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

HOBBITS

Denisovans Lived on the Tibetan Plateau, Researchers Suggest

ByAbdul Moeed

July 6, 2024

Researchers reveal that Denisovans, ancient humans, lived on the Tibetan Plateau. Credit: Dongju Zhang / Wikipedia / CC BY-SA 4.0

Denisovans lived on the high Tibetan plateau for over 100,000 years, as revealed by a recent study. This sheds light on these ancient humans, first discovered in 2010.

Researchers studied many animal bones found at Baishiya Karst Cave, 3,280 meters high near Xiahe County in China’s Gansu province. This cave is one of just three places where these extinct humans lived.

The study found that Denisovans could hunt, cut up, and cook various large and small animals such as woolly rhinos, blue sheep, wild yaks, marmots, and birds

Archaeologists at the cave found a rib bone fragment in sediment dating back to 48,000 to 32,000 years ago. This discovery suggests Denisovans were alive more recently than scientists had thought.

Lived and thrived on the Tibetan plateau

With limited fossil evidence, understanding how our ancient human ancestors, the Denisovans, lived has been challenging. However, the latest study reveals remarkable resilience among those who inhabited Baishiya Karst Cave.

They thrived in one of Earth’s toughest environments through both warm and cold periods, making the most of the diverse animals in the grasslands.

Dongju Zhang, an archaeologist and professor at Lanzhou University in China, co-authored the study published in Nature. Reflecting on the findings, Zhang emphasized the longstanding presence of Denisovans on the Tibetan plateau and posed questions about their lifestyle and environmental adaptation.

“They used all these animals available to them, so that means their behavior is flexible,” Zhang added.

Frido Welker, an associate professor at the Biomolecular Paleoanthropology Group at the University of Copenhagen’s Globe Institute, noted that the rib likely belonged to a Denisovan who lived during a period when modern humans were still spreading throughout Eurasia. He suggested that future research in the area could reveal whether these two groups interacted there.

“It does put this fossil and the (sediment) layer in a context where we know in the wider region humans were likely to be present, and that’s interesting,” he said.

Fossils found in Denisova Cave in the Altai Mountains of Siberia

Denisovans were initially recognized just over a decade ago through DNA analysis of a small piece of finger bone. Since then, fewer than a dozen Denisovan fossils have been unearthed worldwide.

Most of these fossils were discovered in Denisova Cave, nestled in Siberia’s Altai Mountains, which gave the group its name. Genetic studies later revealed that Denisovans, much like Neanderthals, had interbred with early modern humans.

Traces of Denisovan DNA found in present-day populations suggest these ancient people likely once inhabited large parts of Asia.

Notably, it wasn’t until 2019 that researchers identified the first Denisovan fossil outside of Denisova Cave, as reported by CNN.

 

Extinct humans survived on the Tibetan plateau for 160,000 years

UNIVERSITY OF READING

Bone remains found in a Tibetan cave 3,280 m above sea level indicate an ancient group of humans survived here for many millennia, according to a new study published in Nature.  

The Denisovans are an extinct species of ancient human that lived at the same time and in the same places as Neanderthals and Homo sapiens. Only a handful Denisovan remains have ever been discovered by archaeologists. Little is known about the group, including when they became extinct, but evidence exists to suggest they interbred with both Neanderthals and Homo sapiens. 

A research team led by Lanzhou University, China, the University of Copenhagen, Denmark, the Institute of Tibetan Plateau Research, CAS, China, and involving the University of Reading studied more than 2,500 bones from the Baishiya Karst Cave on the high-altitude Tibetan Plateau, one of the only two places where Denisovans are known to have lived.  

Their new analysis, published today (Wednesday, 3 July) in Nature, has identified a new Denisovan fossil and shed light on the species’ ability to survive in fluctuating climatic conditions — including the ice age — on the Tibetan plateau from around 200,000 to 40,000 years ago. 

Dr Geoff Smith, a zooarchaeologist at the University of Reading, is a co-author of the study. He said: “We were able to identify that Denisovans hunted, butchered and ate a range of animal species. Our study reveals new information about the behaviour and adaptation of Denisovans both to high altitude conditions and shifting climates. We are only just beginning to understand the behaviour of this extraordinary human species.” 

