3 species of human ancestors may have mixed and mingled in one Siberian cave 45,000 years ago – altering our evolution

denisova cave
The Denisova cave in Russia’s Anui River Valley.

Denisova Cave, high in the mountains of Siberia, was a happening place for our ancestors 300,000 years ago. Anthropologists have known that for a while: Scientists have excavated bones and teeth there from our Neanderthal and Denisovan cousins – and one of their hybrid children – over the last two decades. They’ve also found stone tools and jewelry.

But according to a recent study in the journal Nature, modern humans appear to have joined the party, too.

An analysis of ancient DNA culled from sediment on the cave floor suggests that these Homo sapiens occupied the cave starting around 45,000 years ago. So they may have overlapped with Neanderthals and Denisovans.

“We now have the first direct evidence for the presence of ancient modern humans at the site,” Elena Zavala, an evolutionary anthropologist at the Max Planck Institute in Germany and a co-author of the study, told Insider.

Neanderthal Evolution
An exhibit shows the life of a Neanderthal family at the Neanderthal Museum in the town of Krapina, Croatia, February 25, 2010.

The findings offer further insight into how our human ancestors interacted and interbred – exchanging genes and tool-making technology that altered the course of our species’ evolution.

“I cannot think of another site where three human species lived through time,” Katerina Douka, an archaeologist who was not involved in the study, told Science.

Ancient DNA tells a 300,000-year story

Zavala’s team collected more than 700 soil samples between 300,000 and 20,000 years old from across the cave’s three chambers.

One-quarter of those samples contained hominin DNA from microscopic bits of human skin, hair, and poop that got mixed into the sediment. The researchers also found DNA from ancient dogs, bears, hyenas, and horses.

denisovan mtDNA lab work
A scientist analyzes ancient DNA in a laboratory at the Max Planck Institute for Evolutionary Anthropology.

From their extensive DNA analysis, they were able to piece together a timeline of the cave’s occupants. Starting about 250,000 years ago, during a period of global warming, Denisovans started using the cave. Then roughly 60,000 years later, as the climate shifted and temperatures started to drop, Neanderthals arrived on scene.

The two hominins shared the cave for another 60,000 years before traces of the Denisovans disappeared from the fossil record.

For 30,000 years, Neanderthals were the cave’s sole occupants. After that, the new study reveals, a second population of Denisovans emerged. That happened about 100,000 years ago, at the start of the last global ice age. DNA evidence suggests both these Denisovans and their Neanderthal cave-mates survived for up to 78,000 years more.

That’s an important part of the timeline, according to the study, because it suggests those two hominin groups were still thriving in Denisova Cave when the first Homo sapiens showed up 45,000 years ago.

denisova cave
Layers of sediment on the walls of the Denisova Cave.

The team found DNA from all three species in a layer of soil that’s between 45,000 and 22,000 years old – which suggests they all overlapped.

A meeting point for hominins

denisovan
A portrait of a young female Denisovan based on a skeletal profile reconstructed from ancient DNA.

The fact that three hominin species all chose the same cave got Zavala thinking: What made this spot so special?

“It’s interesting that Denisovans and Neanderthals kept returning to the cave because it is located at the edge of what is thought to be each of their geographical ranges,” she said. (Neanderthals were predominantly from Europe, and Denisovans from Asia.)

Most likely, according to Zavala, it sat along a migration route between Europe and Asia.

“This cave was repeatedly meeting point between these two regions,” she said.

But to verify this idea, anthropologists would need to find more sites along this potential migratory path.

denisova cave
A view from the Denisova Cave in Russia.

Zavala thinks excavators will continue to find more traces of hominin and animal occupants in Denisova Cave.

Previously, anthropologists had to rely on fossils to assess which ancient species were present in an area. But pulling DNA straight from the soil has increased the amount of evidence scientists have to work with, thereby making findings like Zavala’s possible.

“We are not limited by the rare discovery of skeletal materials,” she said.

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5,000-year-old bacteria is the oldest strain of plague ever seen. Scientists found it in the ancient bones of a Stone Age man.

black plague y. pestis cell reports
The partial skull of a man buried in Riņņukalns, Latvia, who died of the plague around 5,000 years ago.

  • A strain of bacteria that causes the plague infected a hunter-gatherer 5,000 years ago.
  • It’s the oldest strain of plague ever found, a new study says.
  • The ancient strain evolved for four more millennia before causing the Black Death, or bubonic plague.
  • See more stories on Insider’s business page.

