Depiction of a teenage girl with a Neanderthal mother and a Denisovan father
John Bavaro Fine Art/Science Photo Library
This marks the second occasion researchers have successfully retrieved the complete genome of Denisovans, an ancient human lineage that inhabited Asia. The DNA was sourced from a tooth estimated to be 200,000 years old, discovered in a Siberian cave.
The genome indicates that there were at least three distinct groups of Denisovans, each with unique histories. It also suggests that early Denisovans intermixed with an unidentified ancient human group as well as a previously unknown Neanderthal population.
“This research is groundbreaking,” asserts David Reich from Harvard University.
“This study significantly broadened my perspective on the Denisovan ecosystem,” states Samantha Brown from the National Center for Human Evolution Research in Spain.
Denisovans were first described solely via their DNA. Finger bones retrieved from Denisova Cave in Siberia exhibited DNA distinct from both modern humans and Neanderthals found in western Eurasia. Genomic analysis indicates Denisovans mated with modern humans, with populations in Southeast Asia, including the Philippines and Papua New Guinea, carrying Denisovan DNA.
Since their initial discovery in 2010, researchers have found that: a small number of Denisovans also originated from East Asia. In June, a skull unearthed in Harbin, China, was confirmed as Denisovan through molecular evidence, providing the first insight into their physical appearance. However, despite DNA fragments being recovered from various specimens, only the original specimen yielded a high-quality genome.
Researchers led by Stéphane Pèregne from Germany’s Max Planck Institute for Evolutionary Anthropology has introduced an additional researcher. (Pèregne declined to comment as the study is pending peer review.)
In 2020, a team of researchers discovered a male Denisovan molar tooth and sequenced its entire genome from the preserved DNA.
The researchers estimated this individual lived around 205,000 years ago, judging by the number of genetic mutations and comparing them with other ancient human genomes. This timeframe aligns with findings that the deposits containing the teeth are dated between 170,000 to 200,000 years old. In contrast, the other high-quality genome belongs to Denisovans who lived between 55,000 and 75,000 years ago, revealing an earlier chapter in Denisovan history.
The researchers suggest that at least three distinct Denisovan populations likely existed, based on comparisons from various Denisovan cave sites. The oldest group comprised the individuals whose teeth were analyzed. Many millennia later, a second group supplanted this earlier population in Denisova Cave.
“Comprehending how early Denisovans were supplanted by subsequent groups underscores pivotal events in human history,” says Qiao Meifu from the Institute of Vertebrate Paleontology and Paleoanthropology in China.
A third group, absent from the cave, still interbred with modern humans as suggested by genetic testing. Thus, all Denisovan DNA present in modern humans derives from a Denisovan group about which little is known.
The new genome illuminates the fact that Denisovans mated repeatedly with Neanderthals, who resided in and around the Denisovan Cave. Notably, this genome also contained traces of Neanderthals who lived between 7,000 and 13,000 years prior to Denisovan individuals. These traces do not align with any known Neanderthal genomes, indicating that the Denisovans interbred with a Neanderthal group yet to be sequenced.
Moreover, it’s probable that Denisovans also mated with an as-yet unidentified ancient human group that evolved independently of both Denisovans and modern humans for hundreds of thousands of years. One possibility is Homo erectus, the earliest known human species to migrate out of Africa and inhabit regions as far as Java, Indonesia. However, no DNA has been retrieved to confirm this.”H. erectus, so certainty remains elusive.
“It’s endlessly fascinating to uncover these new populations,” Brown remarked.
Currently, we stand alone in our existence. Yet, just hundreds of thousands of years ago, our ancestors coexisted with at least five other ancient human species, including diminutive hobbits and robust Neanderthals.
It may soon be necessary to include another name in that legacy. Recent discussions suggest that “remarkable Denisovan skulls are rewriting the narrative of human evolution,” prompting calls for the recognition of the Denisovans as a distinct species.
Since the initial Denisovan fossils were discovered 15 years ago, this isn’t a hasty conclusion. The ancient DNA retrieved from these fossils indicates they belong to humans with unique evolutionary paths. Furthermore, genetic studies suggest these ancient peoples interbred with Homo sapiens, leading many researchers to reconsider their classification as another species.
Interestingly, various species definitions permit mating as long as the involved species maintain distinct characteristics. The central issue, however, has been the unclear appearance of Denisovans. Yet, earlier this year, the discovery of ancient skulls in China—linked to Denisovan DNA—has strengthened the argument for classifying Denisovans as a distinct species based on their unique morphology.
