Denisovan Sites

DenisovanSites

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General Denisovan Info

Denisovan DNA in Modern Humans

Denisovan Phylogeny

Sedimentary Denisovan DNA

Denisova Cave,Altai Russia

Denisova 25

Denisova 21

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Denisova 20

Denisova 19

Denisova 2

Denisova 8

Denisova 11

Denisova 3

Denisova 4

Over the last, atleast, 200,000 years both Neanderthals and Denisovans have used this cave in the Altai tundra during different periods. However, the Neanderthal/Denisovan hybrid Denisova 11 indicates that there was some direct physical contact between the two species.

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% of Denisovan DNA in Modern Human Genomes

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Data from: Peyrégne, Slon, & Kelso. 2023

The History of the Denisovans

Denisovans were a hominin sister species of Neanderthals and H. sapiens but were more closely related to Neanderthals. Initially, they were known mostly through DNA. However, over the last decade this has changed with increasing fossil evidence being identified, with the Harbin cranium being the most prominent.

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The common ancestor of Neanderthals and Denisovans split from the ancestor of H. sapiens between 750-500 thousand years ago. This likely occurred in Africa.

The ancestors of Neanderthals and Denisovans left Africa and remained in a single population for another 5-10 thousand generations. Assuming a generation length of 28 years, Neanderthals and Denisovan ancestors remained together an additional 140,000-280,000 years after they split from H. sapiens.

Genomic analysis indicates that the long term effective population size of Neanderthals hovered somewhere between 1,500 and 3,600 individuals throughout the life of the species. Considering that Denisovans show higher genetic variation than Neanderthals, their effective population size was likely on the higher end of this range.

The available evidence indicates that after splitting, Neanderthals occupied Western Eurasia while Denisovans occupied Eastern Eurasia as well as Oceania, including Australasia and Melanesia.

As other sections of this website demonstrate, there are limited confirmed Denisovan sites with preserved fossils. Many interesting East Asian hominin fossils have defied classification. Few of these have produced sequenced DNA but the several confirmed Denisovan teeth and mandibles hint that some of these middle Pleistocene hominins may in fact be the physical remains of Denisovans. The confirmation of the Harbin cranium, in 2025 via DNA, strengthens this suspicion. It has been proposed that the majority of these hominins be grouped into three species: Homo longi and Homo juluensis and possibly Homo daliensis.

If these hominins are indeed Denisovans, then this species has two unique features. In males, at least, their molars are gigantic. Second, they possess a cranial capacity of 1500-1800 cubic centimeters. On average that is larger than the brains of modern humans.

The Denisovan lineage likely survived from ~500,000 years ago to 25,000 years ago. Although some genomic modeling hints that pockets of this species might have survived as late as 21,000 years ago.

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DenisovanPhylogeny

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Lineage Identification

Extinction Dates

Sources

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DenisovanSedimentary DNA Sites

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Denisova 11 is the most unique individual found from any Denisovan site. "Denny" was a ~13 year old girl who had a Neanderthal mother and a Denisovan father. Interestingly, ancestors of Denny's Denisovan father interbred, more than once, with a Neanderthal lineage that was different from her Neanderthal mother's lineage. Denny, and her father, are proof of something researchers long assumed. Neanderthals, Denisovans, and sapiens occasionally mated with each other.

• Source: Slon et al., 2018.

• Further reading: Meet Denisova 11: First Known Hybrid Hominin

• Further viewing: First Peoples: Asia

Denisova 11 bone fragment

At Xujiayao the remains of at least 16 individuals have been discovered. All age ranges are represented by the fossils. These hominins were large brained. Individual XYJ 6 had a cranial capacity of 1700 cubic centimeters. DNA or proteins have not been obtained from these fossils but their morphological features are similar to known Denisovan fossils.

The Xujiayao hominin fossils have "traits that are not seen in either archaic or recent humans including other late Middle Pleistocene hominins from the region, except Xuchang, Penghu 1, Xiahe 1, and the Denisovans." -Wu & Bae, 2024

• Source: Wu & Bae, 2024.

• Further reading: 'Large Head People': Mysterious New Form of Ancient Human Emerges

Denisova 25 represents the oldest high quality genome ever recovered from a Denisovan, Neanderthal, or sapiens lineage. The next oldest high coverage genome belongs to the Altai Neanderthal, or Denisova 5, from the same cave site but 80,000 years later. Analysis of this genome found that its ancestors interbred with a never before detected ancient ghost Neanderthal lineage. About 5% of Denisova 25's genome was inherited from these ghost Neanderthals. This Denisovan was not closely related to any of the other Denisovans from this site or from Denisovans that contributed DNA in the genomes of modern humans. His was an ancient lineage.

