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Scientists Decode 200,000-Year-Old Denisovan Genome: Unraveling Ancient Human Ancestry

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A groundbreaking research team at the Max Planck Institute for Evolutionary Anthropology has successfully generated a high-quality Denisovan genome assembly using ancient DNA extracted from molar teeth found in the Denisovan Cave. This genome, dating back approximately 200,000 years, significantly predates the only previously sequenced Denisovan specimen. The findings are prompting a reevaluation of when and where early human groups interacted, mixed, and migrated throughout Asia.

Artist’s concept of Penghu Denisovans walking under the bright sun during the Pleistocene in Taiwan. Image credit: Cheng-Han Sun.

Dr. Stéphane Peregne, an evolutionary geneticist from the Max Planck Institute for Evolutionary Anthropology, along with his team, recovered this Denisovan genome from molars excavated in the Denisova Cave, located in the Altai Mountains of southern Siberia. This cave is historically significant as it was the site where Denisovans were first discovered in 2010 through DNA analysis of finger bones.

This cave continues to be pivotal in the study of human evolution, revealing repeated occupations by Denisovans, Neanderthals, and even offspring resulting from the interbreeding of these groups.

“The Denisovans were first identified in 2008 based on ancient DNA sourced from Denisova 3, a phalanx found in the Denisova Cave,” Dr. Peregne and his colleagues noted.

“This analysis confirms that Denisovans are closely related to Neanderthals, an extinct human group that thrived in Western Eurasia during the mid-to-late Pleistocene.”

Since then, twelve fragmentary remains and a single skull have been associated with Denisovans through DNA or protein analysis, with Denisova 3 being the only specimen yielding a high-quality genome.

The newly studied molars, belonging to a Denisovan male who lived approximately 200,000 years ago, are predating modern humans’ migration out of Africa.

“In 2020, a complete upper left molar was found in Layer 17, one of the oldest cultural layers within the southern chamber of the Denisova Cave, dating between 200,000 and 170,000 years old based on photostimulated luminescence,” the scientists elaborated.

“Designated as Denisova 25, this molar resembles others found at Denisova Cave, specifically Denisova 4 and Denisova 8, and exhibits larger dimensions compared to Neanderthal and most post-Middle Pleistocene hominid molars, indicating it likely belonged to a Denisovan.”

“Two samples of 2.7 mg and 8.9 mg were extracted by drilling a hole at the cement-enamel junction of the tooth, with an additional 12 subsamples varying from 4.5 to 20.2 mg collected by carefully scraping the outer root layer using a dental drill.”

Thanks to excellent DNA preservation, researchers successfully reconstructed the genome of Denisova 25 with high coverage, matching the quality of the 65,000-year-old female Denisova 3 genome.

Denisovans likely had dark skin, in contrast to the pale Neanderthals. The image depicts a Neanderthal. Image credit: Mauro Cutrona.

Comparisons between the genomes indicate that Denisovans were not a singular, homogeneous population.

Instead, at least two distinct Denisovan groups inhabited the Altai region at various intervals, with one group gradually replacing the other over millennia.

Earlier Denisovans possessed a greater amount of Neanderthal DNA than later populations, suggesting that interbreeding was a regular event rather than an isolated occurrence in the Ice Age landscape of Eurasia.

Even more intriguing, the study uncovered evidence that Denisovans engaged in interbreeding with “hyperarchaic” hominin groups that diverged from the human lineage before the ancestors of Denisovans, Neanderthals, and modern humans branched off.

“This second Denisovan genome illustrates the recurrent admixture between Neanderthals and Denisovans in the Altai region, suggesting these mixed populations were eventually supplanted by Denisovans from other regions, reinforcing the notion that Denisovans were widespread and that populations in the Altai may have existed at the periphery of their geographic range,” the researchers explained.

The Denisovan 25 genome presents valuable insights into the long-standing mysteries regarding the Denisovan ancestry in contemporary populations.