Dietary diversity 

Bone remains from Baishya Karst Cave were broken into numerous fragments preventing identification. The team used a novel scientific method that exploits differences in bone collagen between animals to determine which species the bone remains came from.  

Dr Huan Xia, of Lanzhou University, said: “Zooarchaeology by Mass Spectrometry (ZooMS) allows us to extract valuable information from often overlooked bone fragments, providing deeper insight into human activities.”  

The research team determined that most of the bones were from blue sheep, known as the bharal, as well as wild yaks, equids, the extinct woolly rhino, and the spotted hyena. The researchers also identified bone fragments from small mammals, such as marmots, and birds.  

Dr Jian Wang, of Lanzhou University, said: “Current evidence suggests that it was Denisovans, not any other human groups, who occupied the cave and made efficient use of all the animal resources available to them throughout their occupation.”  

Detailed analysis of the fragmented bone surfaces shows the Denisovans removed meat and bone marrow from the bones, but also indicate the humans used them as raw material to produce tools.  

A new Denisovan fossil 

The scientists also identified one rib bone as belonging to a new Denisovan individual. The layer where the rib was found was dated to between 48,000 and 32,000 years ago, implying that this Denisovan individual lived at a time when modern humans were dispersing across the Eurasian continent. The results indicate that Denisovans lived through two cold periods, but also during a warmer interglacial period between the Middle and Late Pleistocene eras.   

Dr Frido Welker, of the University of Copenhagen, said: “Together, the fossil and molecular evidence indicates that Ganjia Basin, where Baishiya Karst Cave is located, provided a relatively stable environment for Denisovans, despite its high-altitude. 

"The question now arises when and why these Denisovans on the Tibetan Plateau went extinct.” 

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JOURNAL

Nature

DOI

10.1038/s41586-024-07612-9 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave

ARTICLE PUBLICATION DATE

3-Jul-2024

Who Were the Ancestors of the Neanderthals?

It's complicated. But researchers are gaining some clarity in the vast web of early-human species that preceded modern humans.

By Connor Lynch

Dec 17, 2021 

(Credit: LegART/Shutterstock)

In the genus Homo, us sapiens stand alone today. Once we had an abundance of cousins: Neanderthals, Denisovans, Homo heidelbergensis, Homo erectus and others.

Our isolation makes it easier to assume that hominin history has led up to us — that various lines of human-like primates have evolved, had their chance in the sun and perished, leaving their more human-like descendants to approach the form of modern humans. Rudolph Zalliger’s infamous artwork The Road to Homo Sapiens, now more commonly known as The March of Progress, is commonly blamed for creating this perception in the minds of the public, though that was not what Zalliger himself intended.

But when paleontologists and anthropologists look back at the history of hominin evolution, they find a veritable Gordian Knot, one that weaves back into itself, with innumerable dead ends. For a clear example, consider our quest to learn who the ancestors of our closest relatives, the Neanderthals and Denisovans, were.

One Web, Many Threads

The Neanderthals are probably our most famous cousins: short, stocky humans who went extinct around 40,000 years ago, with some surprising theories as to why. Less-well known but equally relevant are the Denisovans. Remains were discovered in Denisova Cave (also called Aju-Tasch) in Russia in 2008, and genetic analysis revealed them to be very close relatives of Neanderthals. Closer than us, in fact. It turned out we had not one, but two closest relatives.

But who were the hominins that gave rise to the Neanderthals and the Denisovans? University of Utah anthropologist Alan Rogers, who specializes in population genetics and evolutionary ecology, has been working on this problem for over a decade. But a paper he published in 2017 in the Proceedings of the National Academy of Sciences (PNAS) led him down a new, unexpected course.

The paper analyzed all the new genetic data available on Neanderthals and Denisovans to advance our understanding of humanity’s demographic history. In the process, the researchers identified a bottleneck in the population of the ancestors of Neanderthals and Denisovans. Some researchers disagreed with those findings, arguing the paper had left out important data. That kicked off a back-and-forth through the pages of PNAS, Rogers says: “The result of it all was that it became pretty clear, once you added the additional pieces of data, that nobody’s models fit very well, neither ours nor theirs.”