• Source: Peyrégne, 2024.

• Further reading: Peyrégne, 2024b. More than a decade of genetic research on the Denisovans

• Further viewing: The Truth about Denisovans by Dawn of sapiens

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PA 831 is represented by a portion of a mandible. The genome or proteome of this fossile has not been analyzed. Morphologically, PA 831 closely resembles Penghu 1, which has been identified as Denisovan via proteomic analysis. Dated to over 400,000 years old, PA 831 could be a basal Denisovan or ProtoDenisovan similar to the 430,000 year old ProtoNeanderthal AT-6672 from the Spanish site Sima de los Huesos.

• Source: Liu et al., 2017.

Jinniushan has not been genetically or proteomically identified as a Denisovan. But remains a candidate.

Based on the analysis of the its pelvis and other skeletal elements, Jinniushan is the largest female hominin ever discovered. At an estimated height of 168 cm, or 5'5", and a mass of 79kg, or 175 lbs, lady Jinni has an identical size to the average male Neanderthal. Rosenberg et al., argue that her large size and short limbs are a response to her cold environment. Because there are so few female Denisovan fossils to analyze, if Jinni proves to be Denisovan she will provide a new understanding of the species.

• Source: Rosenberg, Zune, & Ruff, 2006.

• Further Reading: Pomeroy, 2023.

• Further Reading: Big Woman with a Distant Past

The extinction dates displayed here are inferred from detected admixing events between Denisovans and sapiens populations as found in the genomes of modern humans. Denisovans may have disappeared later than indicated as these dates represent the last mixing events detected.

D0 - Admixture detected with East Asians ~49 kya. This is the source of the Denisovan EPAS1 allele found in modern day Tibetans. Xiah 2 & BKCL3 indicate survival until at least 40 kya.

D1 - An admixture pulse into ancestral Papuans is detected at ~ 46 kya.

D2 - A second unique admixture pulse into ancestral Papuans is detected at ~ 25 kya. This lineage is not detected outside of the Papua region.

D3 - A mixing event into the Philippine Ayta is detected at about the same time as the second Papuan admixture event from a unique lineage not seen anywhere else.

TNH2-1 was a young Denisovan. Proteomic analysis of this molar crown is only able to identifiy this individual as a female (AMELY free) member of the genus Homo.

However, the morphology of this tooth is near identical to Xiahe 1 from China confirming its status as Denisovan. Unlike Xiahe 1 and the Denisovans from Denisova cave, the Annamite Mountians of Laos, where lady TNH2-1 called home, are tropical rather than tundra.

• Source: Demeter et al., 2022.

• Further reading: Tooth from mysterious human relative adds new wrinkles to their story.

• A glimpse of Cobra Cave

The lineage names used in this phylogentic tree come from Jacobs et al., 2019. Other studies use different nomenclature for each branch. To reconcile these differences across studies, it is best to look at the estimated divergence dates. For example, D0 is the root branch and often labeled as the "Altai Denisovan." D2, and it's equivalent in other studies, is the next oldest branch and has estimated divergence dates from 409 kya to 363 kya ago depending on the study. D3 as it's own lineage is less certain but it might have diverged around 315 kya. More research is needed for this branch (see Ongaro & Huerta-Sanchez, 2024). D1 is the youngest branch and is assigned divergence dates from 283 kya to 222 kya.

The lineage names used in this phylogentic tree come from Jacobs et al., 2019.

The proteins of small bone fragments from Denisova cave were analzyed to identify taxonomy. When several fragments were identified as hominin in nature, DNA analysis was conducted. Denisova 20's genome differs from Denisova 21 by four base pair substitutions. It's genome differs 20 base pairs from Denisova 2 and 30 base pairs from Denisova 8. This Denisovan forms a clade with Denisovans 21, 19, 2, and 8. Denisova 8 was the most distantly related in this clade as it lived ~90k years after the rest of the clade.

• Source: Brown et al., 2022

Denisova 20 bone fragments

The DNA of Denisova two was extracted from a deciduous tooth. At the time this female lost the tooth she was 10-12 years old. This age does not necessarily represent the death of the individual. Five thousand years after Denisova 2 lived, a Neanderthal population, represented by Denisova 17, moved into the cave. This likely occurred at the beginning of the last interglacial when this warm period caused Neanderthals to expand into the region.