People in Oceania, parts of South Asia, and East Asia all carry Denisovan DNA, albeit from different Denisovan sources.

Through genetic comparison, scientists have identified at least three separate Denisovan origins, highlighted by their genetic segments found in thousands of modern genomes.

One lineage closely relates to the later Denisovan genome and is linked to widespread ancestry across East Asia and beyond.

A second, more distantly related Denisovan population contributed independently to Oceanian and South Asian ancestry.

Notably, East Asians do not share this highly divergent Denisovan ancestry, implying their ancestors may have taken a different route into Asia, potentially from the north, whereas Oceanian ancestors likely migrated through South Asia.

“Neanderthal-like DNA fragments appear in all populations, including Oceanians, aligning with a singular out-of-Africa migration; however, the distinct Denisovan gene flow points to multiple migrations into Asia,” the researchers stated.

Reconstruction of a young Denisovan woman based on skeletal profiles derived from ancient DNA methylation maps. Image credit: Maayan Harel.

The researchers believe certain Denisovan genetic traits offered advantages that increased their prevalence in modern human populations through the process of natural selection.

By analyzing both Denisovan genomes, the authors pinpointed numerous regions in present-day populations that appear to have originated from Denisovan introgression, particularly in Oceania and South Asia.

Genetic alterations observed in other Denisovans provide intriguing insights into their physical appearances.

Several unique mutations in Denisovans influence genes connected to cranial shape, jaw protrusion, and facial characteristics—attributes that align with the limited fossil record associated with Denisovans.

A shift in regulatory mechanisms is on the horizon. The Fox P2 gene, implicated in brain development and language in modern humans, raises important questions regarding the cognitive capabilities of Denisovans, although researchers emphasize that genetic data cannot replace direct fossil or archaeological evidence.

“The impact of Denisovan alleles on modern human phenotypes might also shed light on Denisovan biology,” the researchers pointed out.

“Examining alleles linked to contemporary human traits, we identified 16 associations with 11 Denisovan alleles, covering aspects like height, blood pressure, cholesterol levels, and C-reactive protein levels.”

“Additionally, we recognized 305 expressed quantitative trait loci (QTL) and 117 alternative splicing QTLs that affect gene expression across 19 tissues in modern humans, with the most significant effects observable in the thyroid, tibial artery, testis, and muscle tissues.”

“These molecular effects can be utilized to explore additional phenotypes that are not retained in the fossil record. This updated catalog provides a more reliable foundation for investigating Denisovan traits, adaptations, and disease susceptibilities, some of which may have influenced modern humans through admixture.”

A Preprint of the team’s research paper was published in bioRxiv.org on October 20, 2025.

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Stephane Peregne et al. 2025. High coverage genome of Denisovans from 200,000 years ago. BioRxiv doi: 10.1101/2025.10.20.683404

Source: www.sci.news

Scientists Decode the Genome of Oat Bread | Science News

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Oats (avena sativa) grain are a traditional food rich in dietary fiber, contributing positively to human health. Recent years have seen a rise in interest in oats as they serve as the foundation for plant-based milk alternatives. Unlike many other cereal crops, oat genomic research is still in its early stages, with limited exploration into structural genomic diversity and gene expression variability. Scientists are currently focused on collecting and annotating the genome. An atlas of gene expression across six tissues at various developmental stages in 33 wild and domesticated oat strains is also being developed.

Oats (avena sativa). Image credit: Christian Wynn.

Oats rank as the seventh most cultivated grain globally, esteemed for their high fiber content and notable health benefits.

In 2022 and 2023, global production exceeded 25 million tons.

Advancements in genetically improved varieties hold the promise of enhanced productivity and sustainability in oat farming; however, much of this potential remains untapped, with the first oat reference sequences released only in recent years.

The complexity of the oat genome adds to the slow progress.

“Pangenomes encapsulate the complete genetic diversity of cultivated plants like oats and are essential for our understanding,” remarked lead author Raz Avni, Ph.D., from the Leibniz Institute for Plant Genetics and Crop Research.