Five thousand years ago, a rodent bit a Stone Age hunter-gatherer. The creature carried a strain of pernicious bacteria called Yersinia pestis – the pathogen that caused the Black Death, or bubonic plague in the 1300s.

The bacteria likely killed the Stone Age man, who died in his 20s, according to a study published Tuesday. It’s the oldest strain of plague known to science so far.

The strain’s genome closely resembles the version of plague that wrecked medieval Europe more than 4,000 years later, killing up to half the region’s population over the course of seven years. But it’s missing a few key genes – notably, traits that helped it spread.

Unlike its microbial descendants, the plague that sickened the ancient hunter was a slow-moving disease and not very transmissible, according to Ben Krause-Kyora, a professor of ancient DNA analysis at Kiel University in Germany.

“It lacked the genes that enabled transmission by flea,” Krause-Kyora, who co-authored the new study, told Insider. During the Black Death, bites from fleas and lice were the key source of infections.

So in the millennia between the hunter-gatherer’s demise and the Black Death, Y. pestis bacteria mutated in a way that gave it the ability to jump between species via fleas.

“The change was a major driving force of a fast and widespread plague,” Krause-Kyora said.

Bacteria in the bloodstream

black plague bacteria y. pestiris
Yersinia pestis bacteria as seen under a microscope. This bacteria is the cause of the Bubonic plague.

The Stone Age hunter-gatherer died in a region that’s now Latvia. Near his bones, anthropologists also excavated the remains of another man, a teenage girl, and a newborn, but none had been infected.

Krause-Kyora’s group hadn’t gone looking for ancient plague victims – rather, they wanted to see if the four buried people were related. But before completing their planned genetic analysis, the team screened ancient DNA extracted from the bones and teeth for traces of pathogens. That’s how they found the bacteria.

black plague y. pestis cell reports
The Riņņukalns site on the banks of the Salaca River in Latvia, where 5,000-year-old bones were found.

The researchers then compared the bacteria’s genome to other ancient plague strains. A previous study described other strains that are roughly 5,000 years old, but Krause-Kyora said this particular one is a couple hundred years older. So his team concluded it was the earliest-known version of Y. pestis.

The hunter-gatherer’s DNA also showed that he had a large quantity of bacteria in his body, which suggests that he died from it. His grave site indicated that other members of his group meticulously buried him, according to the study.

“It’s hard to tell if he died quickly,” Krause-Kyora said, adding, “from the number of bacteria present, it seems he survived a higher dose and lived longer or in a more chronic way with it.”

black plague y. pestis cell reports
The jawbone of a Stone Age hunter-gatherer buried in Riņņukalns, Latvia, around 5,000 years ago.

The plague can take three forms. Bubonic is the type that ravaged Europe and left victims with swollen, painful lymph nodes. Septicemic refers to infections in which the bacteria enters the bloodstream and the patient’s skin turns black and dies. Pneumonic plague, meanwhile, can cause respiratory failure.

Krause-Kyora thinks the ancient hunter had septicemic plague, which could explain why no other members of his small group got the disease.

“They would’ve had to have direct contact with his blood,” he said – or another infected rodent would have had to bite them.

An evolving plague

black plague bubonic plague art
A painting titled “Carting the Dead,” by French artist Jean-Pierre Moynet, depicts a cart of bodies from people who died from the Black Plague in the 1300s.

The plague is mostly zoonotic, meaning it hops from animal hosts to humans.

Krause-Kyora said that the hunter-gatherer’s case can show epidemiologists how zoonotic pathogens – like Ebola, swine flu, and (most likely) the new coronavirus – change over time.

“We really have to think about how evolution of zoonotic events could take thousands of years,” he said.

black plague y. pestis cell reports
A lab specializing in ancient DNA at Kiel University.

During the era when the Stone Age man lived, the plague didn’t cause widespread outbreaks. Y. pestis would pop up here and there in groups of hunter-gatherers, farmers, and nomads across Eurasia, but there was never a Black Death-level event.

“The finding confirms the early strains are associated with sporadic outbreaks that didn’t spread far,” Krause-Kyora said.

What changed by medieval times, he thinks, is that people started to live in bigger communities and in closer proximity. That shift might have influenced the evolution that led the plague to live in fleas – which bite people more easily.

“It’s the bacteria adapting to population density,” Krause-Kyora said.

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A human ancestor previously unknown to science lived alongside ancient humans and Neanderthals – and they all interbred

Nesher Ramla Homo
The partial skull and jaw bone of a newly discovered human ancestor named Nesher Ramla homo.