“
The Denisovans might help us decode why we are the last humans standing. “
The inclination among biologists to categorize nature into distinct species can sometimes be trivialized as mere stamp collecting. The intention is to classify life forms rather than genuinely understand them. However, in this context, the effort is meaningful. Anatomical insights from Denisovan fossils hint at a captivating possibility: these mysterious humans are closely related to our species, offering potential clarity into early behavioral advancements of Homo sapiens by juxtaposing them with Denisovans.
At a certain point, our ancestors developed new behaviors that positioned us ahead of other human races. It’s conceivable that Denisovans could shed light on how we became the last standing humans.
This excerpt is from our human stories newsletter, focused on the archaeological revolution—sign up to receive it monthly.
In human stories, I aim to address common questions about human evolution. In February 2021, I tackled a query that many find perplexing—whether Neanderthals and modern humans are distinct species (short answer: species boundaries are ambiguous).
This month, we confront another frequently asked question: Do Denisovans, the extinct human group once prevalent in Asia, have a designated species name? If so, what should that name be?
The debate regarding the “official” name of the Denisovans has been lively since their discovery in 2010. Notably, in June, the skull of Harbin, dubbed the Dragon Man from northern China, was classified as Denisovan through molecular evidence. This marked the first acquisition of a Denisovan skull, giving us insights into their facial features.
While participating in New Scientist discussions, host Rowan Hooper asked why Denisovans lack a species name. Why can’t we refer to them as Homo Denisovanensis, similar to how Neanderthals are called Homo Neanderthalensis?
I preferred a straightforward explanation: insufficient information has hindered a definitive classification of Denisovans. Their DNA shows significant divergence from Neanderthal DNA; yet, we require detailed insights into their anatomy and skeletal structure.
However, this inquiry is multifaceted. First, we must identify which fossils unequivocally belong to Denisovans. This involves analyzing numerous specimens and decades of research, complicating the resolution. Secondly, we need to determine which of the assigned names should take precedence under our classification norms—a legal question that adds to the complexity.
Who’s Included and Who’s Excluded?
A brief reminder about Denisovans: they are an enigmatic group of humans initially identified in 2010 from fragments of a finger bone discovered in the Denisova Cave in Siberia’s Altai Mountains. Genetic analysis revealed they were distinct from both modern humans and Neanderthals. Moreover, many contemporary individuals, especially in Southeast Asia and Melanesia, carry Denisovan DNA.
This suggests that Denisovans were quite widespread in East Asia over the past several hundred thousand years. So, where are the Denisovan fossils?
Fifteen years later, a handful of Denisovan fossils have been actively categorized. For example, mandibles discovered on the Tibetan Plateau were identified through fossil proteins and sediment DNA. Similarly, a jawbone retrieved from the Pengle waterway off the coast of Taiwan was confirmed as Denisovan in April.
Nonetheless, we still lack a complete skeleton. Identifying the Harbin skull as Denisovan brought us closer to understanding their appearance, yet many more discoveries are necessary.
Numerous human fossils in East Asia potentially belong to Denisovans. However, categorizing these remains has proven challenging, as they often do not resemble established species like modern humans, Neanderthals, or even Homo Erectus. If adequate specimens surface, thus confirming their Denisovan identity, our understanding could significantly improve, leading to a formal classification.
But how do we determine which fossils are Denisovan? Ideally, we seek molecular evidence of preserved DNA or protein for comparison with the original Denisovan remnants. However, many fossils remain unanalyzed or inaccessible.
One notable effort to address this issue was a preliminary study submitted by a team led by Xijun Ni from the Chinese Academy of Sciences in March 2024. By comparing 57 human fossils for various physical traits, they constructed familial relationships between these findings.
The team found three primary groups among Eurasian hominins: Modern Humans, Neanderthals, and a third group composed of the original Denisovan fossil, the Tibetan cave jawbone, the Pengle jawbone, and the Harbin skull. This third category appears to represent those we refer to as Denisovans.
This is an intriguing proposition, but others disagree.
A collection of contentious fossils from Hualongdong, southern China, offers a wealth of material: an almost complete skull, 14 teeth, an upper jaw, six isolated teeth, and additional fragments dating back around 300,000 years.
While the NI team classified the Hualongdong specimens as part of the Denisovan group, a study led by Xiujie Wu in July suggested that these teeth did not show clear correlations, proposing instead that they may belong to a different hominin group. Another interpretation could be that the Denisovans at Hualongdong were somewhat disparate from those in other regions.