“They comprise genes common to all plants and those unique to specific species, providing a kind of roadmap.”

“The pantranscriptome reveals which genes are active across various tissues, such as leaves, roots, and seeds, and at different developmental stages. It serves as a gene expression atlas.”

“However, deciphering how genetic variations influence traits in individual plants poses a challenge, particularly in oats.”

“The oat genome’s complexity arises from its hexaploid nature, having six sets of chromosomes from three ancestral sources.”

During their study, the authors sequenced and analyzed the genomes of 33 oat lines, including cultivated varieties and related wild types.

They also constructed an oat pan transcriptome by scrutinizing gene expression in six tissues across various developmental stages in 23 of these oat lines.

The research aimed to identify structural changes, such as chromosome inversions and translocations.

“Our pangenome illustrates the extensive genetic diversity present in oats,” stated Dr. Avni.

“This insight aids in identifying key genes associated with yield, adaptation, and health.”

The researchers uncovered intriguing findings during their study.

“For instance, we observed the loss of many genes in one of the three subgenomes,” the team noted.

“Nevertheless, other gene copies seem to compensate for the functions, ensuring the plant’s productivity remains intact.”

“Sequencing the oat pangenome highlights how modern genomic methods can propel foundational research and directly influence health, agriculture, and breeding,” commented lead author Dr. Martin Mascher from Murdoch University’s Leibniz Institute for Plant Genetics and Crop Research.

“We also discovered that structural variations in the genome influence the regulation of flowering time.”

The team’s results are published in the journal Nature.

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R. Avni et al. Pangenome and pantranscriptome of hexaploid oat. Nature, published online October 29, 2025. doi: 10.1038/s41586-025-09676-7

Source: www.sci.news

AFP Creates AI Tool to Decode Gen Z Slang Amid Concerns Over ‘Criminal Influencers’ Targeting Young Women

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The Australian Federal Police is set to create an AI tool designed to understand Gen Z and Alpha slang and emojis as part of its efforts to combat sadistic online exploiters and “criminal influencers”.

During a speech at the National Press Club on Wednesday, AFP Commissioner Chrissy Barrett highlighted the increasing presence of online criminal networks predominantly led by boys and men who target vulnerable teenage and pre-teen girls.

The police chief detailed how these individuals, mainly from English-speaking nations, groom their victims, coercing them into “engaging in severe acts of violence against themselves, their siblings, other individuals, and even their pets”.

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“They act as criminal influencers, driven by chaos and the desire to inflict harm, with most of their victims being teenagers, specifically teenage girls,” she remarked, addressing parents and guardians.

“The motivations behind these networks are not financial or sexual in nature; they are purely for entertainment, fun, or gaining online popularity, often without an understanding of the repercussions.”

“This perverse form of gamification encourages the production of increasingly extreme and depraved content, allowing offenders to elevate their status within the group.

“In some instances, these perpetrators will swap victims much like in online gaming scenarios.”

The Federal Police confirmed they have identified 59 suspects involved in these networks, taking action against an undisclosed number of them, all aged between 17 and 20.

Barrett mentioned that AFP is collaborating with Microsoft to create artificial intelligence tools capable of “interpreting emojis and Gen Z and Gen Alpha slang in encrypted communications and chat groups to detect sadistic online exploitation.”

“This prototype is intended to assist our teams in swiftly removing children from dangerous situations,” she stated in a pre-released version of her speech.

“While it may feel like an endless struggle to safeguard children, I urge parents and caregivers to understand they are not alone and that there are straightforward steps they can take.”

Barrett also addressed the radicalization of youth, noting that four young individuals faced terrorism-related charges this year due to 10 investigations.

Since 2020, a total of 48 youths aged between 12 and 17 have been investigated for suspected terrorist activities, resulting in 25 charges.

