Ancient brown bear genomes sheds light on Ice Age losses and survival

Peer-Reviewed Publication

UNIVERSITY OF COPENHAGEN - THE FACULTY OF HEALTH AND MEDICAL SCIENCES

The brown bear is one of the largest living terrestrial carnivores, and is widely distributed across the Northern Hemisphere. Unlike many other large carnivores that went extinct at the end of the last Ice Age (cave bear, sabretoothed cats, cave hyena), the brown bear is one of the lucky survivors that made it through to the present. The question has puzzled biologists for close to a century - how was this so?

Brown bears are ecologically flexible and have a broad dietary range. While they are carnivores, their diets can also consist primarily of plant matter making them adaptable to environmental changes. However, brown bears also experienced extensive range reductions and regional extinctions during the last Ice Age. Brown bears used to occupy a much wider range including Ireland, Honshu, the largest island of Japan, and Quebec (Canada). 

Did the decline or disappearance of bear populations in certain areas happen because bears left those places for better ones that they still currently live, or did unique groups of bears with distinct genes inhabit those areas and go extinct, leading to a loss in the overall diversity of the species?

By studying the genomes of ancient brown bears dated to between 3,800 and 60,000 years old, including several individuals from outside their current range, researchers from the University of Copenhagen, Denmark and the University of Yamanashi, Japan sought to address this question by investigating the evolutionary relationships between brown bears across space and time. 

Their study showed that brown bears did not simply move with the shifting environment, but populations went extinct. “Our analyses showed that ancient brown bears represent genetic diversity absent in today’s populations” says Takahiro Segawa, lead author of the study. “While brown bears survived global extinction, they suffered considerable losses of their historical range and genetic diversity”. This new perspective highlights a crucial period in the brown bear’s history and that they also faced challenges during and after the last Ice Age.

“As we continue to grapple with the challenges of coexistence between humans and wildlife, insights from the deep past are invaluable in shaping a sustainable future.” adds Michael Westbury, the senior author of the study. “Although studying recent specimens can provide some insights, by including samples from the past and from areas a species no longer exists, we can better quantify how patterns of current diversity arose, and inform predictions about how they may respond to future environmental change.” 

You can read more about this in the study “The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations” in Proceedings of the Royal Society B.

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JOURNAL

Proceedings of the Royal Society B Biological Sciences

DOI

10.1098/rspb.2023.2411 

ARTICLE PUBLICATION DATE

24-Jan-2024

COI STATEMENT

The authors declare no competing interests.

 

Neanderthal Nuclear DNA Found in Paleolithic Cave Sediments

Apr 16, 2021 by News Staff / Source

An international team of scientists has developed new methods for the enrichment and analysis of nuclear DNA from sediments, and applied them to cave deposits in Europe and Siberia dated to between approximately 200,000 and 50,000 years ago.

Vernot et al. extracted Neanderthal nuclear DNA from cave sediments. Image credit: Tyler B. Tretsven.

Skeletal remains are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites.

Mitochondrial DNA (mtDNA) has been retrieved from cave sediments, but provides limited value for studying population relationships.

Although nuclear DNA contains far more information, its retrieval from sediments presents substantial challenges. It’s far less abundant than mtDNA and difficult to distinguish from other non-hominin mammalian and microbial DNA, which dominates the genetic material often present in ancient sediments.

To address these challenges, Dr. Benjamin Vernot from the Department of Evolutionary Genetics at the Max-Planck-Institute for Evolutionary Anthropology and his colleagues developed methods to recover, enrich and analyze nuclear DNA from cave sediments.

“There are lots of places in the human genome that are very similar to a bear’s DNA, for example,” Dr. Vernot said.

“We specifically targeted regions in the genome where we could be confident of isolating only human DNA, and we also designed methods to measure our success in removing non-human DNA.”

“We wanted to be confident that we weren’t accidentally looking at some unknown species of hyena.”

Specifically, the researchers applied their approach to extract nuclear DNA from more than 150 sediment samples from three caves: Galería de las Estatuas in northern Spain and Chagyrskaya and Denisova caves in the Altai Mountains of southern Siberia.

They detected a population replacement in Spain approximately 100,000 years ago, accompanied by a turnover of mtDNA.

They also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene.

“The dawn of nuclear DNA analysis of sediments massively extends the range of options to tease out the evolutionary history of ancient humans,” Dr. Vernot said.

“By freeing the field of ancient DNA from the constraints of finding human remains and expanding the number of sites potentially suitable for investigation, we can now study the DNA from many more human populations, and from many more places, than has previously been thought possible,” added Dr. Matthias Meyer, also from the Department of Evolutionary Genetics at the Max-Planck-Institute for Evolutionary Anthropology.