In the meantime, other intriguing fossils from Asia continue to emerge. Among them are specimens from Dariscal and Jinniushan, both around 260,000 years old, which Ni’s team has suggested might also belong to the Denisovan lineage.
As the list of contending Denisovan fossils grows, we must decide how to categorize them.
The Harbin Skull
Hebei Geo University
Homo — What Does It Mean?
Interestingly, I was part of the team that described the Harbin skull in 2021, and we named it Homo Longhi. So, could that be the name we assign to Denisovans?
However, last year a competing proposition was put forth by Woo and Christopher Beh from the University of Hawaii, who suggested that we should center around fossils from Xujiayao in northern China, proposing to call this new species Homo Jurensis—fossils that would include the original Denisovan findings.
This idea’s strength lies in the resemblance of Xujiayao fossils to Denisovan remains, a point also observed by the NI team. However, Bae and Wu aimed to designate the Xujiayao fossils as “type specimens.”
This raises two issues: the classification of fossils and the naming protocols. Let’s examine each aspect separately.
In classification, the Homo Jurensis proposal faces challenges. Bae and Wu classify the Harbin skull as Homo Jurensis or Denisovan, yet it lacks sufficient resemblance to warrant such designation. A study published in June demonstrated molecular evidence clearly linking the Harbin skull to Denisovans. Hence, identifying those fossils as Denisovan would contravene objective realities, making Homo Jurensis seem unfounded.
What about taxonomy? This area is intricate. A crucial factor is the concept of priority, where the first proposed name tends to gain precedence. Hence, Homo Longhi might likely take precedence over Homo Jurensis as it was suggested three years earlier.
Are there alternative names for Denisovans?
The excavators of Denisova Cave never formally classified Denisovans as a distinct species. Anatoly Derebianco, part of that team, suggested the name Homo Sapiens Altaiensis, implying they would serve as a modern human subspecies—yet this proposal lacked formal status, rendering it typically insignificant.
This year, Derebianco has published a series of papers discussing what Denisovans could be. His references include locations in Mongolia, Uzbekistan, Tajikistan, and Iran, referring to them collectively as Homo sapiens denisovan. I remain unsure if formal explanations were provided, as only abstracts were published, and if completed, it occurred post the naming of Homo Longhi.
Lastly, it’s possible that one of the names was assigned to an Asian human fossil within an obscure publication decades ago. If the fossil is ultimately identified as Denisovan, the name takes precedence (assuming it was adequately introduced). Nevertheless, Wu, Bae, Ni, and others assessed this notion in 2023 and concluded that many crucial fossils were not appropriately named. For instance, there was a suggestion to label Dali’s skull as Homo Dariensis, yet such ideas amounted to informal statements rather than formally recognized classifications.
Your head might be swirling from this cascade of names and species classifications, so let’s recap: the critical takeaway is our evolving understanding of Denisovans, which brings us closer to officially designating their name.
Given our comprehension of taxonomic norms and their significance, Homo Longhi could emerge as the official designation. Although I can’t influence the decision, they will always remain Denisovans in my mind.
The human skull from Harbin, China, is currently identified as Denisovan
Hebei Geo University
Denisovans, an enigmatic group of ancient humans, were initially recognized solely through their DNA, but now they have a distinct appearance.
With molecular data, Qiaomei Fu and her team at the Institute for Vertebrate Paleontology and Paleoanthropology have validated long-held suspicions among researchers.
This aligns with additional evidence that Denisovans were robust and heavyset. “I believe we observe individuals weighing around 100 kg of lean body mass: a truly massive individual,” stated Bens Viola, who was not part of the research team from the University of Toronto, Canada.
Denisovans were first discovered in 2010 in the Denisova Cave in Siberia’s Altai Mountains, where researchers found fragments of an unknown ancient hominin’s finger bone. The preserved DNA concluded that it was neither modern humans (Homo sapiens) nor Neanderthals (Homo neanderthalensis), but rather an entirely new species.
Moreover, genetic findings indicated that Denisovans interbred with contemporary humans. Today, populations in Southeast Asia and Melanesia carry up to 5% of Denisovan DNA, signifying their earlier presence in Asia.
Following these revelations, researchers commenced their quest for Denisovan fossils in both fieldwork and museum collections. Several fossils have since been discovered, with a notable mandible found in the Baishaya Karst Cave on the Tibetan Plateau, confirmed through fossil and DNA protein analysis from surrounding sediments. Recently, a jawbone recovered from the Peng Channel off Taiwan’s coast was also confirmed as Denisovan through preserved proteins.