She pointed out that 54% had a religious motivation, 22% had an ideological motivation, 11% had a mixed or unclear ideology, and 13% had undetermined motives.

In one notable case from 2022, a 14-year-old was investigated after posting on Snapchat about violent extremism, Barrett revealed.

This 14-year-old boy had access to firearms and explosives, with a tip-off suggesting he was plotting a school shooting in Australia.

During his arrest, police discovered a tactical vest, a bulletproof helmet, and “extremist-style” drawings.

Barrett’s address also referred to the AFP’s ongoing investigation into the arson at the Adas Israel synagogue, asserting that the suspect is linked to several incendiary bombings targeting tobacco shops.

“This individual represents a national security threat to our nation,” she stated.

“Among all the criminals who pose a threat to Australia, he is my primary concern, and I have directed my most seasoned investigators to focus on him.”

Barrett’s recent appointment as AFP’s chief, succeeding the retiring Reece Kershaw, suggests a shift in the police’s mission.

The AFP is now mandated to “protect Australia and its future from both domestic and global security threats,” implying increased international actions and operations.

Barrett mentioned the AFP’s collaboration with Colombian law enforcement, highlighting that AFP personnel were dispatched to a remote area of the Colombian jungle to “deliberately dismantle a cocaine manufacturing facility.”

“The AFP is determined to prevent criminal organizations from targeting Australia and will persist in collaborating with local law enforcement to confront criminals in our own vicinity when legally feasible,” she said.

“In recent years, AFP and Colombian cooperation has led to the seizure of over eight tonnes of cocaine.”

In partnership with Colombian authorities, a cache of arms and explosives from narco-terrorist groups, employed in assaults on police and military personnel, was also confiscated.

Barrett stated that AFP assisted in the seizure of 295 military grenades, 200 detonators, firearms, and ammunition.




Source: www.theguardian.com

AI can rapidly decode digital data stored in DNA in a matter of minutes instead of days

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DNA can store digital data such as visual and audio files

Science Picture Co / Alamy

Artificial intelligence can read data stored in DNA strands within 10 minutes, not the day required for previous methods, and DNA storage approaches practical use of computing.

“DNA stores huge amounts of data in a very compact form and remains intact for thousands of years.” Daniella Bar-Lev At the University of California, San Diego. “In addition, DNA is naturally replicable and offers a unique advantage for long-term data storage.”

However, getting encoded information within DNA is a monumental challenge as the strands become confused when mixed and stored. During the data encoding process, individual strands may be replicated incompletely, and some fragments may be lost completely. As a result, data readings stored in DNA are similar to reconstructing books from boxes filled with pages that go beyond the finest, varied.

“The traditional methods suffer from this confusion and require several days of processing,” says Bar-Lev. The new approach “rationalizes this with AI trained to find patterns of noise,” she says.

Bar-Lev and her colleagues developed an AI-driven method called DNAFormer. The system includes a deep learning AI model trained to reconstruct DNA sequences, another computer algorithm to identify and correct errors, and a third decoding that brings everything back to digital data while correcting any remaining mistakes. Includes algorithms.

In experiments, DNAFormer can read 100 megabytes of DNA storage data 90 times faster than the next fastest method developed with traditional rules-based computing algorithms, while achieving better or equivalent accuracy. I did. The decoded data included colored images of the test tube, a 24-second audio clip from astronaut Neil Armstrong's famous Moonlanding speech, and text on why DNA is a promising data storage medium .

The team says they plan to develop a version of DNAFormer tailored to new technologies for encoding data into DNA. Omar Savery Technion – Israel Institute of Technology.

“Crucially, our approach doesn't rely specifically on us. [DNA] Synthesis or sequencing methods can be adapted to future, still undeveloped technologies that are more commercially viable,” he says.

