Denisovan (updated)

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

 

The Denisovans or Denisova hominins ( /dɪˈniːsəvə/ di-NEE-sə-və) are an extinct species or subspecies of archaic humans in the genus Homo. Pending its taxonomic status, it currently carries temporary species or subspecies names Homo denisova, Homo altaiensis, Homo sapiens denisova, or Homo sp. Altai. In 2010, scientists announced the discovery of an undated finger bone fragment of a juvenile female found in the Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. The mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from Neanderthals and modern humans. The nuclear genome from this specimen suggested that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans, with about 3% to 5% of the DNA of Melanesians and Aboriginal Australians and around 6% in Papuans deriving from Denisovans. Several additional specimens were subsequently discovered and characterized.

A comparison with the genome of another Neanderthal from the Denisova cave revealed local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, and evidence of interbreeding with an as yet unidentified ancient human lineage, while an unexpected degree of mtDNA divergence among Denisovans was detected.

The lineage that developed into Denisovans and Neanderthals is estimated to have separated from the lineage that developed into "anatomically modern" Homo sapiens approximately 600,000 to 744,000 years ago. Denisovans and Neanderthals then significantly diverged from each other genetically a mere 300 generations after that. Several types of humans, including Denisovans, Neanderthals and related hybrids, may have each dwelt in the Denisova Cave in Siberia over thousands of years, but it is unclear whether they ever co-habitated in the cave.

Discovery

Denisova Cave

Location of Denisova Cave in the Altai Mountains of Siberia

 

The Denisova Cave, where the "X woman" was found

 

The Denisova Cave is in south-western Siberia, Russia in the Altai Mountains near the border with Kazakhstan, China and Mongolia. It is named after Denis, 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. 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. They found the finger bone of a juvenile hominin, originally referred to as the "X woman" (referring to the maternal descent of mtDNA), or the Denisova hominin. Artifacts (including a bracelet) excavated in the cave at the same level were dated using radiocarbon and oxygen isotopes to around 40,000 BP. Excavations have since revealed human artifacts showing an intermittent presence going back 125,000 years.

A team of scientists led by Johannes Krause and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced mtDNA extracted from the fragment. The cool climate of the Denisova Cave preserved the DNA. The average annual temperature of the cave is 0 °C, which has contributed to the preservation of archaic DNA among the remains discovered. The analysis indicated that the Denisova hominin "diverged from a common ancestor well before Neanderthals and modern humans did"—around 1 million years ago.

The mtDNA analysis further suggested that this new hominin species was the result of an earlier migration out of Africa, distinct from the later out-of-Africa migrations associated with modern humans, but also distinct from the even earlier African exodus of Homo erectus. Pääbo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene. This work shows that the Denisovans were actually a sister group to the Neanderthals, branching off from the human lineage 550,000 years ago, and diverging from Neanderthals, probably in the Middle East, 300,000 years ago.

A second paper from the Svante Pääbo group reported the prior discovery of a third upper molar from a young adult, dating from about the same time (the finger was from level 11 in the cave sequence, the tooth from level 11.1). The tooth differed in several aspects from those of Neanderthals, while having archaic characteristics similar to the teeth of Homo erectus. They performed mtDNA analysis on the tooth and found it to have a sequence somewhat similar to that of the finger bone, indicating a divergence time about 7,500 years before, and suggesting that it belonged to a different individual from the same population.

Fossils

So far, the fossils of four distinct Denisovans from Denisova Cave have been identified through their DNA: Denisova 2, Denisova 3, Denisova 4, and Denisova 8. Analysis of a fifth specimen, Denisova 11, proved it to have belonged to an F1 Denisovan-Neanderthal hybrid. Denisova 2 and Denisova 3 are prepubescent or adolescent females, while Denisova 4 and Denisova 8 are adult males. mtDNA analysis of the Denisovan individuals suggests the Denisova 2 fossil is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 are roughly contemporaneous.

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 had survived.

Anatomy

Little is known of the precise anatomical features of the Denisovans, since the only physical remains discovered thus far are the finger bone, two teeth from which genetic material has been gathered, and a toe bone. The single finger bone is unusually broad and robust, well outside the variation seen in modern people. It belonged to a female, indicating that the Denisovans were extremely robust, perhaps similar in build to the Neanderthals. The tooth does not share the derived morphological features seen in Neanderthal or modern human teeth. An initial morphological characterization of the toe bone led to the suggestion that it may have belonged to a Neanderthal-Denisovan hybrid individual, although a critic suggested that the morphology was inconclusive. This toe bone's DNA was analyzed by Pääbo. After looking at the full genome, Pääbo and others confirmed that humans produced hybrids with Denisovans.

Some older findings may or may not belong to the Denisovan line. These include the skulls from Dali and Maba, and a number of more fragmentary remains from Asia. Asia is not well mapped with regard to human evolution, and the above finds may represent a group of "Asian Neanderthals".

Mitochondrial DNA analysis

The mitochondrial DNA (mtDNA) from the finger bone discovered in Denisova Cave 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 contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. This suggested a divergence time around one million years ago. The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic population. Studies suggest that a population related to modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced. It has suggested the species could be Homo heidelbergensis, but that species is now generally considered to be too closely related to the Neanderthals. That it could have been a Homo erectus-like introgression into the Denisovans about 53,000 years ago that is responsible for the anomalously-divergent mtDNA has also been proposed.