The findings were published in the journal Science.

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Benjamin Vernot et al. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science, published online April 15, 2021; doi; 10.1126/science.abf1667

Elephants solve problems with personality

UNIVERSITY OF WYOMING

Research News

 

IMAGE: AFRICAN SAVANNA ELEPHANT TEMBO, AT THE SAN DIEGO ZOO, WAS ONE OF THE ELEPHANT PARTICIPANTS IN THE STUDY. view more 

CREDIT: LISA BARRETT

Just as humans have their own individual personalities, new research in the Journal of Comparative Psychology shows that elephants have personalities, too. Moreover, an elephant's personality may play an important role in how well that elephant can solve novel problems.

The article was written by Lisa Barrett and Sarah Benson-Amram in the University of Wyoming's Animal Behavior and Cognition Lab, led by Benson-Amram. It may be viewed here.

The authors of the paper tested 15 Asian elephants and three African savanna elephants in three zoos across the country -- the San Diego Zoo, the Smithsonian's National Zoological Park and the Oklahoma City Zoo -- with the help of elephant caretakers.

Previous work from Barrett and Benson-Amram demonstrated that Asian elephants can use water as a tool to solve a novel problem -- and reach a tasty marshmallow reward -- in what's called the floating object task. This time, the authors designed new novel tasks, as well as personality tests, for the elephants.

"We took a comprehensive approach by using three different problem-solving tasks and three types of personality assessments to determine if individual personality played a role in which elephants were able to solve these tasks," Barrett says. "Since we couldn't give the elephants a personality test like the ones you're familiar with online, we had to think creatively."

The authors developed novel object tests, in which they presented the elephants with an unfamiliar object, a mylar balloon, a burned log and the scent of a predator (lion or hyena), and recorded the elephants' responses. You can watch videos of the novel object trials: balloon, burned log and urine. They also asked elephant caretakers to fill out a survey about the personalities of the animals in their care; and, finally, they observed the elephants interacting with one another in their zoo habitats.

From those assessments, Barrett and Benson-Amram learned that the surveys and observations were the most reliable methods to get at elephant personality. Overall, Barrett and Benson-Amram measured traits such as active, affectionate, aggressive, defiant, excitable, mischievous, shy and sociable, which have been studied in other animals as well.

"We were eager to see if the personality traits we uncovered through the surveys and observations predicted success on novel problem-solving tasks," Benson-Amram says. "The elephants had an opportunity to solve each task three times, and we measured if they learned to solve faster over time, and then we traced their success back to their personality type."

The three problem-solving tasks included the trap tube task, which is a common test used with primates but which had never been presented outside of primates before. You can watch videos of the problem-solving trials: boxed ball, rod ball and trap tube.

Barrett and Benson-Amram found that elephants did learn to solve two out of the three tasks faster over time, even though the elephants only received three trials on each task. Traits including aggressiveness and activity were important predictors of problem-solving overall, but the personality traits measured did not significantly predict learning ability.

This study makes connections between two sources of individual variation, personality and cognition, in threatened species. One reason it is important to examine problem-solving in elephants is that they are faced with new problems that they need to solve regularly in the wild. For example, if certain traits enable elephants to overcome novel problems, elephants may be more likely to invade farmland and contribute to human-elephant conflict. With more research, managers can predict which elephants might overcome or habituate to deterrents, and managers can devote more resources to tracking elephants.

The authors call for more work on different forms of personality assessments to determine which methods would be best for management of zoo and wild elephants.

"Research with free-ranging elephants can extend this study to determine which personality traits are most important for solving novel problems that elephants experience in the wild," says Barrett, a 2020 graduate of UW's Program in Ecology and the Department of Zoology and Physiology.

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Humans Sheltered in This Lava Tube for Thousands of Years

Isaac Schultz

GIZMONDO
Wed, April 17, 2024 

The mouth of the Umm Jirsan lava tube. - Photo: Green Arabia Project


Three needs are famously fundamental to survival: food, water, and shelter. According to new research, ancient humans had at least two of those three needs met by a nearly mile-long lava tube about 77 miles (125 kilometers) north of Medina, Saudi Arabia, for at least 7,000 years.

The lava tube in question is named Umm Jirsan, the longest of the lava tubes in Saudi Arabia’s volcanic field, Harrat Khaybar. Today, wolves, foxes, and snakes inhabit the cave, but it was once a popular spot forhuman pastoralists and their domesticated animals. The new study, published today in the journal PLoS One, examined faunal remains and rock art in the region and adds to a growing body of research into the system.