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Source: www.newscientist.com

Astronomers Decode the Calendar Ring of the Antikythera Mechanism

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The Antikythera Mechanism is a multi-part device recovered from a shipwreck near the Greek island of Antikythera in 1901. It is believed to be the remains of a complex mechanical calculator from ancient times and has undergone considerable scrutiny and analysis to determine its true form and function. In a new study, astronomers from the University of Glasgow have used statistical modelling techniques developed to analyse gravitational waves to identify the location of a hole under the Antikythera Mechanism's calendar ring. Their results provide new evidence that the component was likely used to track the Greek lunar calendar.

Fragment of the Antikythera Mechanism. Image credit: National Archaeological Museum of Athens / CC BY-SA 3.0.

The Antikythera shipwreck is a Roman shipwreck dating back to the 1st century BC (85-50 BC).

It is located at the junction of the Aegean and Mediterranean Seas, east of the Greek island of Antikythera, near Crete.

The Antikythera ships are thought to have been carrying looted treasure from the coast of Asia Minor to Rome in support of a planned triumphal parade for Julius Caesar.

The wreck was discovered in 1900 by a group of Greek sponge diggers on their way to Tunisia, who had taken refuge from a storm near the island and decided to look for sponges while waiting for calmer weather.

Early excavations at the site produced a wealth of finds that are today housed in the National Archaeological Museum in Athens, Greece, including three life-size marble horses, jewels, coins, glassware, and hundreds of works of art, including a statue of Hercules.

The most surprising find was the corroded remains of a complex device known as the Antikythera Mechanism, which is thought to have been an early analog computer used to plan important events such as religious ceremonies, the early Olympic Games and agricultural activities.

Also known as the first mechanical computer, this bronze device was created between 150 and 100 B.C.

It was originally housed in a wooden case with overall dimensions of 31.5 x 19 x 10 cm, with doors at the front and back and much of the exterior covered with astronomical inscriptions.

The surviving fragments contain 30 gears in an incredibly complex arrangement – technological artifacts of similar complexity would not appear until 1,000 years later.

In 2020, new X-ray images of one of the rings in the mechanism, known as the calendar ring, revealed new details about the regular rows of holes underneath the ring.

However, because the ring was broken and incomplete, it was unclear how many holes it originally had.

Initial analysis by Antikythera researcher Chris Budicelic and his colleagues suggests it probably dates to between 347 and 367 B.C.

Above: The 82 surviving fragments of the Antikythera Mechanism. Image courtesy of T. Freeth others2006. Below: Reconstruction of the Antikythera Mechanism by Alan Bromley and Frank Percival. Image courtesy of Alan Bromley.

In the new study, University of Glasgow researchers Graham Warne and Joseph Bayley used two statistical analysis methods to uncover new details about the calendar wheel.

The study found that it was far more likely that the ring had 354 holes corresponding to the lunar calendar, rather than 365 holes according to the Egyptian calendar.

The analysis also shows that the presence of 354 holes is hundreds of times more likely than a ring with 360 holes, which previous studies have suggested as a possible number.

“Late last year a colleague pointed me to some data available from YouTuber Chris Budiselic, who was trying to make a replica calendar ring and was researching ways to work out how many holes there are in the ring,” Prof Warne said.

“I thought this was an interesting problem and thought there might be a different way to solve it over the Christmas holidays, so I set out to answer the question using statistical methods.”

Using a technique called Bayesian analysis, which uses probability to quantify uncertainty based on incomplete data, Professor Warne used the positions of the remaining holes and the arrangement of the ring's six remaining fragments to calculate an estimated number of holes in the mechanism.

His findings provided strong evidence that the mechanism's calendar ring contained either 354 or 355 holes.

At the same time, Dr Bailey had also heard about the problem, and he was applying techniques used by his group to probe the calendar ring by analysing signals picked up by the LIGO gravitational wave detectors, which measure tiny ripples in space-time caused by massive astronomical events such as colliding black holes passing through Earth.

The Markov Chain Monte Carlo and nested sampling methods used by Professor Warne and Dr Bailey provided a comprehensive set of probabilistic results, again suggesting that the ring most likely contained 354 or 355 holes within a circle of radius 77.1mm, with an uncertainty of approximately 1/3mm.

