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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

Study Shows Nearly Two-Thirds of Dog Breeds Share Ancestry with Wolves

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A dog (Canis lupus familiaris) and a wolf (canis lupus) can interbreed to create fertile offspring, but such occurrences are far less common than in domestic and wild populations of other species. In a recent study, researchers from the American Museum of Natural History, the Smithsonian National Museum of Natural History, and the University of California, Davis, combined localized ancestry estimation with phylogenetic analysis of the genomes of 2,693 ancient and modern dogs and wolves. They discovered that 64.1% of contemporary purebred dogs possess wolf ancestry in their nuclear genomes, stemming from admixture that occurred nearly 1,000 generations ago, while all analyzed free-ranging dog genomes showed signs of ancient wolf ancestry.

German shepherd puppy. Image credit: Marilyn Peddle / CC BY 2.0.

“Modern dogs, especially those kept as pets, seem quite distant from the often vilified wolves,” states Dr. Audrey Lin, a postdoctoral fellow at the American Museum of Natural History.

“However, certain wolf-derived traits are highly valued in our current dogs, and we have intentionally preserved them in this lineage.”

“While this research focuses on dogs, it reveals much about their wild relatives, the wolves.”

Dogs evolved from a gray wolf population that faced extinction due to human influence during the late Pleistocene, approximately 20,000 years ago.

Though wolves and dogs inhabit overlapping areas and produce fertile offspring, instances of interbreeding are infrequent.

Aside from rare cases of intentional interbreeding, there is limited evidence of genetic exchange between the two groups following dog domestication, which separated their gene pools.

“Prior to this study, prevailing theories posited that for a dog to be classified as such, it would need to have minimal or no wolf DNA,” remarked Dr. Lin.

“Yet, upon examining the modern dog genome closely, we found wolf DNA present.”

“This indicates that the dog’s genome can incorporate wolf DNA to varying extents without losing its identity as a dog.”

The researchers scrutinized historical gene flow between dogs and wolves utilizing 2,693 publicly accessible genomes from wolves, purebred dogs, village dogs, and other canids from the late Pleistocene to the present, sourced from the National Center for Biotechnology Information and the European Nucleotide Archive.

The findings revealed that 64.1% of breed dogs possess wolf ancestry in their nuclear genomes, a result of crossbreeding occurring about 1,000 generations ago.

Moreover, all genomes from village dogs (free-ranging canines residing near human settlements) displayed detectable wolf ancestry.

The Czechoslovakian wolfdog and Saarlos wolfdog, which were purposefully crossbred with wolves, exhibited the highest levels of wolf ancestry, ranging from 23% to 40% of their genomes.

The breeds considered most “wolf-like” include the Great Anglo-French Tricolor Hound (4.7% to 5.7% wolf ancestry) and the Shiloh Shepherd (2.7% wolf ancestry).

The Shiloh Shepherd is the result of breeding efforts that included wolf-dog hybrids aimed at producing healthier, family-friendly sheepdogs in the U.S., while the origins of the significant wolf ancestry in the Great Anglo-French Tricolor Hound (the prevalent modern hunting dog in France) remain enigmatic.

The Tamaskan is another “wolf-like” breed that emerged in the UK during the 1980s by selectively breeding huskies, malamutes, and others to achieve a wolf-like appearance, containing roughly 3.7% wolf ancestry.

Researchers identified several patterns within the data. Larger dogs and those bred for specific tasks, such as arctic sled dogs, “pariah” breeds, and hunting dogs, exhibited higher levels of wolf ancestry.

Terriers, gundogs, and scent hounds typically have the least wolf ancestry on average.

While some large guardian breeds have wolf ancestry, others, such as the Neapolitan Mastiff, Bullmastiff, and St. Bernard, showed no signs of wolf ancestry.

Interestingly, wolf ancestry was also detected in a variety of dog breeds, including the miniature Chihuahua, which has around 0.2% wolf ancestry.

“This shouldn’t surprise anyone who owns a Chihuahua,” Dr. Lin noted.

“What we’ve discovered is that this is actually common. Most dogs have a hint of ‘wolfishness’ in them.”

The authors also analyzed the frequency with which personality traits were assigned to breeds labeled with high versus low levels of wolf ancestry by Kennel Clubs.

Breeds with lower wolf ancestry were often described as “friendly,” followed by terms like “eager to please,” “easy to train,” “courageous,” “active,” and “affectionate.”

Conversely, dogs exhibiting higher wolf ancestry were more frequently characterized as “independent,” “dignified,” “alert,” “loyal,” “discreet,” “territorial,” and “suspicious of strangers.”

Traits such as “smart,” “obedient,” “good with kids,” “dedicated,” “calm,” and “cheerful” appeared with relative consistency across both groups of dogs.

The researchers clarified that these traits reflect a biased assessment of behavior and that it’s uncertain whether wolf genes directly influence these characteristics, though their findings lay the groundwork for future explorations in canine behavioral science.

Additionally, significant adaptations inherited from wolves were uncovered. For instance, the wolf ancestry in village dogs enhances their olfactory receptor genes, crucial for locating human food waste, and distributions of Tibetan wolf-like genes assist Tibetan mastiffs in surviving low-oxygen conditions on the Tibetan Plateau and Himalayas.

