Differing uses for local and imported donkeys in Early Bronze Age Israel

 Archaeological excavations of an Early Bronze Age III (c. 2900–2600/2550 BCE) domestic neighborhood at the site of Tell eṣ-Ṣâfi/Gath, Israel, uncovered four complete skeletons of young female donkeys that were buried immediately below house floors as ritual foundation deposits. Multi-isotope analyses (carbon, oxygen and strontium) of their teeth document that each of the donkeys was born and raised in Egypt before being brought to Tell eṣ-Ṣâfi/Gath where they were slaughtered and buried beneath house floors in a non-elite domestic neighborhood. 

In contrast, isotopic analysis of teeth from a single isolated donkey mandible and additional sheep and goat teeth that displayed evidence of being used for food consumption and not associated with a complete burial, identify the donkey as born and raised among local livestock in the vicinity of Tell eṣ-Ṣâfi/Gath. The intentionally buried of specifically imported and highly valued young jennies reveal what appears to be a ritually charged characteristic when constructing domestic residences at the site.

Gantangqing site in southwest China yields 300,000-year-old wooden tools

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New discoveries from the Pleistocene-age Gantangqing site in southwestern China reveal a diverse collection of wooden tools dated from ~361,000 to 250,000 years ago, marking the earliest known evidence of complex wooden tool technology in East Asia. The findings reveal that the Middle Pleistocene humans who used these tools crafted the wooden implements not for hunting, but for digging and processing plants. Although early humans have worked with wood for over a million years, wooden artifacts are quite rare in the archaeological record, particularly during the Early and Middle Pleistocene. Most ancient wooden tools have been found in Africa and western Eurasia, with notable examples that include spears and throwing sticks from Germany and the UK, dating back 300,000 to 400,000 years, as well as structural elements like interlocking logs from Zambia and wooden planks and digging sticks from sites in Israel and Italy. While the long-standing Bamboo Hypothesis argues that early East Asian populations relied on bamboo for toolmaking, archaeological evidence for organic material-based tools from the region is scarce.

 

Here, Jian-Hui Liu and colleagues present new findings from the Gantangqing site in southwestern China, which has yielded a wide range of artifacts. Among these are 35 wooden artifacts that exhibit clear evidence of intentional shaping and use, including signs of carving, smoothing, and wear, suggesting that they were purposefully crafted by hominins. These tools, most of which were fashioned from pine, range from large two-handed digging sticks to smaller hand-held implements, and even include hook-like tools potentially used for cutting plant roots. According to Liu et al., compared to other well-known contemporaneous wooden tool sites in Europe, which are generally characterized by medium-sized hunting gear, Gantangqing stands out for its broader and more diverse array of small, hand-held tools designed primarily for digging up and processing plants. The sophistication of these wooden tools underscores the importance of organic artifacts in interpreting early human behavior, particularly in regions where stone tools alone suggest a more “primitive” technological landscape, say the authors.

Monumental structures built by hunter-gatherer groups: burial mounds in the Peruvian Andes

 Archaeologists have long thought that monumental architecture — large, human-built structures that emphasize visibility — were products of societies with power structures, including social hierarchy, inequality and controlled labor forces. But this notion is being questioned as researchers uncover evidence that hunter-gatherer groups also built such structures.

In new research published June 24 in the journal Antiquity, University of California researchers report evidence of monumental structures built by hunter-gatherer groups at Kaillachuro, a collection of burial mounds located in the Titicaca Basin of the Peruvian Andes. The discovery places monumental architecture in the region 1,500 years earlier than previously thought, researchers said.

“Most researchers in the Andes argue that monumental architecture is a product of elites, intentionally constructed as a space of centralized power,” said the study’s corresponding author Luis Flores-Blanco, who conducted the research while a doctoral student in anthropology at UC Davis. “We propose that monumentality can emerge from hunter-gatherer groups without institutionalized inequality.”

The study — co-authored by Mark Aldenderfer, a professor emeritus of anthropology and heritage studies at UC Merced — suggests that ritual memory of the dead played a key role in the rise of monumental architecture in the region.

Burial activity began modestly, researchers said, with simple pits in the ground.

Over time, these practices evolved into the construction of stone masonry burial boxes that were eventually covered by mounds of debris resulting from ongoing rituals and remembrances of the community’s ancestors.