  • Scientists uncovered a new species of human ancestor named the Nesher Ramla homo in a sinkhole.
  • This ancestor lived between 140,000 and 120,000 years ago in Israel and Arabia alongside humans.
  • New research suggests Nesher Ramla homo interbred with humans, as well as our Neanderthal cousins.
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The eastern Mediterranean coast was a crowded place 120,000 years ago.

By that time, Homo sapiens – anatomically modern humans – had migrated out of Africa and settled in modern-day Israel and Arabia. Meanwhile, Neanderthals – our genetic cousins – had started to thrive in Eurasia.

Now, new research reveals that a third human ancestor was hunting and gathering in the same landscape. Two studies published Thursday in the journal Science describe a previously unknown hominin called the Nesher Ramla homo. The group not only shared tools and technology with their neighbors, they also interbred.

“They lived together and interacted with another,” Rachel Sarig, an anthropologist from Tel Aviv University and co-author of the new studies, told Insider.

Nesher Ramla Homo
A virtual reconstruction of the Nesher Ramla lower jaw bone.

Sarig and her colleagues uncovered a partial jaw bone, which they pieced together from 17 fragments like a puzzle, deep in a sinkhole at an Israeli site called Nesher Ramla – hence the ancestor’s name. There were also chunks of skull and a tooth belonging to the same individual.

Notably, the human ancestor had no chin – a feature distinct to Homo sapiens – and a flatter, squatter head. Those features suggest Nesher Ramla was a more ancient species than the region’s other occupants.

“It was some kind of pre-Neanderthal,” Sarig said.

The team had expected the bones to belong to a modern human.

“Homo sapiens were the dominant population in the Levant” between 100,000 and 200,000 years ago, Sarig said. “We were very surprised when we started looking at the fossils, and it was clear right away that Nesher Ramla was not the same.”

A sinkhole in the Judean Hills

Nesher Ramla Homo
The Nesher Ramla sinkhole in Israel, west of Jerusalem.

The discovery was a decade in the making. In 2011, workers were expanding a limestone quarry in the Judean Hills – between Israel’s Mediterranean coast and Jerusalem – when they found a huge sinkhole.

In sediment about 25 feet down, Sarig’s team uncovered animal teeth and bones, flint stone tools, and the Nesher Ramla bones. They suspect the sinkhole was an ancient watering hole, where animals came to drink and our human ancestors gathered to butcher game.

The researchers calculated that the animal teeth and flint were between 120,000 and 140,000 years old, suggesting Nesher Ramla homo lived then, too. But Hila May, a co-author of the new studies, told Insider that it’s possible this prehistoric human started occupying the area up to half a million years ago.

Nesher Ramla Homo
The patch of sediment inside the Nesher Ramla sinkhole where scientists excavated the fossils.

Typically, hominins that lived during the Middle Pleistocene era in Israel, as Nesher Ramla homo did, are classified as part of the species Homo heidelbergensis. These ancestors are characterized by their use of fire to make tools and cook. But the authors of the study chose not to put this new human in that species, since its anatomical features do not align closely.

Still, May said this ancestor had a very similar way of life to Neanderthals and Homo sapiens.

“They were hunter-gatherers living in small groups, hunting animals like rhinos, horses, and deer,” she said, adding that Nesher Ramla were “not very different in their abilities from other groups.”

Interbreeding among human ancestors

Neanderthal
An artist’s conception of a Neanderthal.

The new study suggests that once Neanderthals migrated to Europe about 100,000 years ago, the Nesher Ramla group played a key role in shaping what they looked like and how they lived.

The new discovery might also solve a genetic mystery. Previous research found that some Neanderthals from the Middle Pleistocene era have genes that come from Homo sapiens. But these modern humans didn’t arrive in Europe until about 45,000 years ago – long after the Neanderthals.

nesher ramla
A stone tool found in the Nesher Ramla sinkhole.

So if Nesher Ramla interbred with both Neanderthals and modern humans in the Levant before Neanderthals expanded west, that could explain the migration of the genes.

“We needed some explanation how Homo genes got to Europe before Homo got there,” May said.

And the three hominins did more than just interbreed – evidence from the sinkhole also suggests they shared tool-making technologies, using the same types of flint tools made in the same way.

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The carcass of a young woolly rhinoceros that died thousands of years ago was found almost perfectly preserved in the Siberia permafrost. Researchers even found the animal’s horn.

woolly rhino siberia
Researchers discovered a frozen woolly rhinoceros carcass in the permafrost of Yakutia, Siberia.