Rogers wouldn’t have a satisfactory resolution to that puzzle until 2020. The models improved some after adding in various supplementary factors — such as the gene flow from older hominins, known as “super-archaics." Also, evidence of Acheulean hand-axes, which first appeared in Africa nearly 2 million years ago and then spread to Eurasia, suggested another possible explanation. What if ancient hominins, likely H. erectus, had colonized Eurasia as early as 2 million years ago — not just traveling there and dying out, but forming sustainable populations? Then the ancestors of the Neanderthals and Denisovans, the “Neandersovans,” as Rogers calls them, interbred with those hominins around 750,000 years ago. “Suddenly everything fit,” he and his co-authors wrote in their paper.

Tracking the Neandersovans

These Neandersovans, the researchers say, spread from Africa around 750,000 years ago and encountered their cousins, the super-archaics, likely descendants from Homo erectus. The groups interbred before dispersing across the continent, with Neanderthals later emerging in the West, and the Denisovans emerging in the East. “Exactly like what happened 50,000 years ago,” Rogers says, “when modern humans expanded, interbred, and separated into eastern and western populations.”

But nailing down who these earlier hominins were, or what they looked like, is extraordinarily difficult, for a number of reasons.

The single greatest problem is time. The oldest hominin DNA ever retrieved was 450,000 years old. Some research suggests that the upper-limit to retrieve sequenced DNA is somewhere in the range of 400,000 years to 1.5 million years. And while we know a fair bit about H. erectus, which likely formed some, if not all, of Eurasia’s super-archaic population 2 million years ago, those hominins had over a million years to evolve before they interbred with the Neandersovans.

And there are other basic questions that remain to be answered in this quest. For instance, where did the Neandersovan lineage branch off from the rest of the hominins in the first place? Was it in Africa? Or Eurasia?

The simplest answer, and the one that best fits the available evidence, says Rogers, is that they branched off in Africa. “It’s a story I can tell without too much moving back and forth between Africa and Eurasia,” he says. The genetic evidence supports this as well, since it appears that the ancestors of Neanderthals and Denisovans split off from the lineage that leads to modern humans, and modern humans are believed to have evolved in Africa.

While there are hominins that are good candidates to be representatives of Neandersovans after they interbred with the super-archaics of Eurasia, nailing those down is simply impossible, he says. Homo antecessor, a hominin that lived in what’s now Spain around 800,000 to 1.2 million years ago, could be one. “I would like to think it’s the hominin fossil that interbred with these Neandersovans. But I can’t know that. So there’s this ambiguity about the relationship between the genetics and the fossil record,” he says. Though, a protein analysis of the 800,000-year-old tooth enamel of a H. antecessor published last year lends his theory credence.

Perhaps H. heidelbergensis was modern humanity’s last common ancestor with Neanderthals. As Rogers put it, paraphrasing a colleague arguing with some paleontologists years ago, “paleontologists never know whether any fossil had descendants; but geneticists always know the fossils had ancestors.” There’s no guarantee the organism you’re looking at had any descendants at all, he explains, or that its species didn’t go extinct before any other species split off from it.

Further complicating the picture are discoveries of yet more hominins, and long-standing debates about how to even classify them. Some anthropologists argue that what is commonly called H. sapiens is actually composed of a number of different species. What makes us human has become as much a taxonomic problem as a philosophical one, especially for the time period 400,000 to 700,000 years ago. Rogers believes that is around when the Neandersovans would have interbred with the super-archaics and then branched off into Neanderthals and Denisovans. “The taxonomy of that time, I think, is confused,” he says. “Maybe I’m just confused. But I’m not comfortable with the taxonomy of that given part of history.”

A climate-orchestrated early human love story

Peer-Reviewed Publication

INSTITUTE FOR BASIC SCIENCE

 

IMAGE: PHOTO OF THE REMAINING DENISOVA 11 (DENNY) BONE FRAGMENT FROM DENISOVA CAVE IN RUSSIA, THAT COMES FROM A DAUGHTER TO A NEANDERTHAL MOTHER AND A DENISOVAN FATHER. (PHOTO CREDIT: KATERINA DOUKA, TOM HIGHAM). view more 

CREDIT: INSTITUTE FOR BASIC SCIENCE

A new study published in the journal Science by an international team finds that past changes in atmospheric CO2 and corresponding shifts in climate and vegetation played a key role in determining when and where early human species interbred.

