Study provides snapshots of mammoth genetic diversity throughout the last million years

Stockholm University

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Woolly mammoth molar (Mammuthus primigenius) from the Old Crow river, Yukon Territory Canada.

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Credit: Photo credit: Hans Wildschut

A new genomic study has uncovered long-lost genetic diversity in mammoth lineages spanning over a million years, providing new insights into the evolutionary history of these animals.

The new study has successfully extracted and analysed 34 new mammoth mitochondrial genomes (mitogenomes), including specimens dating back to the Early and Middle Pleistocene geological periods. A total of 11 specimens come from these periods, with their ages spanning from 1.3 million to 125 000years ago. The findings, published in Molecular Biology and Evolution, shed light on mammoth evolutionary history and demonstrate the power of ancient DNA in characterising past genetic diversity.

“Our analyses provide an unprecedented glimpse into how major deep-time demographic events might have shaped the genetic diversity of mammoths through time”, said Dr J. Camilo Chacón-Duque, researcher at the Department of Zoology, Stockholm University, and Centre for Palaeogenetics and lead author of the study.

A million years of mammoth evolution

Most of today’s biodiversity evolved during the last 2.5 million years. Understanding the evolutionary processes that shaped this diversity requires access to genetic information throughout this timeframe. Until now, very few DNA samples have surpassed the 100-thousand-year threshold due to preservation challenges. By recovering DNA from mammoth specimens spanning over more than a million years, this study showcases the importance of temporal sampling to characterise the evolutionary history of species.

By analysing these new mitogenomes alongside over 200 previously published mammoth mitogenomes, the researchers were able to find that diversification events across mammoth lineages seem to coincide with well described demographic changes during the Early and Middle Pleistocene. Their findings support an ancient Siberian origin for major mammoth lineages and reveal how shifts in population dynamics might have contributed to the expansion and contraction of distinct genetic clades.

“With the ever-decreasing costs of sequencing technologies, mitogenomes have been somewhat forgotten. However, our study shows that they remain crucial for evolutionary biology since they are more abundant than nuclear DNA,” said Dr Jessica A. Thomas Thorpe, researcher at the Wellcome Sanger Genome Institute (UK) and co-first author of the study.

A big contribution to evolutionary biology

The study not only advances our understanding of mammoth evolution but also contributes to the broader field of ancient DNA research. The team developed and applied an improved molecular clock dating framework, refining how genetic data can be used to estimate the ages of specimens beyond the radiocarbon dating limit. This methodological advancement offers a powerful tool for future research on extinct and endangered species.

“These results add to our earlier work where we reported million-year-old genomes for the first time. I’m very excited that now we have genetic data from many more mammoth specimens sampled across the last million years, which helps us understand how mammoth diversity has changed through time,” said senior author professor Love Dalén at Stockholm University and Centre for Paleogenetics.

Read article in Molecular Biology and Evolution https://doi.org/10.1093/molbev/msaf065

Read more about Centre for Palaeogenetics
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Key Findings and Future Implications

• The study includes 34 newly sequenced mammoth mitogenomes, with 11 dating back over 100 000 years, increasing substantially the number of mammoth DNA samples beyond this time point, pushing the boundaries of ancient DNA research.
• The team identified the oldest known mammoth DNA in North America, from a specimen found in the Old Crow River, Yukon Territory, Canada and dating to more than 200 000 years ago.
• Their results confirm previous research (van der Valk et al., 2021), showing that mammoths from around a million years ago do not closely resemble later mammoths.
• The study refines DNA-based methods for estimating the ages of ancient specimens, paving the way for more accurate reconstructions of evolutionary histories.

By combining cutting-edge molecular techniques with computational advances, this research highlights the critical role of deep-time DNA in uncovering the genetic past of extinct species. Future studies may apply these methodologies to other long-extinct or endangered species, further enriching our understanding of evolutionary biology.