“The findings at Umm Jirsan provide a new type of archaeological site in the region, and one where organic material like bone and deeply layered sediments are much better preserved,” said Mathew Stewart, a zooarchaeologist at Griffith University in Australia and the study’s lead author, in an email to Gizmodo. “We had no expectations to find archaeology at Umm Jirsan. In fact, we were mostly interested in seeing the large caches of bones that had been previously reported.”


Indeed, a team that included Stewart found evidence in 2021 that striped hyenas were creating bone caches in the back of the cave. There are hundreds of thousands of bones in Umm Jirsan, the team found, belonging to at least 40 species and dating from the Neolithic to as recently as the Victorian Era.

Though the oldest dated faunal remains in the cave are about 7,000 years old, Stewart told Gizmodo that animals have likely used the lava tubes since they formed, millions of years ago. Seven of the lava flows in Harrat Khaybar are less than 1,500 years old, according to the Smithsonian Institution’s Global Volcanism Program, and the region still has the potential for activity, according to a 2022 study.

The interior of the lava tube. - Photo: Green Arabia Project

In their new paper, the researchers reported evidence for human occupation of the lava tube between the Neolithic and the Bronze Age—in other words, humans made use of the tube for millennia. Isotopic analysis of the human remains in the cave revealed an increase of foods in their diet that had high levels of a certain isotope of carbon associated with oasis agriculture.

But the team concluded that Umm Jirsan was probably not permanently occupied. Rather, they think it was a convenient spot for herders to stop and provide their flocks with shade and water. Based on human use of the surrounding area—evinced by nearby rock art and other faunal records—the team posited that the lava tube “was situated along a pastoral route linking key oases.” So you can think of Umm Jirsan more as an ancient truck stop than a place of residence.

The rock art described by the team was found at a nearby collapsed lava tube northeast of Umm Jirsan. The researchers reported 16 rock art panels depicting cattle, sheep, goats, and possibly ibexes.

Even though humans didn’t have a permanent presence in the lava tube, the natural structure provided shelter for people and their herds for thousands of years. In the harsh desert environment, the promise of a break from the sun, wind, and heat would’ve made Umm Jirsan a perfect prehistoric pit stop.

Humans were living in a lava tube 7,000 years ago on the Arabian Peninsula

Owen Jarus

LIVE SCIENCE
Wed, April 17, 202

A large cave-like lava tube that is dark and underground. We see a researcher with a light in the corner

Archaeologists in Saudi Arabia have discovered that humans were living in a lava tube at least 7,000 years ago and possibly earlier, a new study finds.

The lava tube, called Umm Jirsan, is located in a volcanic field called Harrat Khaybar, approximately 78 miles (125 kilometers) north of Medina, researchers said in a statement.

"Umm Jirsan is currently the longest reported lava tube in Arabia in terms of the horizontal length of passages, at 1481 metres [4,859 feet]," the scientists wrote in the paper published Wednesday (April 17) in the journal PLOS One.

Although ancient humans are known to have lived on the Arabian Peninsula during prehistoric times, organic remains are scant due to poor preservation in the arid region. So the researchers looked for areas that would have preserved artifacts because they were sheltered from the sun, wind and wild temperature changes over the past millennia. Umm Jirsan met these criteria, so the team decided to look there.

Their hunch turned out to be good. They found artifacts such as fragments of cloth and worked wood; rock art of domesticated animals; and the skeletal remains of nine human bones. These finds suggest that people occupied the lava tuba for at least the past 7,000 years and possibly as far back as 10,000 years, according to radiocarbon dating and optically stimulated luminescence dating, which examines when the last time certain minerals were exposed to heat or sunlight. Some of the dates are relatively recent and the tube appears to have been used into modern times, Stewart said.

The humans who used the lava tube left a few clues about their lives. These include bones of domesticated sheep and goats, as well as rock art depicting these animals, suggesting that these creatures were key to the humans' survival. A chemical analysis of the human remains showed an increase in certain plants, like cereals and fruits, over time — possibly because of a rise in oasis agriculture in the Bronze Age, the team said in the statement.

The analysis suggested that humans weren't living in the lava tube for long periods at a time, however. "The lava tube does not appear to have served as a permanent habitation location, but rather as a site that likely lay on herding routes and that allowed access to shade and water for passing herders and their animals," the authors wrote in the study. "Prior to this, as well as during pastoral periods, the lava tube was likely also linked with hunting activities, which probably remained a cornerstone of local economies into the Bronze Age."