They also found that the holes were precisely positioned with exceptional precision, with the average radius variation between each hole being just 0.028mm.

“Previous studies had suggested that the calendar ring was likely lunar based, but the dual techniques we applied in this study make it much more likely that this was the case,” Dr Bailey said.

“It gave me a new appreciation for the Antikythera Mechanism and the effort and care that Greek artisans put into creating it. Getting the holes exactly where they were would have required extremely precise measuring techniques and an incredibly steady hand to drill them.”

“This is a fascinating symmetry that allows us to apply techniques used to study the universe today to better understand the mechanisms that helped people around 2,000 years ago to understand the movements of celestial bodies,” Prof Warne said.

“While our discoveries about the Antikythera Mechanism are not as supernaturally spectacular as the Indiana Jones mechanism, we hope they will help us better understand how this incredible device was built and used by the Greeks.”

a paper A paper on the findings was published in the July 2024 issue. Watch Journal.

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Graham Warne & Joseph Baillie. 2024. The number of holes in the Antikythera Mechanism’s improved calendar ring: a new analysis. Watch Journal

This article has been adapted from an original release from the University of Glasgow.

Source: www.sci.news

Researchers successfully decode the genome of the elusive night parrot

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CSIRO researchers first genome of night parrot (Pezoporus occidentalis)one of the rarest and most elusive birds in the world.

night parrot (Pezoporus occidentalis). Image credit: Arianna Urso / Western Australian Museum.

The night parrot is a relatively small, short-tailed parrot species endemic to Australia.

This species is also known as the porcupine parrot, nocturnal ground parakeet, midnight parrot, solitaire, spinifex parrot, and nocturnal parakeet. first explained It was published in 1861 by British ornithologist John Gould.

The night parrot is one of the most elusive and mysterious birds in the world, with no confirmed sightings from 1912 to 1979.

They were once widespread in the arid regions of Australia, but their numbers have declined due to environmental changes such as predation by cats and foxes.

It is now known only from localized areas in south-west Queensland and Western Australia.

“Dozens of scientific specimens were collected in the 19th century, with one specimen collected in 1912. A specimen was then discovered in south-west Queensland in 1990,” says the CSIRO Australian National Wildlife Collection. said Dr. Leo Joseph, Director.

“A live bird was reported from the same area in 2013, and a live parrot was finally captured and tagged in 2015.”

“This genome will allow us to explore the genetic basis of why parrots are nocturnal, a trait that is very rare in parrots,” he added.

“We investigate functions such as navigation, sense of smell, beak shape, and suboptimal night vision.”

“Researchers will also be able to perform statistical analysis of this individual's genome to estimate the historical population size of Australia's night parrot.”

“We can now compare this annotated genome with other closely related parrot species, revealing the reasons behind its rarity and limited distribution compared to many closely related species. You can.”

Dr Joseph and his colleagues sequenced the armyworm genome using tissue obtained from specimens found in the Pilbara region.

“Access to high-throughput sequencing technology through CSIRO's Applied Genomics Initiative is accelerating genomics research in Australia,” said Dr Gunjun Pandey, CSIRO Environment Directorate Night Parrot Genomics Project Leader.

“We can now generate very high-quality genomes from very small tissue samples, as small as an ant's head or a single mosquito.”

“This level of quality and detail was not possible even five years ago.”

“Genetic data can be used to maximize diversity in conservation programs, so species are resilient and have the best chance of long-term survival.”

The night parrot genome is an exciting scientific resource for understanding more about this bird, but protecting this species from cats, foxes, fire, and habitat loss is also important for its conservation.

“The night parrot genome will open up many opportunities for further research that will help protect this species,” Dr. Pandey said.

“This will allow scientists to develop a plan to save the night parrot, with the ultimate goal of sequencing and publishing the genome.”

Source: www.sci.news