Their DNA survives in diverse populations across the world – but who were the Denisovans?

The Conversation
November 27, 2024

This finger bone discovered in Siberia in 2008 led to the original Denisovan discovery. Wikimedia, CC BY-SA

It started with a finger bone found in a cave in the Altai mountains in Siberia in the late 2000s. Thanks to advances in DNA analysis, this was all that was required for scientists to be able to identify an entirely new group of hominins, meaning upright primates on the same evolutionary branch as humans.

Now known as the Denisovans (De-NEE-so-vans), after the Denisova cave in which the finger bone was found, the past few years have seen numerous other discoveries about these people. I’ve recently co-published a paper collating everything we know so far.

So who were the Denisovans, where did they live, and why are they important to the story of humanity?


Around 600,000 years ago, early humans in Africa diverged into groups. Some migrated out of Africa, becoming Neanderthals in eastern and western Eurasia and Denisovans in eastern Eurasia.

Modern humans later evolved in Africa, spread across the globe, and encountered Neanderthals, Denisovans and possibly other unknown archaic human groups. Yet by 40,000 years ago, only modern humans remained on the archaeological record.
The genetic legacy


Unlike Neanderthals, whose fossils are relatively abundant, Denisovan remains continue to be very scarce. Apart from that Siberian finger bone, the main other discovery was a jawbone found in China, in a limestone cave located on the northeastern edge of the Tibetan Plateau. It had been believed that the Denisovans had been confined to Siberia, but this jawbone demonstrated that they had lived much further afield.

Their DNA has enabled scientists to build on this insight, since it survives in contemporary populations, particularly in Oceania, parts of Asia, and even Indigenous American populations. This shows that the Denisovans were widely distributed across these areas.


From Tibet to the Americas, the Denisovans certainly got around. Dmitry Kalinovsky

Strikingly, recent studies reveal that Denisovans interbred with modern humans multiple times. For instance, east Asians harbour ancestry from at least two distinct Denisovan populations. Also, the people of Papua New Guinea, which retain up to 5% Denisovan ancestry, a much higher proportion than other groups, interbred with at least two Denisovan groups at different times.

Additionally, research has shown that some populations from the Philippines carry a distinct Denisovan ancestry compared to their neighbouring groups. These various genetic differences highlight that the interbreeding between modern humans and Denisovans has a complex history.

Adaptations

While much about the Denisovans’ lifestyle, appearance and culture remains unknown, the discovery of the Tibetan jawbone showed that these people lived in diverse environments, and that they must have been very adaptable. Sure enough, we now know that Denisovan ancestry in modern humans has contributed to adaptive traits, particularly in challenging environments.

A notable example is the EPAS1 gene. Inherited from Denisovans, it helps regulate the body’s response to low oxygen levels, giving Tibetans a physiological advantage in the high altitudes of the Tibetan plateau.


Other human adaptations possibly derived from Denisovan interbreeding relate to being able to tolerate cold weather, and being able to metabolise lipids, which include fats and oils. These may have been beneficial for populations in northern regions, such as the Arctic. For example, Inuit populations carry Denisovan genes that help to regulate body fat and maintain warmth.


The Inuit may have the Denisovans to thank for their ability to tolerate harsh climes. Chris Christopherson


Some genes that aid in fighting infections also appear to have Denisovan origins. These immune-related genes might have played crucial roles in protecting ancient and modern humans from south and east Asia, the Americas and Papua New Guinea against specific pathogens, illustrating how Denisovan heritage continues to affect human health today.
Unanswered questions

Many questions about the Denisovans remain unanswered. For instance, how genetically distinct were these populations, and how many distinct groups existed? We know that at least four distinct Denisovan populations interbred with modern humans. However, with further analyses, this number might increase, revealing an even more complex story.

We’re also looking for a better understanding of the biological impact of Denisovan DNA in modern humans. While many beneficial traits have been identified as derived from Neanderthals, only a few have been found for Denisovans so far. Many other potential contributions remain to be explored.

This will be possible only if additional Denisovan remains are discovered and DNA is extracted and sequenced. We need more data, especially from diverse geographical regions and time periods, to provide new insights into these people’s adaptations, interactions with other hominins, and lasting legacy in human evolution.

To address these questions, our research capabilities will need to improve. For example, we need new tools to more accurately distinguish Denisovan genetic material from Neanderthal and modern human DNA.

Additionally, studying Denisovan ancestry in populations beyond east Asia and Oceania, such as Indigenous Americans, could shed light on exactly which Denisovan sources have contributed to modern humans genomes.

The discoveries to date highlight the power of genetic studies in uncovering hidden chapters of our past. Each discovery brings us closer to understanding who the Denisovans were and how their lives and adaptations continue to affect humans today.

Linda Ongaro, Research Fellow in Genetics, Trinity College Dublin

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Fossilized tooth proves extinct Denisovans lived in southeast Asia


An ancient tooth found in southeast Asia links extinct Denisovans to modern day humans, according to findings published Tuesday in the journal Nature Communications. A close-up of the 3D printed reconstruction of a female Denisovan. File Photo by Debbie Hill/UPI | License Photo

May 17 (UPI) -- A fossilized tooth dug from a mountain cave in northern Laos is the first evidence to show the extinct human species, the Denisovans, lived in southeast Asia.