 

Contact:
J Camilo Chacón-Duque, researcher at the Department of Zoology, Stockholm University, and Centre for Palaeogenetics
Phone: +44 76 112 9754 E-mail: camilo.chacon-duque@su.se

Love Dalén, professor at the Department of Zoology, Stockholm University, and Centre for Palaeogenetics
Phone: ++46 707772794 E-mail: love.dalen@zoologi.su.se

Jessica A. Thomas Thorpe, researcher at the Wellcome Sanger Genome Institute
E-mail: jt30@sanger.ac.uk

Love Dalén Photo: Gleb Danilov

J Camilo Chacón-Duque  Photo credit: Natalia Romagosa

Photos:
The Old Crow mammoth.
Woolly mammoth molar (Mammuthus primigenius) from the Old Crow river, Yukon Territory Canada. Photo credit: Hans Wildschut 

J Camilo Chacón-Duque  Photo Natalia Romagosa

Love Dalén Photo: Gleb Danilov

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Journal

Molecular Biology and Evolution

DOI

10.1093/molbev/msaf065 

Subject of Research

Animals

Article Publication Date

9-Apr-2025

 

Jurassic fossil sheds light on evolutionary origins of thorny-headed worms

Chinese Academy of Sciences Headquarters

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Juracanthocephalus (a, overall view; b, artistic reconstruction) and the comparison with extant Acanthocephala (c). Scale bars, 2.0 mm (a, b), 0.5 mm (c).

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Credit: Image by YANG Dinghua

A research team from the Nanjing Institute of Geology and Palaeontology of the Chinese Academy of Sciences has identified a fossil acanthocephalan, Juracanthocephalus, from the 160-million-year-old Daohugou Biota in Inner Mongolia, China. This finding was published in Nature.

Acanthocephalans, commonly known as thorny-headed or spiny-headed worms, are a group of endoparasitic worms found in both marine and terrestrial ecosystems. These medically significant parasites infect a wide range of hosts, including humans, pigs, dogs, cats, and fish. Acanthocephalans are characterized by their worm-like body shape and a retractable proboscis armed with rows of recurved (i.e., backward-facing) hooks for anchoring to the digestive tracts of their hosts. Historically classified as a distinct animal phylum, their highly specialized body plan has led to ongoing debates regarding their phylogenetic position.

Morphological studies have proposed various hypotheses linking acanthocephalans to Platyhelminthes (flatworms), Priapulida (penis worms), or Rotifera (wheel animals). However, molecular phylogenetic analyses strongly suggest that acanthocephalans are a highly specialized subgroup within Rotifera. Despite this, the morphological disparity between endoparasitic acanthocephalans and free-living rotifers remains striking.

Furthermore, the fossil record of acanthocephalans is exceptionally sparse due to their soft bodies—which were less likely to fossilize than harder ones—and concealed habitats. Until now, the only known fossil evidence consisted of four putative acanthocephalan eggs discovered in the coprolites of a Late Cretaceous crocodyliform. Due to the lack of body fossils, the origin and early evolution of acanthocephalans thus remain poorly understood.

Using scanning electron microscopy (SEM) and energy-dispersive spectroscopy (EDS), the research team conducted a detailed anatomical analysis of Juracanthocephalus and  updated the morphological matrix of worm-like animals to support a comprehensive phylogenetic analysis.

The results indicate that Juracanthocephalus represents a transitional form between free-living, jawed rotifers and jawless, endoparasitic acanthocephalans, bridging an evolutionary gap. This finding provides the first direct fossil evidence to help resolve the long-standing mystery of acanthocephalan origins.

Juracanthocephalus has a fusiform body divided into a proboscis, neck, and trunk. The proboscis is equipped with strongly sclerotized, slightly curved hooks, while the ventral surface of the trunk features 38 lines of transverse, setaceous combs—a trait comparable to modern acanthocephalans. A possible alimentary tract is preserved in the proboscis, though no clear gut is visible in the trunk. The terminal end of the fossil displays a structure resembling the bursa of male acanthocephalans.

Notably, Juracanthocephalus has a jaw apparatus composed of clustered, tooth-like units arranged in converging paired rows, with the jaws increasing in size posteriorly. This structure closely resembles that found in Gnathifera, a group that includes Gnathostomulida, Micrognathozoa, and Syndermata (which encompasses Rotifera and Acanthocephala).