Lava tubes form when lava creates underground passages that can transport large quantities of molten rock; when the lava supply ends or if the lava is diverted elsewhere, the empty tube is left behind, according to the National Park Service. And while they may sound inhospitable, they can be a good source of shelter. For instance, scientists at JAXA, Japan's space agency, have suggested that future humans could live in lava tubes on the moon.

Study co-author Mathew Stewart, a research fellow at the Australian Research Centre for Human Evolution at Griffith University in Australia, said lava tubes like this one continue to be used by modern-day people in the region "whether it be for corralling animals, accessing water resources, or simply for leisure," Stewart told Live Science in an email.

Related: 4,000-year-old wall found around oasis in Saudi Arabia likely defended 'against raids from nomads'


We see 8 square images. The top four are of rock art of sheep, goats, people, long-horned cattle and an ibex. The bottom four are digital enhancements of the top four.

It's difficult to say when Umm Jirsan was last filled with lava, Stewart said, although volcanic activity has occurred intermittently in the region. "There have been some 1500 volcanic eruptions in Arabia over the past 1500 years, and many more in antiquity," Stewart said.

Scholars not involved with the research spoke positively of the team's work. It is "wonderful work by this team that has made a strong reputation for excellent fieldwork and interpretation," Gary Rollefson, a professor emeritus of anthropology at Whitman College and San Diego State University, told Live Science in an email. "Although the excavation produced relatively little in the way of artifacts and faunal remains, the material nevertheless reveals strong connections of material recovered in other parts of northern Saudi Arabia," Rollefson said, noting that there are similarities with material excavated in parts of Jordan.

Anthony Sinclair, a professor of archaeological theory and method at the University of Liverpool in the U.K., said in an email that in addition to providing shelter, the lava tube also would have been a "defendable position — in terms of allowing the pastoralists to safeguard their flocks at night against local predators. There would have been wolves, hyena and quite possibly lion and leopard across Arabia." Today, some of these animals are endangered or no longer present in Arabia.

SMART DOGS
African wild dogs cope with human development using skills they rely on to compete with other carnivores

The Conversation
February 18, 2022

African wild dogs (Screen Grab)

Large carnivores in Africa are important from ecological, economic and cultural perspectives, but human activities put them at risk. Increasingly, lions, hyenas and African wild dogs are restricted to protected areas like national parks. Within these limited areas, they must compete for the same food sources.

Competition is, of course, nothing new. For several million years, African wild dogs have evolved within a set of large carnivores that all prey on the same large herbivore species, like wildebeest and warthogs. Wild dogs are lanky, long-distance hunters that always live in groups, usually of eight to 10 adults. Cooperation with pack mates allows them to hunt prey much larger than themselves. Weighing in at about 40-62 pounds (18-28 kilograms), wild dogs have been shaped by the necessity to compete with larger species like the lion and spotted hyena.

There may be a silver lining to being the bottom dog in the competitive hierarchy. Research that my colleagues with the Zambian Carnivore Programme and I have conducted in Zambia and Tanzania suggests why smaller, subordinate species like wild dogs are better able to move through human-modified landscapes. Understanding how is essential for their conservation.


A pack of African wild dogs makes a formidable hunting team.
slowmotiongli/iStock via Getty Images Plus

Meeting the African wild dog

In the late 1980s, I was studying dwarf mongooses in Tanzania’s Serengeti National Park when an extraordinary thing happened. While I sat on the roof of an ancient Land Rover watching mongooses on a nearby termite mound, a wild dog trotted past. And then another, and another. Wild dogs had been missing from most (perhaps all) of the Serengeti for years due to a combination of intense competition from larger carnivores and outbreaks of rabies. But here they were, back again.

Over the next year, I occasionally followed the dogs to watch them hunt on the shortgrass plains, where they were constantly shadowed by spotted hyenas. Several hyenas often trailed the dogs even as they set out to hunt, and hyenas quickly aggregated when the dogs killed a gazelle or wildebeest – often alerted by the unmistakable sound of vultures plummeting through the air in their own race to the fresh carcass.

Although they are half the size, wild dogs do not easily give up a kill to hyenas. A pack of wild dogs making a coordinated attack on one or two hyenas can easily drive them off. But hyenas are also social animals, and researchers found that the dogs generally lost their kills to hyenas when their numbers were equal. Given the large population of hyenas in Serengeti, they took nine out of 10 kills that the dogs made. And lions are simply too dangerous to fight, so the big cats could always take over a kill from the dogs, and kill them surprisingly often.

At that time, very little was known about wild dogs in places other than Serengeti and South Africa’s Kruger National Park, a more wooded ecosystem where researchers had found a flourishing population that often hunted impala. Biologists started to rethink the prevailing view that wild dogs were specialized to live and hunt in open grasslands.