Scientists published their findings Tuesday in the journal Nature Communications and said the large ancient molar, found in Cobra Cave, appears to be from a young Denisovan girl who died between 164,000 and 131,000 years ago.

"We've always assumed that Denisovans were in this part of the world, but we've never had the physical evidence," said study co-author Laura Shackelford, a paleoanthropolotist at the University of Illinois Urbana-Champaign. "This is one little piece of evidence that they were really there."


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Denisovan teeth and finger bones were first discovered in Siberia and Tibet in 2010. DNA testing revealed these extinct hominids interbred with Neanderthals and modern humans, and are among the ancestors to current populations in Australia and the Pacific. But until now, scientists could not track the ancient species to the area.

Tuesday's published discovery of a Denisovan fossilized tooth in southeast Asia provides the geographical link between these ancient hominids and people living today.

It also shows the Denisovans occupied a wide range of areas and were able to adapt to different climates. It shows that 131,000 years ago the Denisovans could survive in temperate conditions as well as frigid temperatures, making them more similar to our own species.

RELATED Earliest evidence of hominin interbreeding revealed by DNA analysis

University of Toronto researcher Bence Viola said the molar was in the "right place and right time" to belong to a Denisovan. "In its size, it is comparable to hominins that lived two or three million years ago... but the age of it shows that it is very recent."

Scientists were convinced five years ago there were Denisovan fossils in southeast Asia.

"The genetic data shows that these guys were spread over large parts of Asia, so we must have them," Viola said in 2017.

Child’s 130,000-year-old tooth could offer clues to extinct human relative

Researchers believe the discovery in a Laos cave proves that Denisovans lived in the warm tropics of southeast Asia

A view of the molar thought to belong to a young female child from the extinct human species called the Denisovans, was found in cave Tam Ngu Hao in northeastern Laos.
Photograph: Fabrice Demeter/Reuters

Agence France-Presse

Tue 17 May 2022

A child’s tooth at least 130,000 years old found in a Laos cave could help scientists uncover more information about an early human cousin, according to a new study.

Researchers believe the discovery proves that Denisovans – a now-extinct branch of humanity – lived in the warm tropics of southeast Asia.

Very little is known about the Denisovans, a cousin of Neanderthals.

Scientists first discovered them while working in a Siberian cave in 2010 and finding a finger bone of a girl belonging to a previously unidentified group of humans.

Using only a finger and a wisdom tooth found in the Denisova Cave, they extracted an entire genome of the group.

Researchers then found a jawbone in 2019 on the Tibetan Plateau, proving that part of the species lived in China as well.

Aside from these rare fossils, the Denisovans left little trace before disappearing – except in the genes of human DNA today.

Through interbreeding with Homo sapiens, Denisovan remnants can be found in current populations in southeast Asia and Oceania.

Aboriginal Australians and people in Papua New Guinea have up to five percent of the ancient species’ DNA.

Scientists concluded “these populations’ modern ancestors were ‘mixed’ with Denisovans in southeast Asia”, said Clement Zanolli, a paleoanthropologist and co-author of the study published Tuesday in Nature Communications.

But there was no “physical proof” of their presence in this part of the Asian continent, far from the freezing mountains of Siberia or Tibet, the researcher at the French National Centre for Scientific Research told AFP.

This was the case until the group of scientists began searching in the Cobra Cave in northeast Laos.

Cave specialists discovered the area in a mountain in 2018 next to Tam Pa Ling Cave, where the remains of ancient humans have already been found.

The tooth immediately appeared to have a “typically human” shape, explained Zanolli.

The study said, based on ancient proteins, the tooth belonged to a child, likely female, aged between 3.5 and 8.5 years old.

But the tooth is too old for carbon-dating, and the DNA has been badly preserved because of heat and humidity, said paleoanthropologist and study co-author Fabrice Demeter.

After analysing the shape of the tooth, scientists reckon it was most likely a Denisovan who lived between 164,000 to 131,000 years ago.

They then studied the tooth’s interior through different methods including analysing proteins and a 3D X-ray reconstruction.


'Spectacular' jawbone discovery sheds light on ancient Denisovans

The tooth’s internal structure was similar to that of the molars found in the Tibetan Denisova specimen. It was clearly distinguishable from modern humans and other ancient species that lived in Indonesia and the Philippines.

“The proteins allowed us to identify the sex – female – and confirm its relation to the Homo species,” said Demeter, a researcher at the University of Copenhagen in Denmark, where the tooth is temporarily based.

The tooth’s structure had common characteristics with Neanderthals, who were genetically close to Denisovans. The two species are thought to have diverged about 350,000 years ago.

But Zanolli explained that the researchers concluded it was a Denisova specimen because no Neanderthal traces have been found so far east.

For Demeter, the discovery shows that Denisovans occupied this part of Asia and adapted to a wide range of environments, from cold altitudes to tropical climates, whereas their Neanderthal cousins seemed more “specialised” in cold western regions.