• Source: Slon et al., 2017

• Further reading: Brown et al., 2022

• Further reading: Another Denisovan from Denisova Cave by John Hawks.

• Further viewing: 2024 in Neanderthals, Denisovans, and Hobbits.

The proteins of small bone fragments from Denisova cave were analzyed to identify taxonomy. When several fragments were identified as hominin in nature, DNA analysis was conducted. The mitochondria of Denisova 21 matches the mitochondria of Denisova 19. This indicates these bone fragments either came from the same person or are from the same maternal lineage. Denisova 21's genome differs from Denisova 20 by four base pair substitutions. It's genome differs 20 base pairs from Denisova 2 and 30 base pairs from Denisova 8. This Denisovan forms a clade with Denisovans 20, 19, 2, and 8. Denisova 8 was the most distantly related in this clade as it lived ~90k years after the rest of the clade.

• Source: Brown et al., 2022

The BKCL sedimentary samples consist of several layers. Layers 2-4 have produced Denisovan mtDNA. The dating of layers 3, and especially 2, are questionable as both layers have been disturbed to different extents. At Baishiya Karst Cave, the presence of Xiahe Denisovans 160 kya and BKCL Denisovans to at least 60 kya indicates the existence of Denisovans on the Tibetan Plateau, at least sporadically, for a stretch of 100 thousand years. The mitochondrial DNA in BKCL3 and BKCL4 form a clade with Denisova 3 and Denisova 4. This does not necessarily mean Baishiya Karst Denisovans were directly related to Denisova cave Denisovans, but it does show that they are from the same lineage, D0 (see the phylogenetic tree). It is from this lineage that Tibetan ancestors likely inherited the adaptive EPAS1 allele.

• Source: Zhang et al., 2020

• Further reading: Scientists Extract DNA From Ancient Humans Out of Cave Dirt

• Further reading: Extinct Humans Passed High-Altitude Gene to Tibetans

The discovery of Denisova 3 made headlines around the world and brought with her the realization that Neanderthals were not the only human relative living during the pleistocene. Up until 2024, Denisova 3 was unique for producing the only high coverage Denisovan genome. This changed when the genome of Denisova 25 was sequenced. Although, the Denisova 25 genome has not yet been published. Like Denny (Denisova 11), Denisova 3 was a ~13 year old girl. The analysis of the D3 genome showed that Denisovans had lower genetic diversity than Homo sapiens but a bit more diversity than Neanderthals.

• Source: Meyer et al., 2012.

• Further reading: New Type of Human Discovered via Single Pinky Finger

• Further viewing: The mysterious hominids from the Denisova Cave

The Denisova 4 molar is some of the latest evidence of Denisovan occupation at this site. He lived at roughly the same time a group of Neanderthals occupied the nearby Chagyrskaya cave.

This male individual groups in a clade with Denisova 3. The mtDNA differed with the mtDNA of Denisova 3 by two nucleotide substitutions.

• Source: Sawyer et al., 2015.

• Further reading: Brown et al., 2022.

Figure 3b. Brown et al., 2022.

In July of 2025, Harbin became confirmed as the most complete Denisovan cranium discovered to date. By extracting DNA from dental calculus, or tartar, from a tooth of this specimen, researchers were able to determine that Harbin was Denisovan.

In July of 2025, Harbin became the face of Denisovans. He is also the most complete Densiovan cranium discovered yet. By extracting DNA from dental calculus, or tartar, from a tooth of this specimen, researchers were able to determine that Harbin was Denisovan.

This finding will allow researchers to compare the morphology of genetically unidentified specimens to determine if they are likely Denisovan. This identification also brings into question whether Denisovans will be designated as Homo longi.

This finding will allow researchers to compare the morphology of genetically unidentified specimens to determine if they are likely Denisovan. This identification also brings into question whether Denisovans will be designated as Homo longi.

• Source: Fu et al., 2025.

• Source: Fu et al., 2025.

• Further Reading: Ni et al., 2021.

• Further Reading: Ni et al., 2021.

• Further Viewing: Chris Stringer's first impression of the Harbin cranium, 2019.

• Further Viewing: Chris Stringer's first impression of the Harbin cranium, 2019.