The mtDNA from a tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population. 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.

Nuclear genome analysis

The isolation and sequencing of nuclear DNA from the Denisova finger bone revealed an unusual degree of DNA preservation with only low-level contamination, allowing near-complete genomic sequencing and detailed comparison with the genomes of Neanderthals and modern humans. Despite the apparent divergence of their mitochondrial sequence, the Denisova population share a common branch with Neanderthals, with a more distant split from the lineage leading to modern African humans. The Denisovan and Neanderthal sequences were estimated to have diverged about 640,000 years ago, with divergence of the branch leading to these groups from modern Africans dating to about 800,000 years ago. The authors of the study speculated that the anomalous more-divergent Denisovan mtDNA resulted either from the persistence of an ancient mtDNA lineage purged from the other branches of humanity through genetic drift or else an introgression from an older hominin lineage.

The mtDNA sequence from the femur of a 400,000-year-old Homo heidelbergensis from the Sima de los Huesos cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to the latter. Analysis of nuclear DNA sequences from two specimens showed they were more closely related to Neanderthals rather than to Denisovans, yet one of these samples also had the Denisovan-related mtDNA. The studies' authors posited that the mtDNA found in these specimens represents an archaic sequence indicative of Neanderthal's kinship with Denisovans that was subsequently lost in Neanderthals due to replacement by modern-human-related sequence.

Epigenetics

An analysis of the natural degradation processes of ancient DNA, which differs between methylated and unmethylated cytosines, has provided insight into Denisovan and Neanderthal epigenetics. Because changes in cytosine methylation are correlated with gene regulation, the full DNA methylation maps allowed an assessment of gene activity throughout the Denisovan genome, as compared to that of modern humans and Neanderthals. About 200 genes were identified that show distinct regulatory patterns in Denisovans.

Interbreeding

A detailed comparison of the Denisovan, Neanderthal, and modern human genomes has revealed evidence for a complex web of interbreeding among the lineages. Through such interbreeding, 17% of the Denisova genome represents DNA from the local Neanderthal population, while evidence was also found of a contribution to the nuclear genome from an ancient hominin lineage yet to be identified, perhaps the source of the anomalously ancient mtDNA. DNA from this unidentified but highly archaic species that diverged from other populations over a million years ago represents as much as 8% of the Altai Denisovan genome. The only widespread remains of archaic humans in the Late Pleistocene Asian region are from Homo Erectus, although East Asian variants such as Dali Man have Neanderthal characteristics. The Denisovan genome shared more derived alleles with the Altai Neanderthal genome from Siberia than with the Vindija cave Neanderthal genome from Croatia and 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. The web of archaic human intermixing is highlighted by the genome from a 90,000-year-old bone fragment from the Denisova cave, found to have belonged to a Denisovan-Neanderthal hybrid female. Her 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.

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) and Denisovans, and that such interbreedings occurred on multiple occasions. Approximately 1–4% of the DNA of non-African modern humans is shared with Neanderthals as a result of interbreeding. Tests comparing the Denisova hominin genome with those of six modern humans – a ǃKung from South Africa, a Nigerian, a Frenchman, a Papua New Guinean, a Bougainville Islander and a Han Chinese – showed that between 4 and 6% of the genome of Melanesians (represented by the Papua New Guinean 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). This DNA was possibly introduced during the early migration to Melanesia. These findings are in concordance with the results of other comparison tests which show a relative increase in allele sharing between the Denisovan and the Aboriginal Australian genome, compared to other Eurasians and African populations; however, Papuans, the population of Papua New Guinea, have more allele sharing than Aboriginal Australians.

Melanesians are not the only modern-day descendants of Denisovans. David Reich of Harvard University and Mark Stoneking of the Planck Institute team found genetic evidence that Denisovan ancestry is shared also by Australian Aborigines, and smaller scattered groups of people in Southeast Asia, such as the Mamanwa, a Negrito people in the Philippines, though not all Negritos were found to possess Denisovan genes; Onge Andaman Islanders and Malaysian Jehai, for example, were found to have no significant Denisovan inheritance. This suggests that interbreeding occurred in mainland South-East Asia, and that Denisovans once ranged widely over eastern Asia. Based on the modern distribution of Denisova DNA, Denisovans may have crossed the Wallace Line, with Wallacea serving as their last refugium. Small amounts of Denisovan DNA, representing around 0.2% Denisovan ancestry, are also found in mainland Asians and Native Americans.

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed, and that a second introgression event from Denisovans into humans occurred. A study of Han Chinese, Japanese and Dai genomes revealed that modern East Asian populations 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 the Altai cave. These components were interpreted as representing separate introgression events involving two divergent 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. Though there is no genomic evidence to support the hypothesis, the Red Deer Cave people of China have been suggested to have been the result of interbreeding between Homo sapiens and Denisovans within a few thousands years of the end of the last glacial period.

The immune system's HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin. The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. 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. The Denisovan genome also contains a variant region around the EPAS1 gene that in Tibetans assists with adaptation to low oxygen levels at high altitude. In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.