The last Denisovans could have therefore met and interbred with modern humans, who passed on their genetic heritage to southeast Asia’s modern populations, in the Pleistocene epoch.

 IN TIBET

First evidence of mysterious, ancient humans called Denisovans found outside of their cave

By Ashley Strickland, CNN
Wed May 1, 2019

CNN —

A 160,000-year-old Denisovan jawbone fossil has been found in a cave on the Tibetan plateau, according to a new study. This marks the first evidence of Denisovans found outside Denisova Cave in Siberia since the mysterious ancient human group was discovered in 2010.

Denisovans, who lived during a time that overlapped with Neanderthals, are known only from a few fossils discovered in a Siberian cave. But they also left a genetic legacy that lives on today in the DNA of some Asian, Australian and Melanesian humans. A Denisovan genome was sequenced in 2012 and compared with that of modern humans, revealing the trait.

Tibetans and Sherpas have a genetic variant that helps them live in low oxygen at high altitudes, which can be traced back to Denisovans.

But before the discovery of this jawbone, researchers wondered why this genetic variant existed. Tiny, fragmented remains of Denisovans had only ever been found in Denisova Cave, which sits at an altitude of 2,296 feet.

Baishiya Karst Cave on the Tibetan Plateau, where the jawbone was found, has an altitude of 10,761 feet.

No DNA was preserved in the fossil, but the researchers were able to extract ancient proteins and analyze them, as well as conduct radioisotopic dating of the fossil. The study on their findings was published Wednesday in the journal Nature.

This cave sheltered some of the first known humans 300,000 years ago

The jawbone was well-preserved and featured a primitive shape, as well as a few large molars that were still attached.

At 160,000 years old, the fossil predates other evidence of ancient humans at such a high altitude in the area, which was previously set at between 30,000 and 40,000 years ago.

The age and features of the fossil are also similar to those of the oldest known Denisovan fossils from Denisova Cave, which suggests that the populations were closely related.



Dongju Zhang/Lanzhou University
The entrance to the Baishiya Karst Cave.

The jawbone was found by a monk in 1980 and eventually made its way to Lanzhou University, where researchers have been studying the cave site since 2010. They began analyzing the jawbone in 2016.

“Archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene and successfully adapted to high-altitude low-oxygen environments long before the regional arrival of modern Homo sapiens,” said Dongju Zhang, study author and lecturer at Lanzhou University’s Research School of Arid Environment and Climate Change, in a statement.


Mysterious Denisovans interbred with modern humans more than once

The discovery shows that Denisovans lived in East Asia and adapted to the conditions there.

“Our analyses pave the way towards a better understanding of the evolutionary history of hominins in East Asia,” Jean-Jacques Hublin, study author and director of the Department of Human Evolution at the Max Planck Institute for Evolutionary Anthropology, said in a statement.

Evolutionary study suggests prehistoric human fossils ‘hiding in plain sight’ in Southeast Asia

A Homo erectus skull from Java, Indonesia. This pioneering species stands at the root of a fascinating evolutionary tree. Scimex

March 23, 2021 

Island Southeast Asia has one of the largest and most intriguing hominin fossil records in the world. But our new research suggests there is another prehistoric human species waiting to be discovered in this region: a group called Denisovans, which have so far only been found thousands of kilometres away in caves in Siberia and the Tibetan Plateau.

Our study, published in Nature Ecology and Evolution, reveals genetic evidence that modern humans (Homo sapiens) interbred with Denisovans in this region, despite the fact Denisovan fossils have never been found here.

Conversely, we found no evidence that the ancestors of present-day Island Southeast Asia populations interbred with either of the two hominin species for which we do have fossil evidence in this region: H. floresiensis from Flores, Indonesia, and H. luzonensis from Luzon in the Philippines.

Together, this paints an intriguing — and still far from clear — picture of human evolutionary ancestry in Island Southeast Asia. We still don’t know the precise relationship between H. floresiensis and H. luzonensis, both of which were distinctively small-statured, and the rest of the hominin family tree.

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And, perhaps more intriguingly still, our findings raise the possibility there are Denisovan fossils still waiting to be unearthed in Island Southeast Asia — or that we may already have found them but labelled them as something else.
An ancient hominin melting pot

Stone tool records suggest that both H. floresiensis and H. luzonensis are descended from Homo erectus populations that colonised their respective island homes about 700,000 years ago. H. erectus is the first ancient human known to have ventured out of Africa, and has first arrived in Island Southeast Asia at least 1.6 million years ago.

This means the ancestors of H. floresiensis and H. luzonensis diverged from the ancestors of modern humans in Africa around two million years ago, before H. erectus set off on its travels. Modern humans spread out from Africa much more recently, probably arriving in Island Southeast Asia 70,000-50,000 years ago.

We already know that on their journey out of Africa about 70,000 years ago, H. sapiens met and interbred with other related hominin groups that had already colonised Eurasia.

The first of these encounters was with Neanderthals, and resulted in about 2% Neanderthal genetic ancestry in today’s non-Africans.

The other encounters involved Denisovans, a species that has been described solely from DNA analysis of a finger bone found in Denisova Cave in Siberia.