2,000 years of communal memorialization

The sites at Kaillachuro were built over a period of 2,000 years. Using radiocarbon dating, researchers suggest that these mounds are the earliest evidence of monumental architecture in the Titicaca Basin, with construction beginning about 5,300 calendar years before the present day. This is 1,500 years earlier than monumental architecture was thought to exist in the region.

“Kaillachuro is an extraordinary find because it shows that mounds were used in ritual contexts for over 2,000 years — though not necessarily continuously,” said Flores-Blanco, who is now a postdoctoral researcher at Arizona State University. “Our study shows that rituals surrounding the dead can, through repeated action, generate visible monumental formations in the landscape.”

Discovered in 1995 by Aldenderfer, Kaillachuro consists of nine low-lying mounds. Subsequent surveys and excavations of the mounds in the succeeding years uncovered human burials and stone tools, including projectile points, among other items.

The researchers theorize that Kaillachuro’s construction started when egalitarian hunter-gatherer groups began living in one place, allowing for population aggregation, low-level food production, expanded exchange networks and the development of bow-and-arrow technology.     

“In this way, Kaillachuro was not initially planned as a mound site, but rather developed gradually through ongoing acts of burial ritual and remembrance tied to the community’s ancestors,” Flores-Blanco said.

An emphasis on remembrance of the dead

The study suggests an alternative pathway to mounded architecture that emphasizes community and ritual memory of the dead over societal power structures. In this instance, memory of the dead didn’t merely remain symbolic, but manifested as a materially visible architectural form.

“In many societies, the burial of ancestors compels us to return, reminisce and mark a space as special,” Flores-Blanco said. “At Kaillachuro, this happened in a similar way — though here, these repetitive practices formed mounds that not only shaped the landscape, but likely also influenced the practices of the living. This form of construction, rooted in communal memory, is what makes it monumental.”

The research was supported by the National Science Foundation, the H. John Heinz III Charitable Trust, the Rust Family Foundation, the American Philosophical Society, the Instituto Francés de Estudios Andinos - Carlos Brignardello Grant, and the National Geographic Society. 

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Journal

Antiquity

DOI

10.15184/aqy.2025.40 

A rare form of leprosy existed in the Americas for thousands of years

 

A new study has reconstructed two 4000-year-old genomes from the rare pathogen Mycobacterium lepromatosis

Peer-Reviewed Publication

Max Planck Institute for Evolutionary Anthropology

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Skeleton that yielded a 4000-year-old M. lepromatosis genome.

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Credit: © Oscar Eduardo Fontana-Silva & Anna Brizuela

To the point

• Hansen’s Disease (leprosy) is thought to have originated in Eurasia: previous studies on Mycobacterium leprae, the dominant form of leprosy, suggest the disease originated in Eurasia. 
• Ancient pathogen genomes from old bones: a team of scientists from Germany and Argentina have reconstructed two genomes of Mycobacterium lepromatosis in 4000-year-old human skeletons from Chile. This pathogen is regarded as a second, less common, cause of Hansen’s Disease.
• A new American chapter for Hansen’s Disease: two pathogens that are responsible for the same disease evolved separately on opposite sides of the world for thousands of years.

Hansen’s Disease, more commonly known as leprosy, is a chronic disease that can lead to physical impairment. Today it exists in over 100 countries, and while the infection is treatable, access to treatment varies widely with socioeconomic conditions. Its mention in historical texts give us a glimpse into its past impact on population health in Europe and Asia. Prolonged untreated infection can result in characteristic changes in bone, and these have been documented in archaeological skeletons as early as 5000 years ago in Europe, Asia, and Oceania. So far, absence of these characteristic changes in the pre-contact American contexts suggests that leprosy was one of the many diseases introduced to the continent in the colonial period. Thereafter it afflicted humans and curiously also armadillos.

From a genetic perspective, Hansen’s Disease is caused by either the globally dominant Mycobacterium leprae or the newly identified and rare Mycobacterium lepromatosis. The recovery of M. leprae from archaeological bone in Europe suggests the disease originated in Eurasia sometime during the Neolithic transition about 7000 years ago. Similar emergence estimates have been proposed for other notorious diseases such as plague, tuberculosis, and typhoid fever. Ancient genomes for M. lepromatosis have remained elusive, and these may hold important clues on the history of Hansen’s Disease.