To determine the phylogenetic position of Juracanthocephalus, the research team compiled an updated morphological matrix incorporating both extant and extinct worm-like animals. The analysis identifies Juracanthocephalus as a stem-group acanthocephalan, sister to all extant acanthocephalans. This finding aligns with molecular phylogenetic analyses, which place acanthocephalans within Rotifera (including Monogononta, Bdelloidea, and Seisonidea).

However, the precise placement of acanthocephalans within Rotifera remains contentious, with six competing hypotheses arising from molecular and morphological studies. When Juracanthocephalus is excluded from the morphological matrix, the results support Seisonidea as the sister group to all other Rotifera, consistent with previous morphological analyses but conflicting with molecular data.

Conversely, incorporating Juracanthocephalus into the matrix positions Seisonidea as the sister group to Juracanthocephalus and all extant acanthocephalans, reconciling morphological and molecular phylogenetic analyses.

The discovery of Juracanthocephalus provides a crucial reference for understanding the evolutionary innovations and body plan of acanthocephalans. Its hooked proboscis and large body size suggest that it was an endoparasite during the Jurassic period. Furthermore, this fossil implies that acanthocephalans may have originated in terrestrial environments and diverged from Rotifera no later than the Middle Jurassic.

This study underscores the importance of transitional fossils in elucidating radical morphological changes in animal body plans. While molecular phylogenetics has revolutionized our understanding of evolutionary relationships, Juracanthocephalus highlights the indispensable role of fossil evidence in reconstructing the history of life.

The research was supported by the National Natural Science Foundation of China, the IUGS "Deep-time Digital Earth" Big Science Program, and the Jiangsu Innovation Support Plan for International Science and Technology Cooperation Programme.

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Journal

Nature

DOI

10.1038/s41586-025-08830-5 

The backscatter scanning electron (BSE) image (a), overlay image of several elements concentrations (b) and elemental maps of carbon from energy-dispersive X-ray spectroscopy (c) of Juracanthocephalus. Scale bar, 2.0 mm.

Simplified cladogram of Gnathifera showing Juracanthocephalus in red color

Phylogenetic tree from 50% majority rule bootstrap consensus tree of parsimony analysis. When Juracanthocephalus is included in the matrix, the results recover Seisonidea as the sister group to Juracanthocephalus + all extant acanthocephalans (a); when Juracanthocephalus is excluded from the morphological matrix, the results support the Seisonidea as the sister group of all other Rotifera (b

Credit

Image by NIGPAS

 

Longest known seafaring venture 8,500 years ago brings hunter-gatherers to Malta before early farmers

Griffith University

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Cave site of Latnija in the northern Mellieħa region of Malta.

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Credit: Huw Groucott

Seafaring hunter-gatherers were accessing remote, small islands such as Malta thousands of years before the arrival of the first farmers, a new international study has found.

Published in Nature, the research team – led by Professor Eleanor Scerri of the Max Planck Institute of Geoanthropology (MPI-GEA) and the University of Malta – found hunter-gatherers were crossing at least 100km of open water to reach the Mediterranean island of Malta 8,500 years ago, a thousand years before the arrival of agricultural practises.

This report documented the oldest long-distance seafaring in the Mediterranean, before the invention of boats with sails – an astonishing feat for hunter-gatherers likely using simple dugout canoes.

At the cave site of Latnija in the northern Mellieħa region of Malta, the research team found the traces of humans in the form of their stone tools, hearths, and cooked food waste.

Small, remote islands were long thought to have been the last frontiers of pristine natural systems.

Humans were not thought to have been able to reach or inhabit these environments prior to the dawn of agriculture, and the technological shift that accompanied this transition.

“Even on the longest day of the year, these seafarers would have had over several hours of darkness in open water,” said Professor Nicholas Vella of the University of Malta, co-investigator of the study.

Dr Mathew Stewart, from Griffith University’s Australian Research Centre for Human Evolution, analysed the animal remains from this site as part of the study.

“At the site we recovered a diverse array of animals, including hundreds of remains of deer, birds, tortoises, and foxes.” Dr Stewart said.

“Some of these wild animals were long thought to have gone extinct by this point in time,” added Professor Scerri.

“They were hunting and cooking red deer alongside tortoises and birds, including some that were extremely large and extinct today.”

In addition to this, the team of researchers found clear evidence for the exploitation of marine resources.