Only a handful of Denisovan fossils have been found, such as this jawbone unearthed in a Tibetan cave. Dongju Zhang/Wikimedia Commons, CC BY-SA

Intriguingly, however, the largest amounts of Denisovan ancestry in today’s human populations are found in Island Southeast Asia and the former continent of Sahul (New Guinea and Australia). This is most likely the result of local interbreeding between Denisovans and modern humans — despite the lack of Denisovan fossils to back up this theory.

Read more: Southeast Asia was crowded with archaic human groups long before we turned up

To learn more, we searched the genome sequences of more than 400 people alive today, including more than 200 from Island Southeast Asia, looking for distinct DNA sequences characteristic of these earlier hominin species.

We found genetic evidence the ancestors of present-day people living in Island Southeast Asia have interbred with Denisovans — just as many groups outside Africa have similarly interbred with Neanderthals during their evolutionary history. But we found no evidence of interbreeding with the more evolutionarily distant species H. floresiensis and H. luzonensis (or even H. erectus).

This is a remarkable result, as Island Southeast Asia is thousands of kilometres from Siberia, and contains one of the richest and most diverse hominin fossil records in the world. It suggests there are more fossil riches to be uncovered.
So where are the region’s Denisovans?

There are two exciting possibilities that might reconcile our genetic results with with the fossil evidence. First, it’s possible Denisovans mixed with H. sapiens in areas of Island Southeast Asia where hominin fossils are yet to be found.

One possible location is Sulawesi, where stone tools have been found dating back at least 200,000 years. Another is Australia, where 65,000-year-old artefacts currently attributed to modern humans were recently found at Madjebebe.

Read more: Buried tools and pigments tell a new history of humans in Australia for 65,000 years

Alternatively, we may need to rethink our interpretation of the hominin fossils already discovered in Island Southeast Asia.

Confirmed Denisovan fossils are extremely rare and have so far only been found in central Asia. But perhaps Denisovans were much more diverse in size and shape than we realised, meaning we might conceivably have found them in Island Southeast Asia already but labelled them with a different name.

Given that the earliest evidence for hominin occupation of this region predates the divergence between modern humans and Denisovans, we can’t say for certain whether the region has been continuously occupied by hominins throughout this time.

It might therefore be possible that H. floresiensis and H. luzonensis (but also later forms of H. erectus) are much more closely related to modern humans than currently assumed, and might even be responsible for the Denisovan ancestry seen in today’s Island Southeast Asia human populations.

If that’s true, it would mean the mysterious Denisovans have been hiding in plain sight, disguised as H. floresiensis, H. luzonensis or H. erectus.

Solving these intriguing puzzles will mean waiting for future archaeological, DNA and proteomic (protein-related) studies to reveal more answers. But for now, the possibilities are fascinating.

Authors

João Teixeira
Research associate, University of Adelaide

Kristofer M. Helgen
Chief Scientist and Director, Australian Museum Research Institute, Australian Museum
Disclosure statement

João Teixeira receives funding from the Australian Research Council.

Kristofer M. Helgen received funding from the Australian Research Council’s Centre for Australian Biodiversity and Heritage (CABAH).

Oldest-known fossils of mysterious human lineage uncovered in Siberian cave


By Charles Q. Choi 

The newly discovered Denisovan bones are 200,000 years old.

Here, one of the Denisovan bones found in Denisova Cave in Siberia. 

(Image credit: Katerina Douka)

Scientists have unearthed the oldest fossils to date of the mysterious human lineage known as the Denisovans. With these 200,000-year-old bones, researchers have also for the first time discovered stone artifacts linked to these extinct relatives of modern humans, a new study finds.

First identified a little more than a decade ago, the Denisovans — an extinct branch of the human family tree — are the closest known relatives of modern humans, along with Neanderthals. Analysis of DNA extracted from Denisovan fossils suggests they might have once been widespread across continental Asia, island Southeast Asia and Oceania, and revealed that at least two distinct groups of Denisovans interbred with ancestors of modern humans.

Until now, scientists had only discovered half a dozen Denisovan fossils. Five were unearthed in Denisova Cave in Siberia, and one was found in a holy site in China, Live Science previously reported.

Now, researchers have discovered another three Denisovan fossils in Denisova Cave. Scientists estimated that they are about 200,000 years old, making them the oldest known Denisovans ever found. Previously, the earliest known Denisovan specimens were about 122,000 to 194,000 years old.

In the new study, researchers examined 3,791 bone scraps from Denisova Cave. They looked for proteins they knew were Denisovan based on previous DNA research on the extinct lineage.

Among these scraps, the scientists identified five human bones. Four of these contained enough DNA to reveal their identity — one was Neanderthal, and the other three were Denisovan. Based on genetic similarities, two of these fossils may either come from one person or from related individuals.

"We were extremely excited to identify three new Denisovan bones amongst the oldest layers of Denisova Cave," study senior author Katerina Douka, an archaeological scientist at the University of Vienna in Austria, told Live Science. "We specifically targeted these layers where no other human fossils were found before, and our strategy worked."