My colleagues and I spent six years in the 1990s observing wild dogs in the Selous Game Reserve, confirming the Tanzania Wildlife Department’s belief that this large ecosystem was a major stronghold for the species. We found that the density of wild dogs in Selous was very good, at least partly because wild dogs were better able to avoid problems with lions and spotted hyenas in the miombo woodland of Selous than in plains of the Serengeti. It was more evidence that not only could they survive outside of grasslands like in the Serengeti, but African wild dogs found advantages to other kinds of environments.

By the mid-1990s, a scientific consensus was emerging that the persistence of wild dogs in an area depends at least partly on their ability to avoid losing food to hyenas or being killed by lions.


African wild dogs have been less separated by human development, like roads, than some other large carnivores.
Simoneemanphotography/iStock via Getty Images Plus

Being bottom dog can pay off

Many studies, including our current research in Zambia, have confirmed that wild dogs are adapted to “live in the cracks” of a landscape where they are outnumbered and outsized by spotted hyenas and lions.

In the short term, wild dogs move quickly away from an encounter with lions – or an experimental playback of their roars over a loudspeaker – in a straight line that would be unusual under other circumstances. Over the long term, wild dogs avoid areas that are heavily used by larger competitors, even though this requires them to hunt in areas with fewer prey.

But there may be a benefit to being at the bottom of the competitive hierarchy. Compared to most species, all of the large African carnivores live in small and isolated populations that must remain connected to maintain genetic diversity. But humans have now modified more than half of the Earth’s terrestrial surface, cutting lines of movement and increasing the isolation of protected areas. Despite this general pattern, some species are better adapted than others to maintain connections between ecosystems.

Our research has used advances in genetic sequencing to test how well connected wild dogs and lions are in several ecosystems across Zambia and Tanzania. The basic idea is that well-connected populations remain genetically similar, but poorly connected populations become genetically distinct from one another over time.

We wondered whether the adaptations of wild dogs that allow them to move through a landscape dominated by lions and hyenas might also help them move through a landscape altered by humans. For example, wild dogs could move more quickly and in a straighter line after an encounter with people, just as they do after an encounter with lions. We hypothesized that genetic data would show that wild dogs have stronger connections between ecosystems than lions, and that their connections are less affected by humans.

And this is just what the data showed when we compared the genotypes of 96 wild dogs and, separately, 208 lions.



Each dot represents an individual wild dog, and similarity in their color represents genetic similarity.


Scott Creel, CC BY-ND

Wild dogs in eastern, central and western Zambia were genetically quite similar, showing that these populations remain well connected. In contrast, lions were much less genetically similar, with distinct populations that were not well connected.




Each dot represents an individual lion, and similarity in their color represents genetic similarity.
Scott Creel, CC BY-ND

We also mapped the degree to which human effects such as land conversion, agriculture and roads hinder animal movement, differentiating between areas with relatively little resistance to animal movement and areas with strong human effects. The genetic differences between lion populations were strongly correlated with human resistance, but there was no such correlation for wild dogs. That is, places that were less hospitable to animal movement had more genetically isolated populations of lions, but didn’t affect the genetic diversity of the wild dogs in the area.

While it is still too early to know if this pattern will apply to other species, it suggests that eons of dealing with lions and hyenas have provided the wild dog with tools that help them maneuver through the unforgiving landscapes that humans create outside of national parks.

Scott Creel, Professor of Conservation Biology & Ecology, Montana State University

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

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

2023 public domain debuts include last Sherlock Holmes work


A Museum of London employee poses for photographers next to an 1897 oil on canvas portrait of Sherlock Holmes author Sir Arthur Conan Doyle by illustrator Sidney Paget on display as part of the exhibition "Sherlock Holmes: The Man Who Never Lived and Will Never Die" at the Museum of London in London, Oct. 16, 2014. Sherlock Holmes is finally free to the public in 2023. The long dispute on contested copyright on Doyle's tales of a whip-smart detective will come to an end in 2022, as the final Sherlock Holmes stories by Doyle will be released on Saturday, Dec. 31, as copyrights from 1927 expire on Jan. 1, 2023. (AP Photo/Matt Dunham, File)


WASHINGTON (AP) — Sherlock Holmes is finally free to the American public in 2023.

The long-running contested copyright dispute over Sir Arthur Conan Doyle’s tales of a whipsmart detective — which has even ensnared Enola Holmes — will finally come to an end as the 1927 copyrights expiring Jan. 1 include Conan Doyle’s last Sherlock Holmes work.