  • A local resident from Yakutia, Siberia found the ancient carcass of a juvenile woolly rhino in melting permafrost.
  • Researchers said the carcass is between 20,000 and 50,000 years old, and the most complete young woolly rhino ever found.
  • Most of the rhino’s fur coat, hooves, and internal organs are intact — researchers even found the animal’s horn nearby.
  • One expert thinks the rhino drowned when it was three or four years old.
  • Visit Business Insider’s homepage for more stories.

Alexei Savvin stumbled upon an unprecedented find walking near the Tirekhtyakh River in Yakutia, Siberia last August: an almost perfectly-preserved woolly rhino carcass.

Most of the rhino’s hooves, teeth, and internal organs were still intact. The animal still had some of its thick, fur coat, and researchers even found its horn, which had broken off but lay nearby.

After analyzing the carcass, Siberian scientists announced on Tuesday that the rhino likely lived between 20,000 and 50,000 years ago. 

It is one of the most intact ancient rhinos ever found.

“The young rhino was between three and four years old and lived separately from its mother when it died, most likely by drowning,” Valery Plotnikov, a paleontologist from the Russian Academy of Sciences, told the Siberian Times.

“The rhino has a very thick short underfur, very likely it died in summer,” Plotnikov added.

woolly rhino siberia
A local resident of Yakutia, Siberia found a frozen woolly rhino in August. The carcass still had intact fur.

The rhino used its horn to forage for food

Siberian scientists hope to take the carcass to a laboratory for radiocarbon dating next month in order to get a better sense of how many thousands of years ago the animal died. There, they aim to also discover what gender the rhino was.

For now, they’re waiting for roads to open up between where Savvin found the rhino and the nearby city of Yakutsk.

woolly rhino siberia
A scientist holds up a tooth from a frozen woolly rhino discovered in Yakutia, Siberia in August 2020.

According to Plotnikov, finding the rhino’s small horn was a stroke of luck.

“This is a rarity, since it decomposes rather quickly,” Plotnikov told local outlet Yakutia 24 TV. The researchers found traces of wear on the horn, which suggests the rhino used it to gather food, Reuters reported.

woolly rhino siberia
Researchers found the woolly rhino’s tusk near its frozen carcass in Siberia.

Woolly rhinos lived throughout Europe and northern Asia until they went extinct about 14,000 years ago near the end of the last Ice Age. The creatures had two horns – one small horn between its eyes and another large one that protruded upward – and were covered in a thick, fur coat.

These herbivores munched on grasses; adults could reach lengths of 13 feet and weigh up to 2.2 tons (4,400 pounds).

Not the first find of its kind

woolly rhino siberia
A woolly rhinoceros replica on display in the Weston Park Museum in Sheffield, UK.

Discoveries like this one are likely to become more common as Earth’s temperatures continue to rise.

As the planet warms, the permafrost – ground in the Northern Hemisphere that remains frozen all year – is beginning to thaw. As it melts, ice-age creatures like this woolly rhino that were entombed for tens of thousands of years are starting to be unearthed.

In 2014, scientists found a baby woolly rhino carcass – nicknamed Sasha – in the same region of Siberia that this new rhino was found.

Sasha lived 34,000 years ago and was covered in strawberry blond-colored fur, according to the Siberian Times.

The baby rhino died at the age of seven months and had two little horns. 

Yakutia yielded another find in 2019: scientists discovered a 40,000-year-old severed wolf’s head, complete with fur, teeth, brain, and facial tissue on the banks of a river.

2019 06 14T063528Z_3_LYNXNPEF5C1KA_RTROPTP_4_RUSSIA PERMAFROST WOLF HEAD.JPG
A severed wolf’s head dating back to the Ice Age was found in Russia

In a similar finding this past September, Siberian researchers announced they’d found a perfectly preserved adult cave bear – with its nose, teeth, and internal organs still intact. Scientists think the bear died 22,000 to 39,500 years ago. Its species, Ursus spelaeus, lived during the last ice age and then went extinct 15,000 years ago.

The Lyakhovsky Islands, where the bear was found, are also replete with remains of woolly mammoths from the last ice age.

ice age bears siberia
A carcass of an Ice Age cave bear found on Great Lyakhovsky Island between the Laptev Sea and the East Siberian Sea in northern Russia.

The Siberian permafrost has also revealed two perfectly preserved extinct cave-lion cubs, as well as an ancient baby horse that died in a mud pit 42,000 years ago. The foal’s hair, skin, tail, and hooves were all intact.

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