The first indication of the existence of Denisovans, in the form of a finger bone, was discovered in this Siberian cave, called the Denisova Cave. (Image credit: Katerina Douka)

The researchers found Denisovan bones within the oldest layers of Denisova Cave. (Image credit: Katerina Douka)

In the new study, researchers looked for Denisovan DNA within 3,791 bone scraps from Denisova Cave. (Image credit: Katerina Douka)

The researchers estimated the age of these Denisovan fossils based on the layer of earth in which they were uncovered. This layer also contained a slew of stone artifacts and animal remains, which may serve as vital archaeological clues on Denisovan life and behavior. Previously, Denisovan fossils were only found in layers without such archaeological material, or in layers that might also have contained Neanderthal material.

"This is the first time we can be sure that Denisovans were the makers of the archaeological remains we found associated with their bone fragments," Douka said.

The new findings suggest these newfound Denisovans lived during a time when, according to previous research, the climate was warm and comparable to today, in a locale favorable to human life that included broad-leaved forests and open steppe. Butchered and burnt animal remains found in the cave suggest the Denisovans may have fed on deer, gazelles, horses, bison and woolly rhinoceroses.

"We can infer that Denisovans were well-adapted to their environments, utilizing every resource available to them," Douka said.

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The stone artifacts found in the same layer as these Denisovan fossils are mostly scraping tools, which were perhaps used for dealing with animal skins. The raw material for these items likely came from river sediment just outside the entrance to the cave, and the river likely helped the Denisovans when they sought to hunt, the scientists noted.

"The site's strategic point in front of a water source and the entrance of a valley would have served as a great spot for hunting," Douka said.

The stone tools linked with these new fossils have no direct counterparts in north or central Asia. However, they do bear some resemblance to items found in Israel dating between 250,000 and 400,000 years ago — a period linked with major shifts in human technology, such as the routine use of fire, the researchers noted.

The new study found that Denisovans may not have been the only occupants of the cave at this time. Bones of carnivores such as wolves and wild dogs suggest Denisovans may have actively competed with these predators over prey and perhaps the cave itself.

"At the moment our team continues to work at Denisova Cave and several other Asian sites and hope to report some interesting new stuff very soon," Douka said.

The scientists detailed their findings online Nov. 25 in the journal Nature Ecology & Evolution.

Originally published on Live Science.

IMAGE: BAISHIYA KARST CAVE view more 

CREDIT: HAN YUANYUAN

HOME OF KOOT HOOMI AND THE SECRET MASTERS

Denisovan DNA found in sediments of Baishiya Karst Cave on Tibetan Plateau

CHINESE ACADEMY OF SCIENCES HEADQUARTERS

Research NewsOne year after the publication of research on the Xiahe mandible, the first Denisovan fossil found outside of Denisova Cave, the same research team has now reported their findings of Denisovan DNA from sediments of the Baishiya Karst Cave (BKC) on the Tibetan Plateau where the Xiahe mandible was found. The study was published in Science on Oct. 29.

The research team was led by Prof. CHEN Fahu from the Institute of Tibetan Plateau Research (ITP) of the Chinese Academy of Sciences (CAS), Prof. ZHANG Dongju from Lanzhou University, Prof. FU Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of CAS, Prof. Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology, and Prof. LI Bo from University of Wollongong.

Using cutting-edge paleogenetic technology, the researchers successfully extracted Denisovan mtDNA from Late Pleistocene sediment samples collected during the excavation of BKC. Their results show that this Denisovan group is closely related to the late Denisovans from Denisova Cave, indicating Denisovans occupied the Tibetan Plateau for a rather long time and had probably adapted to the high-altitude environment.

Denisovans were first discovered and identified in 2010 by a research team led by Prof. Svante Pääbo. Almost a decade later, the Xiahe mandible was found on the Tibetan Plateau. As the first Denisovan fossil found outside of Denisova Cave, it confirmed that Denisovans had occupied the roof of the world in the late Middle Pleistocene and were widespread. Although the Xiahe mandible shed great new light on Denisovan studies, without DNA and secure stratigraphic and archaeological context, the information it revealed about Denisovans was still considerably restricted.

In 2010, a research team from Lanzhou University led by Prof. CHEN Fahu, current director of ITP, began to work in BKC and the Ganjia basin where it is located. Since then, thousands of pieces of stone artifacts and animal bones have been found. Subsequent analysis indicated that the stone artifacts were mainly produced using simple core-flake technology. Among animal species represented, gazelles and foxes dominated in the upper layers, but rhinoceros, wild bos and hyena dominated in the lower layers. Some of the bones had been burnt or have cut-marks, indicating that humans occupied the cave for a rather long time.

To determine when people occupied the cave, researchers used radiocarbon dating of bone fragments recovered from the upper layers and optical dating of sediments collected from all layers in the excavated profile. They measured 14 bone fragments and about 30,000 individual grains of feldspar and quartz minerals from 12 sediment samples to construct a robust chronological framework for the site. Dating results suggest that the deepest excavated deposits contain stone artifacts buried over ~190 ka (thousand years). Sediments and stone artifacts accumulated over time until at least ~45 ka or even later.