Alongside the short-story collection “The Case-Book of Sherlock Holmes,” books such as Virginia Woolf’s “To The Lighthouse,” Ernest Hemingway’s “Men Without Women,” William Faulkner’s “Mosquitoes” and Agatha Christie’s “The Big Four” — an Hercule Poirot mystery — will become public domain as the calendar turns to 2023.

Once a work enters the public domain it can legally be shared, performed, reused, repurposed or sampled without permission or cost. The works from 1927 were originally supposed to be copyrighted for 75 years, but the 1998 Copyright Term Extension Act delayed opening them up for an additional 20 years.

While many prominent works on the list used those extra two decades to earn their copyright holders good money, a Duke University expert says the copyright protections also applied to “all of the works whose commercial viability had long subsided.”

“For the vast majority—probably 99%—of works from 1927, no copyright holder financially benefited from continued copyright. Yet they remained off limits, for no good reason,” Jennifer Jenkins, director of Duke’s Center for the Study of the Public Domain, wrote in a blog post heralding “Public Domain Day 2023.”

That long U.S. copyright period meant many works that would now become available have long since been lost, because they were not profitable to maintain by the legal owners, but couldn’t be used by others. On the Duke list are such “lost” films like Victor Fleming’s “The Way of All Flesh” and Tod Browning’s “London After Midnight.”

1927 portended the silent film era’s end with the release of the first “talkie” — a film with dialogue in it. That was “The Jazz Singer,” the historic first feature-length film with synchronized dialogue also notorious for Al Jolson’s blackface performance.

In addition to the Alan Crosland-directed film, other movies like “Wings” — directed by William A. Wellman and the “outstanding production” winner at the very first Oscars — and Fritz Lang’s seminal science-fiction classic “Metropolis” will enter the public domain.

Musical compositions — the music and lyrics found on sheet music, not the sound recordings — on the list include hits from Broadway musicals like “Funny Face” and jazz standards from the likes of legends like Louis Armstrong and Duke Ellington, in addition to Irving Berlin’s “Puttin’ on the Ritz” and “(I Scream You Scream, We All Scream for) Ice Cream” by Howard Johnson, Billy Moll and Robert A. King.

READ MORE– Silent films to live on in movie theater lobby card project
– 'Pooh,' 'Sun Also Rises' among works going public in 2022


Duke’s Center for the Public Domain highlighted notable books, movies and musical compositions entering the public domain — just a fraction of the thousands due to be unleashed in 2023.

BOOKS

— “The Gangs of New York,” by Herbert Asbury (original publication)

— “Death Comes for the Archbishop,” by Willa Cather

— “The Big Four,” by Agatha Christie

— “The Tower Treasure,” the first Hardy Boys mystery by the pseudonymous Franklin W. Dixon

— “The Case-Book of Sherlock Holmes,” by Arthur Conan Doyle

— “Copper Sun,” by Countee Cullen

— “Mosquitoes,” by William Faulkner

— “Men Without Women,” by Ernest Hemingway

— “Der Steppenwolf,” by Herman Hesse (in German)

— “Amerika,” by Franz Kafka (in German)

— “Now We Are Six,” by A.A. Milne with illustrations from E.H. Shepard

— “Le Temps retrouvé,” by Marcel Proust (in French)

— “Twilight Sleep,” by Edith Wharton

— “The Bridge of San Luis Rey,” by Thornton Wilder

— “To The Lighthouse,” by Virginia Woolf

MOVIES

— “7th Heaven,” directed by Frank Borzage

— “The Battle of the Century,” a Laurel and Hardy film directed by Clyde Bruckman

— “The Kid Brother,” directed by Ted Wilde

— “The Jazz Singer,” directed by Alan Crosland

— “The Lodger: A Story of the London Fog,” directed by Alfred Hitchcock

— “Metropolis,” directed by Fritz Lang

— “Sunrise,” directed by F.W. Murnau

— “Upstream,” directed by John Ford

— “Wings,” directed by William A. Wellman

MUSICAL COMPOSITIONS

— “Back Water Blues,” “Preaching the Blues” and “Foolish Man Blues” (Bessie Smith)

— “The Best Things in Life Are Free,” from the musical “Good News” (George Gard “Buddy” De Sylva, Lew Brown, Ray Henderson)

— “Billy Goat Stomp,” “Hyena Stomp” and “Jungle Blues” (Ferdinand Joseph Morton)

— “Black and Tan Fantasy” and “East St. Louis Toodle-O” (Bub Miley, Duke Ellington)

— “Can’t Help Lovin’ Dat Man” and “Ol’ Man River,” from the musical “Show Boat” (Oscar Hammerstein II, Jerome Kern)