Nevertheless, there remained frustrating gaps, as all confirmed Denisovan fossils obtained via molecular evidence were small, leading to limited insight. Conversely, more complete fossils from Asia were considered candidate Denisovan remains, yet none yielded molecular evidence.
Fu and her team aimed to extract preserved DNA or proteins from the human skull discovered in Harbin, northeastern China. This skull, kept under wraps for decades, was first described in 2021 and is notably large and robust, characterized by prominent brow ridges and brain size similar to modern humans. It has been dubbed Homo longi—or Dragon Man—by its discoverer.
“My impression is that this specimen is representative of what we would expect Denisovan to be, in both size and context,” Viola remarked.
Fu noted that recovering preserved molecules from the Harbin skull was an arduous task. While her team struggled to obtain DNA from the bones, they successfully retrieved 95 proteins, including three variants unique to Denisovans.
Seeking further evidence, Fu turned to dental calculus, a hardened plaque that forms on teeth, which yielded mitochondrial DNA inherited from its maternal lineage. Although she described the quantity as “small,” it was sufficient to confirm the specimen as Denisovan.
“It’s an astonishing outcome, and the efforts made were commendable,” said Saman Subroun from the National Research Centre in Burgos, Spain. “I believe many researchers tend to overlook dental calculus in genetic studies.”
With the identification of the robust Harbin skull as Denisovan, the long-suspected notion of their substantial size is now validated.
“There was a clue,” Brown noted.
The reason for their size remains unclear. Neanderthals’ robust build is linked to the cold climates of Europe and West Asia where they thrived. While Denisovan sites, including Denisova Cave and the Tibetan Plateau, were also cold, others were tropical. “We need to contemplate the implications of this,” Viola stated.
It’s possible that Denisovans varied over time. The fragments from Denisova Cave suggest two distinct groups existed: one from 217,000 to 106,000 years ago and another from 84,000 to 52,000 years ago. The Harbin skull dates back at least 146,000 years, with Fu discovering that its proteins and mitochondrial DNA align with the older group. Nevertheless, we’ve yet to locate any large Denisovan fossils in contemporary times, leaving their full appearance uncertain.
“Numerous different groups inhabited the landscape independently, often isolated from each other for tens of thousands of years,” Viola remarked. We should not presume they all bore a similar appearance.
Archaeologists have discovered a new human rib specimen in the White Cliff Cave, one of two sites known to have been inhabited by Denisovans. Dating from 48,000 to 32,000 years ago, the specimen also belongs to the Denisovan lineage and indicates that the caves were present into the Late Pleistocene.
Portrait of a young Denisovan woman based on a skeletal profile reconstructed from an ancient DNA methylation map. Image courtesy of Maayan Harel.
The Denisovans are an extinct human group first identified from a genome sequence determined from a finger bone fragment found in the Denisova Cave in the Altai Mountains of southern Siberia.
Subsequent genomic analyses revealed that the Denisovans diverged from Neanderthals 400,000 years ago, and that at least two distinct Denisovan populations interbred with the ancestors of modern Asians.
In 2019, a 160,000-year-old jawbone discovered in Baishiyi Cave, a limestone cave on the northeastern edge of the Tibetan Plateau, was identified as being of Denisovan origin.
In 2020, archaeologists found Denisovan mtDNA in deposits from the cave, suggesting they were present around 100,000 years ago, 60,000 years ago, and possibly 45,000 years ago.
The new Denisovan rib, discovered in the Baishigai Karst Cave, dates to approximately 48,000 to 32,000 years ago.
“The combined fossil and molecular evidence indicates that the Amaka Basin, where the Baishiqai Cave is located, was a relatively stable environment for the Denisovans, despite its high altitude,” said Dr Frid Welker, an archaeologist at the University of Copenhagen.
“The question now is, when and why did the Denisovans on the Tibetan Plateau become extinct?”
In their study, Dr Welcker and his colleagues examined more than 2,500 bones discovered in the White Cliff Cave.
“We know that the Denisovans hunted, butchered and ate a wide range of animal species,” said Dr Geoff Smith, a zooarchaeologist at the University of Reading.
“Our study reveals new information about Denisovan behavior and adaptation to high-altitude environments and a changing climate.”
“We are only just beginning to understand the behavior of this incredible human species.”
The bone remains found in the Baixa Karst caves were broken into many fragments, making them difficult to identify.
The researchers used a new scientific technique that uses differences in bone collagen between animals to determine which species the bone remains belong to.