  

To determine who occupied the cave, researchers used sedimentary DNA technology to analyze 35 sediment samples specially collected during the excavation for DNA analysis. They captured 242 mammalian and human mtDNA samples, thus enriching the record of DNA related to ancient hominins. Interestingly, they detected ancient human fragments that matched mtDNA associated with Denisovans in four different sediment layers deposited ~100 ka and ~60 ka.

More interestingly, they found that the hominin mtDNA from 60 ka share the closest genetic relationship to Denisova 3 and 4 - i.e., specimens sampled from Denisova Cave in Altai, Russia. In contrast, mtDNA dating to ~100 ka shows a separation from the lineage leading to Denisova 3 and 4.

Using sedimentary DNA from BKC, researchers found the first genetic evidence that Denisovans lived outside of Denisova Cave. This new study supports the idea that Denisovans had a wide geographic distribution not limited to Siberia, and they may have adapted to life at high altitudes and contributed such adaptation to modern humans on the Tibetan Plateau.

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However, there are still many questions left. For example, what's the latest age of Denisovans in BKC? Due to the reworked nature of the top three layers, it is difficult to directly associate the mtDNA with their depositional ages, which are as late as 20-30 ka BP. Therefore, it is uncertain whether these late Denisovans had encountered modern humans or not. In addition, just based on mtDNA, we still don't know the exact relationship between the BKC Denisovans, those from Denisova Cave in Siberia and modern Tibetans. Future nuclear DNA from this site may provide a tool to further explore thes

Morning Person? You Might Have Neanderthal Genes to Thank.

Carl Zimmer
Thu, December 14, 2023

Neanderthal cranium and mandible of the Chapelle aux Saints (Correze) prehistorical museum in Quinson, France

 (Photo by Xavier Rossi/Gamma-Rapho via Getty Images)


Neanderthals were morning people, a new study suggests. And some humans today who like getting up early might credit genes they inherited from their Neanderthal ancestors.

The new study compared DNA in living humans to genetic material retrieved from Neanderthal fossils. It turns out that Neanderthals carried some of the same clock-related genetic variants as do people who report being early risers.

Since the 1990s, studies of Neanderthal DNA have exposed our species’ intertwined history. About 700,000 years ago, our lineages split apart, most likely in Africa. While the ancestors of modern humans largely stayed in Africa, the Neanderthal lineage migrated into Eurasia.

About 400,000 years ago, the population split in two. The hominins who spread west became Neanderthals. Their cousins to the east evolved into a group known as Denisovans.

The two groups lived for hundreds of thousands of years, hunting game and gathering plants, before disappearing from the fossil record about 40,000 years ago. By then, modern humans had expanded out of Africa, sometimes interbreeding with Neanderthals and Denisovans.

And today, fragments of their DNA can be found in most living humans.

Research carried out over the past few years by John Capra, a geneticist at the University of California, San Francisco, and other scientists suggested that some of those genes passed on a survival advantage. Immune genes inherited from Neanderthals and Denisovans, for example, might have protected them from new pathogens they had not encountered in Africa.

Capra and his colleagues were intrigued to find that some of the genes from Neanderthal and Denisovans that became more common over generations were related to sleep. For their new study, published in the journal Genome Biology and Evolution, they investigated how these genes might have influenced the daily rhythms of the extinct hominins.

Inside the cells of every species of animal, hundreds of proteins react with one another over the course of each day, rising and falling in a 24-hour cycle. They not only control when we fall asleep and wake up, but also influence our appetite and metabolism.

To explore the circadian rhythms of Neanderthals and Denisovans, Capra and his colleagues looked at 246 genes that help to control the body clock. They compared the versions of the genes in the extinct hominins to the ones in modern humans.

The researchers found more than 1,000 mutations that were unique only to living humans or to Neanderthals and Denisovans. Their analysis revealed that many of these mutations probably had important effects on how the body clock operated. The researchers predicted, for example, that some body-clock proteins that are abundant in our cells were much scarcer in the cells of Neanderthals and Denisovans.

Next, the scientists looked at the small number of body-clock variants that some living people have inherited from Neanderthals and Denisovans. To see what effects those variants had on people, they probed the UK Biobank, a British database holding the genomes of a half-million volunteers.

Along with their DNA, the volunteers provided answers to a long list of health-related questions, including whether they were early risers or night owls. To Capra’s surprise, almost all the ancient body-clock variants increased the odds that the volunteers were morning people.

“That was really the most exciting moment of the study, when we saw that,” Capra said.

Geography might explain why the ancient hominins were early risers. Early humans lived in Africa, fairly close to the equator, where the duration of days and nights stays roughly the same over the course of the year. But Neanderthals and Denisovans moved into higher latitudes, where the day became longer in the summer and shorter in the winter. Over hundreds of thousands of years, their circadian clocks may have adapted to the new environment.

When modern humans expanded out of Africa, they also faced the same challenge of adapting to higher latitudes. After they interbred with Neanderthals and Denisovans, some of their descendants inherited body-clock genes better suited to their new homes.