“Dogs are our companions, but it appears that wolves significantly influenced their evolution into the beloved partners we cherish today,” commented Dr. Logan Kistler from the National Museum of Natural History.

“Throughout history, dogs have tackled numerous evolutionary challenges that arise from living alongside humans, such as thriving at high altitudes, foraging for food around villages, and safeguarding their packs. They seem to leverage wolf genes as part of their adaptive toolkit for an ongoing evolutionary success story.”

For more details, check the findings published this week in Proceedings of the National Academy of Sciences.

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Audrey T. Lin et al. 2025. The legacy of genetic intertwining with wolves has shaped the modern dog. PNAS 122 (48): e2421768122; doi: 10.1073/pnas.2421768122

Source: www.sci.news

New DNA research reveals insights into the ancient ancestry of Australia’s dingoes

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Dingo (Dingo) are an iconic element of Australia’s biodiversity, but evidence-based management and conservation of dingoes depends on understanding their origins and population history. New ResearchIssued this week Proceedings of the National Academy of SciencesResearchers have sequenced the genome of an ancient dingo individual, providing clues about the early history of dingoes in Australia, prior to the introduction of modern domestic dogs and the persecution of dingoes by European settlers. The results provide insight into the ancestry and origins of modern dingoes, including their relationship to the singing dogs of New Guinea, and will be a valuable resource for future developments in dingo management and conservation.

Dingoes are culturally and ecologically important free-living canines whose ancestors arrived in Australia more than 3,000 years ago, likely carried by sea voyagers. Image courtesy of Karlel.

Modern dingoes are free-ranging and naturalized Canine They live on most of mainland Australia and some of the nearby islands, including K'gari (known as Fraser Island from the 1840s until 2023).

Between the arrival of their ancestors in Australia at least 3,000 years ago and the introduction of domestic dog breeds as part of European colonisation beginning in the 18th century, dingoes were isolated from domestic dogs for thousands of years and represent an early 'primitive dog' lineage distinct from other free-ranging representatives of modern domestic dogs.

The early branching and free-living nature of dingoes means they were not subjected to the same intensive selective breeding as the ancestors of modern domestic dogs.

As a result, dingoes are behaviorally, genetically and anatomically distinct from domestic dogs and, as the continent's largest and most widespread terrestrial predator, they affect the distribution and populations of many other animal species.

“Dingoes have cultural significance to Aboriginal and Torres Strait Islander people and play a vital role in Australia's ecosystems,” said University of Adelaide researcher Dr Yasin Suirmi.

“Understanding the historical population structure of dingoes will help us to protect their role in Australia's ecosystems and culture.”

“Dingoes are currently under threat from lethal culling programs and our research highlights the importance of protecting populations both inside and outside national parks.”

For the study, Dr Suirmi and his colleagues sequenced genetic data from 42 dingo specimens taken from coastal Western Australia, the Nullarbor Plain and coastal eastern Australia, stretching more than 3,000 kilometres from east to west.

The majority of the dingo specimens the researchers analysed predate the arrival of Europeans in Australia, with some dating back more than 2,000 years, and therefore represent the true genetic diversity of dingoes before they interbred with modern domestic dog breeds.

“This dataset provides a rare glimpse into the genetic landscape of pre-colonial dingoes, without any interbreeding with modern dog breeds,” said Dr Sally Wasef, a palaeogeneticist at Queensland University of Technology.

“As a result, they are behaviorally, genetically and anatomically different from domestic dogs.”

“The ancestors of modern dingoes arrived in Australia more than 3,000 years ago, probably carried there by seafarers.”

“The samples we analysed represent the oldest ancient DNA ever found in Australia and point to broad potential for future DNA and conservation action for dingoes and other animals.”

“Dingo populations have been divided into eastern and western groups and were previously thought to have formed during post-colonial human activity.”

“However, our results show that dingo population structure was already present thousands of years ago, shedding light on the dingo's genetic heritage and highlighting the importance of using ancient DNA for wildlife conservation.”

“For example, all of the K'gari dingoes we analysed are free of domestic dog blood, proving they have retained their ancestral heritage intact.”

“Although we only studied a small number of K'gari dingoes, our results highlight the importance and usefulness of ancient pre-colonial genomic data in conserving our unique native fauna.”

“Bad human behaviour has led some dingoes to take food from tourists so although a few problem dingoes have been culled, this is concerning given the small population.”

“Our unique dataset of ancient dingo DNA has helped us to reveal important details about the ancestry and migration patterns of modern dingoes,” Dr Suirmi said.

“Dingoes existed in Australia long before Europeans arrived, with distinct regional populations roughly separated along the Great Dividing Range, and certainly before the construction of the dingo-proof fence.”

“DNA analysis also shows that there has been less interbreeding between dingoes and modern dogs than previously thought, and our study confirms that today's dingoes retain a significant amount of their ancestral genetic diversity.”

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Yasin Suirmi others2024. Ancient genomes reveal dingo population structure over 2,000 years. PNAS 121(30):e2407584121; doi:10.1073/pnas.240758412

Source: www.sci.news