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Denisova cave, located in the Altai mountains of Siberia, has been the home of several different species of humans across many millennia. 25 years of excavations have unearthed a 280,000-year history of human activity in the cave (Derevianko et al., 2003). Most recently, in the 18th century, it was inhabited by a local religious hermit called Denis of whom the cave is named after. However, it was not Denis who was gained the attention of paleobiologists in 2010 but a young girl who lived around 90,000 years ago.

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In 2008, the finger bone of a 13-year-old female was found in the 11th excavation layer which dates back to 50-30 thousand years ago in the late middle Palaeolithic. Being the third fossil found in this location, it was named ‘Denisova 3’. Analysis of the mitochondrial DNA found within this specimen revealed a new population of archaic humans that shared a common ancestor with anatomically modern humans (AMH) and Neanderthals around 1 million years ago - Homo heidelbergensis ; they were called the Denisovans after the cave where they were discovered (Krause et al., 2010). However, analysis of the nuclear genome of Denisova 3 contradicts this phylogeny and suggests Neanderthals were more closely related to the Denisovans, diverging 500,000 years ago, than to AMH, making the Denisovans a sister group of the Neanderthals (Reich et al., 2010) (Figure 1).

After realisation of this new hominin species, more fossils are increasingly being found and attributed to the Densiovans. The following is a description of those found to date and how they have contributed to our understanding of the species.

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Figure 1: Phylogenetic trees showing the discrepancy between phylogenies of mitochondrial and nuclear DNA of Denisovans, Neanderthals and modern humans (van Holstein, 2016). Mitochondrial DNA analysis of Denisova 3 suggests that Neanderthals are more closely related to humans and Denisovans and thus Denisovans are an out-group of the Neanderthal/modern human lineage. However nuclear DNA analysis of the Denisovan genome suggests that Neanderthals are more closely related to Denisovans than modern humans and thus Denisovans are a sister group of Neanderthals.

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A fourth hominin fossil, this time a molar from the same layer in the cave was also identified as Denisovan in 2010. Analysis of its mtDNA revealed that it differed from Denisova 3 by only two positions suggesting that the two individuals were from the same population (Reich et al., 2010). Subsequent publications in 2015 and 2017 identified two further Denisovan molars, Denisova 8 (Sawyer et al., 2015) and Denisova 2 (Slon et al., 2017). These molars are very large, larger than a Neanderthal’s. It was recognised as more similar to archaic human species as far back a Homo erectus and Homo habilis. The big change in morphology of molars between these two groups may suggest that the Denisovans separated from the Neanderthals early on (more than 300,000 years ago) which allowed Neanderthal dental features to evolve independently. However, it may also be possible that the Denisovan dental features are the result of a reversion (Reich et al., 2010).

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In 1980, a right mandible bone was found by a monk who visited the sacred Baishiya Karst Cave, China located in part of the Tibetan plateau. It wasn’t studied until 40 years after its discovery. There was no accessible DNA but the proteome preserved in the dentine of an accompanying tooth was used for phylogenetic analysis. The results confirmed Denisovan identity and strengthened the hypothesis that the Denisovans are a sister group of Neanderthals as opposed to an outlier of the Neanderthal/Sapien lineage. From this we can assume an evolutionary trail of these groups; it is likely that their common ancestor H.heidelbergensis migrated out of Africa and diverged, first geographically to West Asia/Europe and East Asia and then genetically into Neanderthals and Denisovans respectively. Those that remained in Africa likely evolved into Homo Sapiens that emigrated later.

Although the amino acid polymorphisms mirror that of Denisovan 3, this individual is regarded as a different but closely related population than those belonging to the fossils found in Denisova cave, henceforth referred to as the Altai Denisovans (Chen et al., 2019).

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In 2012, over 2000 fossils from Denisova cave were analysed at Manchester University for hominin remains using collagen peptide mass fingerprinting. It wasn’t until fossil 1227, a fragment of bone or leg, that they struck hominin collagen. mtDNA analysis revealed that it was of Neanderthal descent (Brown et al., 2016). An exciting find but one that only unveiled half the picture; since mitochondria are maternally inherited, this data only revealed that its mother was a Neanderthal. Using nuclear DNA extracted from bone powder, it was later discovered that the individual’s father was a Denisovan making the 13-year-old, affectionately nicknamed ‘Denny’, a Neanderthal-Denisovan hybrid. In fact, deeper analysis into her genome revealed that it was likely the father also had multiple Neanderthal ancestors in his genealogy. These discoveries lead to the realisation that the two species could interbreed and therefore provided concrete evidence that their coexisted and possible cohabited Denisova cave (Slon et al., 2018).

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New hominin fossils are being found and added to the growing number of Denisovan samples, each one adding a piece to the Denisovan jigsaw helping us to learn about their genetics, demographics and morphology of which will be discussed in the following sections.

To date, confirmed Denisovan fossils consist of a finger and arm/leg bone, a mandible, 3 molars and a cranial parietal fragment discovered in Denisova cave in March 2019 but this is yet to be published (Viola et al., 2019). Remarkably, a largely intact hominin skull found 90 years ago in China has recently been rediscovered and may provide a face to the Denisovan name, but this has yet to be confirmed (Ji et al., 2021) (Gibbons, 2021).

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Non-Africans derive 2% of their genome from Neanderthals. When H.sapiens migrated out of Africa, it was beneficial to interbreed with the other species of hominin they encountered as this allowed introgression of alleles already well adapted to the environment into their offspring. This process was not limited to Neanderthals; all ethnicities studied by Browning et al (2018) (Figure 2) possess some Denisovan DNA in their genomes.

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Figure 2: Mean amounts of archaic hominin sequences in individuals of different ethnicities (Browning et al., 2018).