— “Diane” (Erno Rapee, Lew Pollack)

— “Funny Face” and “’S Wonderful,” from the musical “Funny Face” (Ira and George Gershwin)

— “(I Scream You Scream, We All Scream for) Ice Cream” (Howard Johnson, Billy Moll, Robert A. King)

— “Mississippi Mud” (Harry Barris, James Cavanaugh)

— “My Blue Heaven” (George Whiting, Walter Donaldson)

— “Potato Head Blues” and Gully Low Blues” (Louis Armstrong)

— “Puttin’ on the Ritz” (Irving Berlin)

— “Rusty Pail Blues,” “Sloppy Water Blues” and “Soothin’ Syrup Stomp” (Thomas Waller)

Young T. rexes had a powerful bite, capable of exerting one-sixth the force of an adult

Juvenile tyrannosaurs tested their chops as they grew to become bone crushers like their parents

UNIVERSITY OF CALIFORNIA - BERKELEY

VIDEO: UC BERKELEY'S JACK TSENG, SEEN PEERING THROUGH THE EYE SOCKET OF AN ADULT T. REX, EXPLAINS WHY HE MEASURED THE BITE FORCE OF A JUVENILE T. REX, AND WHAT THAT... view more 

CREDIT: UC BERKELEY VIDEO BY ROXANNE MAKASDJIAN AND JEREMY SNOWDEN, WITH FOOTAGE COURTESY OF JACK TSENG

Jack Tseng loves bone-crunching animals -- hyenas are his favorite -- so when paleontologist Joseph Peterson discovered fossilized dinosaur bones that had teeth marks from a juvenile Tyrannosaurus rex, Tseng decided to try to replicate the bite marks and measure how hard those kids could actually chomp down.

Last year, he and Peterson made a metal replica of a scimitar-shaped tooth of a 13-year-old juvie T. rex, mounted it on a mechanical testing frame commonly used in engineering and materials science, and tried to crack a cow legbone with it.

Based on 17 successful attempts to match the depth and shape of the bite marks on the fossils -- he had to toss out some trials because the fresh bone slid around too much -- he determined that a juvenile could have exerted up to 5,641 newtons of force, somewhere between the jaw forces exerted by a hyena and a crocodile.

Compare that to the bite force of an adult T. rex -- about 35,000 newtons -- or to the puny biting power of humans: 300 newtons.

Previous bite force estimates for juvenile T. rexes -- based on reconstruction of the jaw muscles or from mathematically scaling down the bite force of adult T. rexes -- were considerably less, about 4,000 newtons.

Why does it matter? Bite force measurements can help paleontologists understand the ecosystem in which dinosaurs -- or any extinct animal -- lived, which predators were powerful enough to eat which prey, and what other predators they competed with.

"If you are up to almost 6,000 newtons of bite force, that places them in a slightly different weight class," said Tseng, UC Berkeley assistant professor of integrative biology. "By really refining our estimates of juvenile bite force, we can more succinctly place them in a part of the food web and think about how they may have played the role of a different kind of predator from their larger, adult parents."

The study reveals that juvenile T. rexes, while not yet able to crush bones like their 30- or 40-year-old parents, were developing their biting techniques and strengthening their jaw muscles to be able do so once their adult teeth came in.

"This actually gives us a little bit of a metric to help us gauge how quickly the bite force is changing from juvenile to adulthood, and something to compare with how the body is changing during that same period of time," said Peterson, a professor at the University of Wisconsin in Oshkosh and a paleopathologist -- a specialist on the injuries and deformities visible in fossil skeletons. "Are they already crushing bone? No, but they are puncturing it. It allows us to get a better idea of how they are feeding, what they are eating. It is just adding more to that full picture of how animals like tyrannosaurs lived and grew and the roles that they played in that ecosystem."

Tseng, Peterson and graduate student Shannon Brink of East Carolina University in Greenville, North Carolina, will publish their findings this week in the journal PeerJ.

CAPTION

An artist's depiction of a young Tyrannosaurus rex, about 13 years old, chewing on the tail of an Edmontosaurus, a plant-eating, duckbill dinosaur of the late Cretaceous Period. The teeth punctures left in the bone, which the youngster probably scavenged, allowed scientists to estimate the bite force that juvenile tyrannosaurs could exert.

CREDIT

Sketch by Brian Engh, http://dontmesswithdinosaurs.com/

Teeth marks galore, but who was the biter?

Experiments using metal casts of dinosaur teeth to match observed bite marks are rare, not because bite marks on dinosaur fossils are rare, but because the identity of the biter is seldom clear.