Modern-day people carry in their cells a small quantity of DNA deriving from other human species, namely the Neanderthals and the elusive Denisovans. Back in 2018, scientists announced to the world the discovery of an individual [Figure 1], later nicknamed Denny, who lived 90,000 years ago and who was identified as a daughter to a Denisovan father and a Neanderthal mother [Slon et al. 2018]. Denny, along with fellow mixed-ancestry individuals found at Denisova cave, testifies that interbreeding was probably common among hominins, and not limited to our own species Homo sapiens.

To unravel when and where human hybridization took place, scientists usually rely on paleo-genomic analysis of extremely rare fossil specimens and their even scarcer ancient DNA content. In the new Science paper, the team of climate experts and paleo-biologists from South Korea and Italy pursued a different approach. Using existing paleo-anthropological evidence, genetic data and supercomputer simulations of past climate, the team found that Neanderthals and Denisovans had different environmental preferences. More specifically, Denisovans were much more adapted to cold environments, characterized by boreal forests and even tundra, compared to their Neanderthal cousins who preferred temperate forests and grassland. “This means that their habitats of choice were separated geographically, with Neanderthals typically preferring southwestern Eurasia and Denisovans the northeast”, says Dr. Jiaoyang Ruan, postdoctoral researcher at the IBS Center for Climate Physics (ICCP), South Korea and lead author of the study.

However, according to their realistic computer simulations the scientists found that in warm interglacial periods, when Earth’s orbit around the Sun was more elliptic and northern hemisphere summer occurred closer to the Sun, the hominin habitats began to overlap geographically. “When Neanderthals and Denisovans shared a common habitat, there were more encounters and interactions among the groups, which would have increased the chance of interbreeding”, adds Prof. Axel Timmermann, corresponding author of the study and director of the ICCP and professor at Pusan National University.

The simulation of past habitat overlaps does not only put the first generation Neanderthal/Denisovan hybrid Denny into a climatic context, but it also agrees with other known episodes of interbreeding ~78, 120 thousand years ago. Future paleo-genetic reconstructions can be used to test the robustness of the new supercomputer model-based predictions of potential interbreeding intervals around 210 and 320 thousand years ago.

To further determine the climate drivers of the east-west interbreeding seesaw, the scientists looked more closely at how vegetation patterns changed over Eurasia during the past 400 thousand years. They discovered that elevated atmospheric CO2 concentrations and mild interglacial conditions caused an eastward expansion of temperate forest into central Eurasia which created dispersal corridors for Neanderthals into Denisovan lands. “It is as if glacial-interglacial shifts in climate created the stage for a unique and long-lasting human love story, whose genetic traces are still visible today”, comments Dr. Ruan.

One of the key challenges the researchers faced in their study was to estimate the preferred climatic conditions for Denisovans. “To deal with the very sparse Denisovan dataset, we had to devise new statistical tools, which could also account for known ancestral relationships amongst human species”, says Prof. Pasquale Raia from University of Naples, Federico II in Italy, co-author of the study. “This allowed us for the first time to estimate where Denisovans could have lived. To our surprise, we found that, apart from areas in Russia and China, also northern Europe would have been a suitable environment for them”, he adds [Figure 2].

Whether Denisovans ever lived west of the Altai mountains is unknown; but it can be tested using large-sample genetic analyses of Denisovan ancestry in European populations. Such analysis is expected to shed new light on the relationship between early dispersal, habitat encroachment and human genetic diversification.

Illustration of Neanderthal (redscale) /Denisovan (greenscale) preferred habitats. Potential interbreeding areas in Central Asia and northern Europe are indicated by overlapping colors and baby-shapes.

CREDIT

Institute for Basic Science

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JOURNAL

Science

DOI

10.1126/science.add4459 

ARTICLE TITLE

Climate shifts orchestrated hominin interbreeding events across Eurasia

ARTICLE PUBLICATION DATE

11-Aug-2023