All of these conclusions, however, stem from a database limited to British people. Capra is starting to look at other databases of volunteers with other ancestries. If the links hold up, Capra hopes ancient body clocks can inspire some ideas about how we can adapt to the modern world, where circadian rhythms are disrupted by night shifts and glowing smartphones. These disruptions don’t just make it hard to get a good night’s sleep; they can also raise the risk of cancer, obesity and a host of other disorders.

Michael Dannemann, an evolutionary geneticist at the University of Tartu in Estonia who was not involved in the new study, said one way to test Capra’s variants would be to engineer various human cells in the lab so that their genes were more like those of Neanderthals and Denisovans. Then scientists could grow clusters of the cells and watch them go through their daily cycles.

“This step forward not only advances our knowledge of how Neanderthal DNA influences present-day humans,” he said, “but also offers a pathway to expanding our understanding of Neanderthal biology itself.”

c.2023 The New York Times Company

 

Extinct human relatives left a genetic gift that helped people thrive in the Americas

A new study found that a gene passed down from extinct archaic humans provided an adaptive advantage for Indigenous people of the Americas and is still common today in people of Indigenous descent

Brown University

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PROVIDENCE, R.I. [Brown University] — A new study provides fresh evidence that ancient interbreeding with archaic human species may have provided modern humans with genetic variation that helped them adapt to new environments as they dispersed across the globe.

The study, published in Science, focused on a gene known as MUC19, which is involved in the production of proteins that form saliva and mucosal barriers in the respiratory and digestive tracts. The researchers show that a variant of that gene derived from Denisovans, an enigmatic species of archaic humans, is present in modern Latin Americans with Indigenous American ancestry, as well as in DNA collected from individuals excavated at archeological sites across North and South America.

The frequency at which the gene appears in modern human populations suggests the gene was under significant natural selection, meaning it provided a survival or reproductive advantage to those who carried it. It’s not clear exactly what that advantage might have been, but given the gene’s involvement in immune processes, it may have helped populations to fight off pathogens encountered as they migrated into the Americas thousands of years ago.

“From an evolutionary standpoint, this finding shows how ancient interbreeding can have effects that we still see today,” said study author Emilia Huerta-Sánchez, a professor of ecology, evolution and organismal biology at Brown University. “From a biological standpoint, we identify a gene that appears to be adaptive, but whose function hasn’t yet been characterized. We hope that leads to additional study of what this gene is actually doing.”

Huerta-Sanchez co-authored the study with Fernando Villanea, a former post-doctoral researcher at Brown who is now at University of Colorado, Boulder; David Peede, a graduate student at Brown; and an international team of collaborators.

Not much is known about the Denisovans, who lived in Asia between 300,000 and 30,000 years ago, aside from a few small fossils from Denisova cave in Siberia, two jaw bones found in Tibet and Taiwan, and a nearly complete skull from China found this year. The finger fossil from Siberia contained ancient DNA, which enables scientists to look for common genes between Denisovans and modern humans. Prior research led by Huerta-Sánchez found that a version of a gene called EPAS1 acquired from Denisovans may have helped Sherpas and other Tibetans to adapt to high altitudes.

For this study, the researchers compared Denisovan DNA with modern genomes collected through the 1,000 Genomes Project, a survey of worldwide genetic variation. The researchers found that the Denisovan-derived MUC19 gene is present in high frequencies in Latino populations who harbor Indigenous American genetic ancestry. The researchers also looked for the gene in the DNA of 23 individuals collected from archeological sites in Alaska, California, Mexico and elsewhere in the Americas. The Denisovan-derived variant was present at high frequency in these ancient individuals as well.

The team used several independent statistical tests to show that the Denisovan MUC19 gene variant rose to unusually high frequencies in ancient Indigenous American populations and present-day people of Indigenous descent, and that the gene sits on an unusually long stretch of archaic DNA — both signs that natural selection had boosted its prevalence. The research also revealed that the gene was likely passed through interbreeding from Denisovans to another archaic population, the Neanderthals, who then interbred with modern humans.

Huerta-Sánchez said the findings demonstrate the importance that interbreeding had in introducing new and potentially useful genetic variation in the human lineage.

“Typically, genetic novelty is generated through a very slow process,” Huerta- Sánchez said.  “But these interbreeding events were a sudden way to introduce a lot of new variation.”

In this case, she said, that “new reservoir of genetic variation” appears to have helped modern humans as they migrated into the Americas, perhaps providing a boost to the immune system.

“Something about this gene was clearly useful for these populations — and maybe still is or will be in the future,” Huerta-Sánchez said.

She’s hopeful that the recognition of the gene’s importance will spur new research into its function to reveal novel biological mechanisms, especially since it involves coding genetic variants that alter the protein sequence.

The research was supported by The Leakey Foundation, the National Institutes of Health (1R35GM128946- 01, T32 GM128596, R35GM142978, R01NS122766), the Alfred P. Sloan Foundation, the Blavatnik Family Graduate Fellowship in Biology and Medicine, the Brown University Predoctoral Training Program in Biological Data Science (NIH T32 GM128596), the Burroughs Wellcome Fund and the Human Frontier Science Program.