Two dinosaur fossils that Peterson excavated years earlier from the Hell Creek Formation of eastern Montana, however, proved ideal for such an experiment. One, the skull of a juvenile T. rex, had a healed bite mark on its face. "What, other than another T. rex, would be able to chomp another T. rex and puncture its skull?" he reasoned. Tyrannosaurs, like crocodiles today, played rough, and the wound was likely from a fight over food or territory.

In addition, the puncture holes in the skull, which had healed, were the size and shape of juvenile T. rex teeth, and the spacing fit a juvenile's tooth gap. Juvenile T. rexes have teeth that are oval in cross section: more knife-like, presumably to cut and tear flesh. Adult T. rexes have teeth with round cross sections: more like posts, to crush bone. Both juveniles and adults could replace lost or broken teeth from spares buried in the jaw that emerged once the socket was empty.

Because skull bone is harder than other bone, Peterson said, matching these holes with punctures made by the metal tooth in a cow bone provided an upper limit to the bite force.

The other fossil was a tail vertebra from a plant-eating, duckbilled dinosaur, an Edmontosaurus. It had two puncture marks from teeth that matched those of a juvenile T. rex. Peterson said that T. rex was the only predator around at that time -- the late Cretaceous Period, more than 66 million years ago -- that could have bitten that hard on the tailbone of a duckbill. The juvenile likely punctured the bone when chomping down on a meaty part of the tail of the already dead animal.

Because vertebrae are softer, experimentally creating similar punctures in a cow bone gave the researchers a lower limit on bite force.

Tseng employed a testing technique that was used in 2010 by researchers who measured the bite force of a much older and smaller dinosaur from the early Cretaceous: a Deinonychus, made famous under a different name -- Velociraptor -- in the 1993 movie Jurassic Park. Its bite force was between 4,000 and 8,000 newtons.

Tseng, then at the University at Buffalo in New York, and Peterson made a replica of a juvenile T. rex tooth from the middle of the jaw using a dental-grade cobalt chromium alloy, which is much harder than dinosaur tooth enamel, Tseng said.

CAPTION

Jack Tseng of UC Berkeley measuring punctures produced in a cow bone by a metal cast of a tyrannosaur tooth.

CREDIT

UC Berkeley photo by Juan Liu

They then mounted the metal tooth in a mechanical testing frame and pushed it slowly, at a millimeter per second, into a fresh-frozen and thawed humerus of a cow. Bones are easier to fracture at low speed than with a rapid chomp. Because the middle of the humerus has a thicker cortex than the bone near the joint ends, the middle was used to replicate the facial punctures. The ends were used to simulate the vertebra punctures.

"What we did, an actualistic study, is to say, 'Let's actually stab the thing with a tooth and see what it does,'" Peterson said. "What we are finding is that our estimates are slightly different than other models, but they are within a close enough range -- we are on the same page."

Tseng emphasized that there is no one number describing the bite force of any animal: it depends on how the creature bites and adjusts the prey in its mouth for the best leverage.

"They probably were not just chomping down. If you look at modern predators, even reptilian predators, sometimes there is adjustment. Maybe they are finding the most mechanically advantageous place, or the strongest tooth to make their bite," said Tseng, who is a 2004 graduate of UC Berkeley's Department of Integrative Biology and an assistant curator in the University of California Museum of Paleontology. "Presumably, there is some tuning involved before they make that bite, so they can literally take the best bite forward to make that kill or to damage whatever they are trying to get into."

Nevertheless, the measurements are a start in charting the increase in tyrannosaurs' bite force as they mature, similar to how paleontologists have charted T. rex size and weight with age.

"Just as you can do a growth curve for such an organism, you can also do a strength curve for their bite force -- what was their bite force at 12 or 13 years old, what was it at 30, 35 or 40 years old. And what does that potentially mean about the role that those animals played in that ecosystem at the time?" Peterson said. "What's cool about finding bite marks in bone from a juvenile tyrannosaur is that it is tells us that at 13 years old, they weren't capable of crushing bone yet, but they were already trying, they were puncturing bone, pretty deep. They are probably building up their strength as they get older."

Tseng, whose primary interest is mammals, is eager to resume studies interrupted by the pandemic to measure the bite force of various living and extinct animals in order to infer the ecosystem niches of predators no longer alive. For those creatures, fossils are all that paleontologists have, in order to "interpret behavior and breathe some life into these extinct animals," said Peterson.

"I use a biomechanical lens when I look at everything, living or extinct," Tseng added. "Ecologists today studying food webs and ecosystems don't rely much on bones; they have physical animals and plants. It is really the paleontologists who are interested in this approach, because the majority of what we have to study are bones and bite marks."

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