DMCL 21 is the oldest hominin mtDNA detected in sediment samples of Denisova cave. The mtDNA of M71 forms a clade with Denisova 2 and Denisova 8. M71 is the more basal, or ancient, genome of this clade. Sequencing mtDNA throughout multiple layers allows scientists to begin to reconstruct the occupency of Denisova cave over time. Denisovans first arrived sometime after 250 kya. Neanderthals arrived after 150 kya and would sporadically occupy the cave. For the most part if one species' mtDNA is found in a layer, the other species' DNA is absent. Denisovans were absent from the cave from 120 to 97 kya. This is likely because the population that the Altai Neanderthal belonged to occupied this cave during this time. By 90 kya Denisovans had returned as it is about this time that the Neanderthal/Denisovan hybrid "Denny" was born.

• Source: Zavala et al., 2021.

• Further reading: DNA from sediments reveals epic history of Denisova Cave

This partial cranium has not been confirmed as Denisovan through DNA or proteomics but is a candidate Denisovan based on morphology.

Narmada is essentially the only known hominin fossil from India. It has not been formally described and has been characterized as "post-erectus-grade Homo" and "Middle Pleistocene Homo".

This specimen cannot be ruled out as a Denisovan

• Source: Kaifu et al., 2017.

• Further Reading: Narmada: Human History Hub

• Further Reading: Was Narmada hunting giant elephants 300,000 years ago?

Penghu 1 was dredged from the sea floor off the western shore of Taiwan. This mandible, and its teeth, share a similar robustness as other known Denisovan specimens. It has been identified as Denisovan through proteomic analysis. It is also morphologically similar to Xiahe 1, which resided 1,300 miles away on the Tibetan Plateau. Based on trace elements and stratigraphy, the age of this specimen can only be narrowed to two possible layers: ~160 kya or ~45 kya. Penghu 1 provides the furthest direct evidence of Denisovans in the southeast. When paired with TNH2-1, Denisovans existing in Sundaland, Sahul, and the Philippines appears feasible.

• Source: Tsutaya, 2025.

• Further reading: Mysterious Jawbone Found at an Antique Shop in Taiwan Belonged to a Male Denisovan, Scientists Say

• Further reading: Denisovan Fossil Shows Enigmatic Human Cousins Lived from Siberia to Subtropics

Although Xiahe 1 has not produced genetic material, its proteins show an affinity towards Denisovans over both Neanderthals and sapiens. This is the first confirmed Denisovan fossil outside of Altai, Russia and Denisova cave. The location of this site being on the Tibetan Plateau, indicates this specimen belonged to the Denisovan lineage from which modern day Tibetans received the Denisovan EPAS 1 allele. This allele is adaptive as it reduces hypoxia in high elevations.

• Source: Chen et al., 2019.

• Further reading: How We Found an Elusive Hominin in China

At 110 thousand years ago, Denisova 8 is the youngest of the clade that includes Denisova 21, Denisova 20, Denisova 19, and Denisova two. Like all Denisovan teeth found to date, the Denisova 8 molar is massive compared to both Neanderthals and modern humans. It's interesting to note that, like Denisova 8, nearly all jaw and tooth specimens recovered of the species are male. This may bias our understanding of the species as the female morphology is unknown and could be similar or more gracile.

• Source: Sawyer et al., 2015.

• Further reading: Brown et al., 2022.

• Further reading: The problem when all the fossils are male by John Hawks.

• Further viewing: A Year in Paleoanthropology.

Xuchang 1 had a cranial capacity of 1800 cubic centimeters. While not confirmed to be Denisovan by genomic or proteomic analysis, this specimen is consistent with other fossilized Denisovan remains.

• Source: Bae & Wu, 2024.

• Further Reading: Ancient skulls give clues to China human history

Choin et al., 2019

Jacobs et al., 2019

Jinam et al., 2017

Maffesoni & Prufer, 2017

Ongaro & Huerta-Sanchez, 2024

The proteins of small bone fragments from Denisova cave were analzyed to identify taxonomy. When several fragments were identified as hominin in nature, DNA analysis was conducted. The mitochondria of Denisova 19 matches the mitochondria of Denisova 21. This indicates these bone fragments either came from the same person or are from the same maternal lineage. Denisova 19's genome differs from Denisova 20 by four base pair substitutions. It's genome differs 20 base pairs from Denisova 2 and 30 base pairs from Denisova 8. This Denisovan forms a clade with Denisovans 21, 20, 2, and 8. Denisova 8 was the most distantly related in this clade as it lived ~90k years after the rest of the clade.

• Source: Brown et al., 2022