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Remarkably, Melanesians and Australasia aboriginals share 3% of their genome with Denisovans. In fact, the majority of Denisovan DNA resides in those of Asian ethnicity although this is thought to originate from introgression events from two separate Denisovan populations; East Asians carry DNA from individuals more closely related to the Altai Denisovans whereas Paupans and South Asians carry DNA from individuals more distantly related to the Altai Denisovans (Browning et al., 2018).

In a study by Larena et al (2021), 1107 Filipino genomes across 118 different ethnicities were analysed for archaic hominin DNA. They found that levels of Neanderthal DNA were similar within the sample group and standard compared to levels around the world. However, they found that there was variation in the levels of Denisovan DNA in the genomes studied. Interestingly they discovered the Ayta Magbukon people had the highest levels of Denisovan DNA in the world, 5% of their genome is derived from Denisovans. The Ayta Magbukon people are a group indigenous Filipinos and ethnic sub-group of Negritos. Negritos are descendants of the first modern humans to inhabit the Philippines (Jinam et al., 2017). This suggests that Denisovans and Negrito ancestors co-inhabited the Philippines and interbred.

Denisovan DNA has also made it into the further, more isolated corners of western Europe, Iceland. Of the total archaic hominin sequences in an Icelandic genome, 84.5% are of Neanderthal origin and 3% are of Denisovan origin (the remaining are of unknown origin). Overall, Denisovan DNA makes up less than 0.1% of the Icelandic genome. However, unlike the Ayta Kagnukon, this does not imply that Denisovans interbred with Icelandic ancestors, instead it is more likely that it was introduced into the genome via interbreeding with a Neanderthal containing mosaic DNA. Over time, the Denisovan DNA becomes diluted to the low levels we see today (Skov et al., 2020).

Iceland isn’t the only isolated area to be touched by the Denisovans. The Xiahe mandible, as previously discussed, was the first Denisovan fossil to be found outside of the Denisovan cave and its location on the Tibetan plateau was surprising to paleoanthropologists. It was previously thought that only H.sapiens adapted to live at such high altitudes as the Tibetan plateau but discovery of the fossil at this location shows that H.sapiens were not the first. Atmospheric oxygen in this region is 40% lower than sea level. This requires inhabitants to be specially adapted to the hypoxic conditions. This is achieved by a mutation in the EPAS1 gene, creating a new allele that improves oxygen transport under these conditions (Yi et al., 2010). This allele is created by five SNPs (AGGAA); although it is exclusive to Tibetans today, it is not unique to this species. In. fact, it was likely inherited into their genome via introgression events with the population of Altai Denisovans (Huerta-Sánchez et al., 2014).

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Denisovans were the first hominin species to be described completely by DNA as no fossils detailing their morphology have yet been found. Recent advances in genome analysis and forensic anthropology technology have allowed us to determine the morphological features of the Denisovan skeleton and create a facial portrait using the pattern of DNA methylation, a new technique presented by Gokhman and colleagues in 2019. This method was first tested on Neanderthals and Chimps and achieved more than 85% accuracy of traits before being applied to the genome of Denisova 3. 56 traits were identified in total, 21 of which are thought to be shared with Neanderthals including: a wide pelvis and large ribcage, a low cranium and forehead with robust jaws and thick enamel as well as wide fingertips. 11 of the 56 traits are thought to be unique to Denisovans including: an elongated dental arch, enlarged mandible joint, a large distance between the cranial parietal bones, wider temporal bones compared to the width of the anterior mandible and premature loss of permanent teeth. Putting all of these features together allows us to visualise the morphology of a Denisovan compared to Neanderthals and modern humans (Gokhman et al., 2019) (Figure 3).

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The mandible fossil was discovered after these predictions were made, during the peer review of this publication. This discovery allowed the team to test the validity of their predictions - 7 out of 8 of these predictions were correct. Additionally, if the recently rediscovered hominin skull from China mentioned previously does in fact belong to a Denisovan then this will only confirm our confidence in these predictions and enhance our understanding of their anatomy.

Following publication, this data enabled computational biologists to create a portrait of a juvenile female Denisovan based on the traits discovered by deciphering the Denisova 3 genome. This is exciting as it finally puts a face to the name and gives us the opportunity to come face to face for the first time with a Denisovan (Figure 4).

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Figure 3a: Skeletal morphology of a Denisovan compared to Neanderthals and AMH as predicted from DNA methylation analysis (Gokhman et al., 2019).

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Figure 3b: Cranial morphology of a Denisovan compared to Neanderthals and AMH as predicted from DNA methylation analysis (Gokhman et al., 2019).

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The mandible fossil was discovered after these predictions were made, during the peer review of this publication. This discovery allowed the team to test the validity of their predictions - 7 out of 8 of these predictions were correct. Additionally, if the recently rediscovered hominin skull from China mentioned previously does in fact belong to a Denisovan then this will only confirm our confidence in these predictions and enhance our understanding of their anatomy.

Following publication, this data enabled computational biologists to create a portrait of a juvenile female Denisovan based on the traits discovered by deciphering the Denisova 3 genome. This is exciting as it finally puts a face to the name and gives us the opportunity to come face to face for the first time with a Denisovan (Figure 4).

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Figure 4a: An artist’s interpretation of the 13-year-old Denisovan based off of predicted traits by DNA methylation analysis. Artwork: Maayan Harel, created for Carmel Lab, Hebrew University of Jerusalem.

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Figure 4b: An artist’s interpretation of the 13-year-old Denisovan based off of predicted traits by DNA methylation analysis. Modelling: Maayan Harel, created for Carmel Lab, Hebrew University of Jerusalem.

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