
Using a dentistry drill, the surface material was removed and 10.2 mg of tooth powder was extracted at the apical end of the root.[20] FR695060
Denisova 8 (permanent upper 3rd molar)[12] Homo sp. 136.4–105.6 ka[7] 2010 Denisova cave (Russia) Adult male 2015 KT780370
Denisova 2 (deciduous 2nd lower molar)[11] Homo sp. 194.4–122.7 ka[7] 1984 Denisova cave (Russia) Adolescent female 2017 KX663333
Xiahe mandible (partial)[15] Homo sp. > 160 ka 1980 Baishiya Cave (China) 2019 Xiahe mandible.jpg Deposited at Lanzhou University in the 1980s. Several bone and tooth samples were taken along with samples from the crust adhering to the mandible. These samples were destroyed through a variety of testing methods including U–Th dating, DNA analysis, and protein extraction. [21]
Denisova 11
(aka Denny)
(arm or leg bone fragment)[9][22]
Homo sp. x H. neanderthalensis 118.1–79.3 ka[7] 2012 Denisova cave (Russia) 13 year old adolescent female 2016 Denisova-111.jpg

KU131206

Denisova 13 (parietal bone fragment)[23] Homo spp. Found in layer 22[23] which dates to ~285±39 ka[8] 2019 Denisova cave (Russia) pending

Divergence times[edit]

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.[5]

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.[19] 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.[24] 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.[25] H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans.[26]

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.[19] 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[edit]

Wallacea (between the Wallace and Weber Lines) may have been the Denisovans' last refugium

Though their remains have only been identified in only two locations, traces of Denisovan DNA in modern humans suggest they ranged across East Asia.[35][36] Three distinct populations of Denisovans have been identified in Siberia, East Asia, and Papua New Guinea.[37] As revealed by the genomic DNA of Papuans, the latter was extremely divergent from the former two populations.[38] Based on the modern distribution of Denisova DNA, Denisovans may have crossed the Wallace Line, with Wallacea serving as their last refugium.[39][40]

Denisovans are theorized to have migrated at least three times into Southeast Asia, the first of which had spread throughout Southeast Asia and had settled in Papua New Guinea 46,000 years ago. The second wave came 30,000 years ago and also reached Papua New Guinea. The third wave was thought to have introgressed into East Asia, but there is not enough evidence in Denisovan DNA to pinpoint a solid timeframe.[41]

The mtDNA from Denisova 4 bore a high similarity to that of the phalanx, indicating that they belonged to the same population.[19] From a second tooth, an mtDNA sequence was recovered that showed an unexpectedly large number of genetic differences compared to that found in the other tooth and the finger, suggesting a high degree of mtDNA diversity. These two individuals from the same cave showed more diversity than seen among sampled Neanderthals from all of Eurasia, and were as different as modern-day humans from different continents are to each other.[42]

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.[8] Conversely, Baishiya Karst Cave is situated at a high elevation, an area characterised by low temperature, low oxygen, and poor resource availability. Colonisation of high-altitude regions, due to such harsh conditions, was previously assumed to have only been accomplished by modern humans.[15]

Anatomy[edit]

Little is known of the precise anatomical features of the Denisovans, since the only physical remains discovered so far are a finger bone, two teeth, a toe bone, and a partial jawbone.[14] The finger bone is within the modern human range of variation for women, while differing from that of Neanderthals.[13] The tooth does not share the derived morphological features seen in Neanderthal or modern human teeth.[19] An initial morphological characterization of the toe bone led to the suggestion that it may have belonged to a Neanderthal-Denisovan hybrid individual, but this was not supported by genomic DNA.[43] Denisovan teeth are more robust than those of modern humans.[15][18]

Though the only fossil preserving facial bones of Denisovans to be recovered is a partial jaw, a facial reconstruction has been generated by comparing methylation at individual genetic loci associated with facial structure.[44][45][46][47] This analysis suggested that Denisovans, much like Neanderthals, had a long, broad, and projecting face; big nose; sloping forehead; protruding jaw; elongated and flattened skull; and wide chest and hips. However, the Denisovan tooth row is longer than that of Neanderthals and anatomically modern humans.[45][48]

A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today.[49] 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,[50][51][15] and in a region containing the WARS2 and TBX15 loci which affect body-fat distribution in the Inuit.[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]

Artifacts[edit]

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.[8]

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.[8]

Early Upper Paleolithic artefacts 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.[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 verified to have inhabited the cave until 55 ka; the dating of these 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 a species identity, so the attribution of Upper Paleolithic artefacts is unclear.[54][8]

Interbreeding[edit]

Analysis of genomes of modern humans show that they mated with at least two groups of archaic humans: Neanderthals (more similar to those found in the Caucasus than those from the Altai region)[42] and Denisovans,[19][55] and that such interbreedings occurred on multiple occasions.[56] A detailed comparison of the Denisovan, Neanderthal, and modern human genomes has revealed evidence for a complex web of interbreeding among these lineages.[42]

Archaic humans[edit]

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.[57] 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.[58]

About 4% of the Denisovan genome derives from an ancient unidentified hominin,[42] perhaps the source of the anomalous ancient mtDNA, indicating this highly archaic species diverged from other populations over a million years ago. The only identified Homo species of Late Pleistocene Asia are H. erectus and H. heidelbergensis.[57]

Modern humans[edit]

There is a relative increase in allele sharing between the Denisovan and the Australian Aborigines genome compared to other Eurasians and African populations; however, Papuans have more allele sharing than Australian Aborigines.[59] A comparison of the Denisovan genome with those of six modern humans—a ǃKung from South Africa, a Nigerian, a Frenchman, a Papuan, a Bougainville Islander and a Han Chinese—showed that 4–6% of the genome of Melanesians (represented by the Papuan and Bougainville Islander) derives from a Denisovan population; a later study puts the amount at 1.11% (with an additional contribution from some different and yet unknown ancestor).[60] Introgression possibly occurred during an early modern human migration to Melanesia.[59] A study of Han Chinese, Japanese and Dai genomes revealed that modern East Asians include two Denisovan DNA components: 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.[61]

Denisovan ancestry is shared also by smaller, scattered peoples in Southeast Asia, such as the Mamanwa, a Negrito people in the Philippines, though not all Negritos were found to possess Denisovan genes. For example, the Onge Andaman Islanders and Malaysian Jehai were found to have no significant Denisovan inheritance. This suggests that interbreeding occurred in mainland Southeast Asia.[35][36][62] Around 0.2% Denisovan ancestry are found in mainland Asians and Native Americans.[63]

The 11,500-year-old Longlin 1 from the Red Deer Cave

Though there is no genomic evidence to support the hypothesis, the 14.5–11.5 ka Red Deer Cave people of China have been suggested to have been the result of interbreeding between modern humans and Denisovans within a few thousands years of the end of the last glacial period.[64]

Denisovan genes may have helped early H. sapiens migrating out of Africa to acclimatize. Although not present in the sequenced Denisova 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 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.[65] A haplotype of EPAS1 likely introgressed into Tibetans from Denisovans allows them to live at high elevations in a low-oxygen environment.[50][15]

See also[edit]

References[edit]

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