“We found remains of seal, various fish, including grouper, and thousands of edible marine gastropods, crabs and sea urchins, all indisputably cooked,” said Dr James Blinkhorn of the University of Liverpool and MPI-GEA, one of the study’s corresponding authors.

“The incorporation of a diverse range of terrestrial and, especially, marine fauna into the diet likely enabled these hunter-gatherers to sustain themselves on an island as small as Malta,” added Dr Stewart.

These discoveries also raised questions about the extinction of endemic animals on Malta and other small and remote Mediterranean islands, and whether distant Mesolithic communities may have been linked through seafaring.

“The results add a thousand years to Maltese prehistory and force a re-evaluation of the seafaring abilities of Europe’s last hunter-gatherers, as well as their connections and ecosystem impacts,” Professor Scerri said.

The findings ‘Hunter-gatherer sea voyages extended to remotest Mediterranean islands’ have been published in Nature.

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Journal

Nature

DOI

10.1038/s41586-025-08780-y 

Article Title

Hunter-gatherer sea voyages extended to remotest Mediterranean islands

Mediterranean hunter gatherers navigated long-distance sea journeys well before the first farmers

Max Planck Institute of Geoanthropology

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Hunter-gatherers were crossing at least 100 km of open water to reach the Mediterranean island of Malta 8,500 years ago, a thousand years before the arrival of the first farmers

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Credit: Daniel Clark / MPI GEA

Small, remote islands were long thought to have been the last frontiers of pristine natural systems. Humans are not thought to have been able to reach or inhabit these environments prior to the dawn of agriculture, and the technological shift that accompanied this transition.

In a paper published in Nature, new evidence shows that hunter-gatherers were crossing at least 100 kilometers (km) of open water to reach the Mediterranean island of Malta 8,500 years ago, a thousand years before the arrival of the first farmers. This report documents the oldest true long-distance seafaring in the Mediterranean, before the invention of boats with sails - an astonishing feat for hunter-gatherers likely using simple dugout canoes.

“Relying on sea surface currents and prevailing winds, as well as the use of landmarks, stars, and other wayfinding practices, a crossing of about 100 km is likely, with a speed of about 4 km per hour. Even on the longest day of the year, these seafarers would have had over several hours of darkness in open water,” explains Professor Nicholas Vella of the University of Malta, co-investigator of the study.

The discoveries were made by a scientific consortium led by Professor Eleanor Scerri of the Max Planck Institute of Geoanthropology (MPI-GEA) and the University of Malta. At the cave site of Latnija in the northern Mellieħa region of Malta, the researchers found the traces of humans in the form of their stone tools, hearths, and cooked food waste. “We found abundant evidence for a range of wild animals, including Red Deer, long thought to have gone extinct by this point in time,” explains Prof. Scerri. “They were hunting and cooking these deer alongside tortoises and birds, including some that were extremely large and extinct today.”

In addition to this, the team of researchers found clear evidence for the exploitation of marine resources. “We found remains of seal, various fish, including grouper, and thousands of edible marine gastropods, crabs and sea urchins, all indisputably cooked,” adds Dr James Blinkhorn of the University of Liverpool and MPI-GEA, one of the study’s corresponding authors.

These discoveries also raise questions about the extinction of endemic animals on Malta and other small and remote Mediterranean islands, and whether distant Mesolithic communities may have been linked through seafaring.

“The results add a thousand years to Maltese prehistory and force a re-evaluation of the seafaring abilities of Europe’s last hunter-gatherers, as well as their connections and ecosystem impacts,” adds Prof. Scerri.

The research was supported by Malta’s Superintendence of Cultural Heritage, and funded by the European Research Council and the University of Malta’s Research Excellence Award

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Remains found at the site during excavations

Credit

Eleanor Scerri

Excavations at the cave site of Latnija by the scientific consortium led by Professor Eleanor Scerri of the Max Planck Institute of Geoanthropology (MPI-GEA) and the University of Malta.

Credit

Huw Groucutt

Hunter-gatherer sea voyages ex [VIDEO] 

Journal

Nature

DOI

10.1038/s41586-025-08780-y 

Article Title

Hunter-gatherer sea voyages extended to remotest Mediterranean islands

Article Publication Date

9-Apr-2025