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Journal

Science

DOI

10.1101/2023.09.25.559202 

Method of Research

Experimental study

Subject of Research

People

Article Title

The MUC19 gene: An Evolutionary History of Recurrent Introgression and Natural Selection

Article Publication Date

21-Aug-2025

 

DNA from extinct hominin may have helped ancient peoples survive in the Americas

University of Colorado at Boulder

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Thousands of years ago, ancient humans undertook a treacherous journey, crossing hundreds of miles of ice over the Bering Strait to the unknown world of the Americas.

Now, a new study led by the University of Colorado Boulder suggests that these nomads carried something surprising with them—a chunk of DNA inherited from a now-extinct species of hominin, which may have helped humans adapt to the challenges of their new home.

The researchers will publish their results Aug. 21 in the journal Science.

“In terms of evolution, this is an incredible leap,” said Fernando Villanea, one of two lead authors of the study and an assistant professor in the Department of Anthropology at CU Boulder. “It shows an amount of adaptation and resilience within a population that is simply amazing.”

The research takes a new look at a species known as Denisovans. These ancient relatives of humans lived from what is today Russia south to Oceania and west to the Tibetan Plateau. The Denisovans likely went extinct tens of thousands of years ago. Their existence, however, remains poorly understood: Scientists identified the first known Denisovan just 15 years ago from the DNA in a fragment of bone found in a cave in Siberia. Like Neanderthals, Denisovans may have had prominent brows and no chins.

“We know more about their genomes and how their body chemistry behaves than we do about what they looked like,” Villanea said.

A growing body of research has shown that Denisovans interbred with both Neanderthals and humans, profoundly shaping the biology of people living today.

To explore those connections, Villanea and his colleagues including co-lead author David Peede from Brown University, examined the genomes of humans from across the globe. In particular, the team set its sights on a gene called MUC19, which plays an important role in the immune system.

The group discovered that humans with Indigenous American ancestry are more likely than other populations to carry a variant of this gene that came from Denisovans. In other words, this ancient genetic heritage may have helped humans survive in the completely new ecosystems of North and South America.

A little-known gene

Villanea added that MUC19’s function in the human body is about as mysterious as Denisovans themselves. It’s one of 22 genes in mammals that produce mucins. These proteins make mucus, which, among other functions, can protect tissues from pathogens.

“It seems like MUC19 has a lot of functional consequences for health, but we’re only starting to understand these genes,” he said. 

Previous research has shown that Denisovans carried their own variant of the MUC19 gene, with a unique series of mutations, which they passed onto some humans. That kind of admixture was common in the ancient world: Most humans alive today carry some Neanderthal DNA, whereas Denisovan DNA makes up as much as 5% of the genomes of people from Papua New Guinea. 

In the current study, Villanea and colleagues wanted to learn more about how these genetic time capsules shape our evolution.

The group pored through already published data on the genomes of modern humans from Mexico, Peru, Puerto Rico and Colombia where Indigenous American ancestry and DNA is common. 

They discovered that one in three modern people of Mexican ancestry carry a copy of the Denisovan variant of MUC19—and particularly in portions of their genome that come from Indigenous American heritage. That’s in contrast to people of Central European ancestry, only 1% of whom carry this variant.

The researchers discovered something even more surprising: In humans, the Denisovan gene variant seems to be surrounded by DNA from Neanderthals. 

“This DNA is like an Oreo, with a Denisovan center and Neanderthal cookies,” Villanea said.

A new world

Here’s what Villanea and his colleagues suspect happened: Before humans crossed the Bering Strait, Denisovans interbred with Neanderthals, passing the Denisovan MUC19 to their offspring. Then, in a game of genetic telephone, Neanderthals bred with humans, sharing some Denisovan DNA. It’s the first time scientists have identified of DNA jumping from Denisovans to Neanderthals and then humans. 

Later, humans migrated to the Americas where natural selection favored the spread of this borrowed MUC19.

Why the Denisovan variant became so common in North and South America but not in other parts of the world isn’t yet clear. Villanea noted that the first people who lived in the Americas likely encountered conditions unlike anything else in human history, including new kinds of food and diseases. Denisovan DNA may have given them additional tools to contend with challenges like these.

“All of a sudden, people had to find new ways to hunt, new ways to farm, and they developed really cool technology in response to those challenges,” he said. “But, over 20,000 years, their bodies were also adapting at a biological level.”

To build that picture, the anthropologist is planning to study how different MUC19 gene variants affect the health of humans living today. For now, Villanea said the study is a testament to the power of human evolution. 

“What Indigenous American populations did was really incredible,” Villanea said. “They went from a common ancestor living around the Bering Strait to adapting biologically and culturally to this new continent that has every single type of biome in the world.”

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Other co-authors of the new study include researchers at Brown University; the University of Washington School of Medicine; Universidad Nacional Autónoma de México; University of Copenhagen; Clemson University; University of Padova; University of Turin; University of California, Berkeley; Université Paris- Saclay; and Trinity College Dublin.

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Journal

Science

DOI

10.1126/science.adl0882 

Article Title

The MUC19 gene: An evolutionary history of recurrent introgression and natural selection

Article Publication Date

21-Aug-2025