“Zooarchaeology by mass spectrometry (ZooMS) allows us to extract valuable information from bone fragments that are often overlooked, providing deeper insights into human activities,” said Dr Huan Xia, a researcher from Lanzhou University.
Scientists have determined that most of the bones belong to blue sheep called bharals, as well as wild yaks, horses, the extinct woolly rhinoceros and spotted hyenas.
Bones from small mammals, such as marmots, and birds were also identified.
“Current evidence suggests that it was the Denisovans, and not other human groups, who lived in caves and made effective use of all available animal resources during their occupation,” said Dr Jiang Wang, also from Lanzhou University.
“Detailed surface analysis of the bone fragments shows that the Denisovans removed the meat and marrow from the bones, but also suggests that humans used them as raw material for making tools.”
H. Shea othersMiddle and Late Pleistocene Denisovan life in the Baishi Cliff karst caves. NaturePublished online July 3, 2024; doi: 10.1038/s41586-024-07612-9
The snow leopard was one of the animals hunted by the Denisovans
Klaus Honal / Alamy
The ancient humans known as the Denisovans hunted a wide variety of animals on the Tibetan Plateau, including blue sheep, yaks, and snow leopards. This diverse diet allowed them to thrive at high altitudes tens of thousands of years before the arrival of modern humans.
“The Denisovans were very behaviorally flexible,” Fried Welcker “They're really able to adapt to their local environment and the species that live there,” say researchers from the University of Copenhagen in Denmark.
The Denisovans are one of the most mysterious groups of humans that ever lived on Earth. They were first described in 2010 based on DNA extracted from a finger bone fragment found in the Denisova Cave in the Altai Mountains of Russia. This was the first time a group of humans had been identified based solely on DNA.
Denisovans were likely once widespread in South Asia because many people in South and Southeast Asia today carry Denisovan DNA. The Denisovans were highly adaptive, inhabiting various regions from Siberia to Southeast Asia. However, very little is known about their physical characteristics due to the scarcity of remains.
In 2019, Welcker and other researchers described a 160,000-year-old jawbone found in the Baishiya karst caves of Xiahe, on the northeastern Tibetan Plateau. Proteins extracted from one of the teeth were identified as Denisovan.
The following year, another group Denisovan DNA in cave sedimentsThe DNA could have been dated to 100,000, 60,000 or even 45,000 years ago, suggesting the Denisovans lived there for more than 100,000 years.
The Tibetan Plateau is 4,000 meters above sea level. The air is thin, cold, and dry – a tough place to live. To understand how the Denisovans managed to survive for so long, Welcker and his colleagues studied animal bones from the Baishiqiao cave. By observing the bones' shapes and extracting characteristic proteins, they were able to identify 2,005 of the 2,567 bones or bone fragments found.
The most numerous were blue sheep (Pseudo Nayaur) Among them were sheep and goats, Welcker said. Other medium-sized herbivores included wild yaks, Tibetan gazelles, and red deer. There were also small animals with grooved teeth, such as flying squirrels and porcupines. Plus larger carnivores, such as spotted hyenas, wolves, and snow leopards, as well as birds, such as golden eagles.
Most of the bones appear to have been brought there by Denisovans – 19 percent bear clear evidence, such as cuts made by stone tools – while less than 1 percent bear tooth marks or other signs indicating they were brought there by rodents or carnivores.
View of the white cliff caves on the Tibetan Plateau
Zhang Dongzhu Group (Lanzhou University)
“This is the second site where we can be absolutely certain that Denisovans were present and that the associated assemblages concretely represent their behavior.” Samantha Brown At the University of Tübingen, Germany.
Stone tools but no human remains have been found at other sites on the Tibetan plateau, so it's unclear who lived there. Further afield, a single molar found in 2022 at Tam Ngu Hao 2 limestone cave in Laos may point to a mysterious human presence. Tentatively identified as Denisovan.
Brown says it's not possible to draw many inferences about Denisovan capabilities from so few remains, “but we expect that Denisovans were once found as far north as Siberia, and possibly as far south.” [the islands of] Southeast Asia. As more of their remains are discovered, we may really begin to understand that the Denisovans were highly adaptive.”
One of the bones found in the White Cliff Cave, a rib fragment, turned out to belong to another Denisovan. It was found in sediments dating back 48,000 to 32,000 years ago, making it the youngest Denisovan specimen known to date. Stone tools found at Nuwia Devou on the plateau This provides evidence that modern humans were living there by 40,000 years ago, suggesting that Denisovans and modern humans coexisted in the region.
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