Past disease in the American continent

We know comparatively little about the infectious disease experience of the diverse communities of people living in the Americas before the colonial period. This accounts for almost 20,000 years of human history, and the diverse ecosystems into which humans integrated across the continent would have presented challenges to the immune system not otherwise encountered in other parts of the world. We know very little of these diseases, as they were smothered by the onslaught of pathogens that Europeans later brought with them. Archaeological study of human bones from the pre-contact Americas confirm that the time was far from disease-free, but often the traces seen on the bones aren’t specific enough to assign to a known disease. 

“Ancient DNA has become a great tool that allows us to dig deeper into diseases that have had a long history in the Americas”, says Kirsten Bos, group leader for Molecular Paleopathology at the Max Planck Institute for Evolutionary Anthropology. She and her team have been studying pathological bone from American context for over a decade. Some diseases that the group has found were expected – just last year they found evidence that the family of diseases closely related to syphilis had its roots in the Americas, which many had suspected. “The advanced techniques now used to study ancient pathogen DNA allows us to look beyond the suspects and into other diseases that might not be expected from the context”, she adds.

Re-writing the history of Hansen’s Disease

Bos’s team worked closely with researchers from Argentina and Chile to both identify bones suitable for analysis and to carry out the meticulous work of isolating the DNA of ancient pathogens. Doctoral candidate Darío Ramirez of the University of Córdoba, Argentina, worked extensively with such material, and was the first to identify a genetic signature related to leprosy in some 4000-year-old skeletons from Chile. “We were initially suspicious, since leprosy is regarded a colonial-era disease, but more careful evaluation of the DNA revealed the pathogen to be of the lepromatosis form”. This provided the first clue that M. lepromatosis and M. leprae, though nominally both pathogens that cause Hansen’s Disease, might have very different histories. Reconstruction of the genome was key in looking into this. While putting the molecular puzzle of an ancient genome back together is never an easy task, these pathogens in particular had “amazing preservation, which is uncommon in ancient DNA, especially from specimens of that age”, comments Lesley Sitter, a postdoctoral researcher in Bos’s team who carried out the analysis. 

The pathogen is related to all known modern forms of M. lepromatosis, but as there are so few genomes available for comparison, there is still much to be learned about it. This work has shown that a pathogen considered rare in a modern context caused disease for thousands of years in the Americas. Rodrigo Nores, professor of Anthropology at the University of Córdoba, Argentina is convinced that more cases, both ancient and modern, will be identified in the coming years: “this disease was present in Chile as early as 4000 years ago, and now that we know it was there, we can specifically look for it in other contexts”. Once more genomes surface, we’ll be able to piece out further details of its history and better understand its global distribution today. The pathogen has recently been discovered in squirrel populations from the United Kingdom and Ireland, but in the Americas it has yet to be found in any species other than humans. With such little data, mystery still surrounds its origin. “It remains to be determined if the disease originated in the Americas, or if it joined some of the first settlers from Eurasia”, adds Bos. “So far the evidence points in the direction of an American origin, but we’ll need more genomes from other time periods and contexts to be sure."

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Journal

Nature Ecology & Evolution

DOI

10.1038/s41559-025-02771-y 

Human fishing reshaped Caribbean reef food webs, 7000-year old exposed fossilized reefs reveal

 

A groundbreaking study of 7000-year-old exposed coral reef fossils reveals how human fishing has transformed Caribbean reef food webs: as sharks declined by 75% and fish preferred by humans became smaller, prey fish species flourished

Peer-Reviewed Publication

Smithsonian Tropical Research Institute

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Fieldwork at an exposed fossilized Caribbean reef located in the Dominican Republic

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Credit: Sean Mattson

When we think of fossils, giant prehistoric creatures like dinosaurs may come to mind. But the fossil record also holds the remains of smaller organisms, such as fish and corals, that tell us about our oceans’ past.

Scientists at the Smithsonian Tropical Research Institute (STRI) recently studied exposed fossilized coral reefs from Panama's Bocas del Toro Province and the Dominican Republic, comparing them with nearby modern reefs. These exceptionally well-preserved reefs date back 7,000 years, offering a unique window into what Caribbean reefs looked like before human impact. Within the fine sediments of these ancient reefs, the team discovered thousands of tiny fish ear bones and shark scales, allowing them to reconstruct entire ancient fish communities.

The results revealed a dramatic shift in fish communities over time: sharks have declined by 75% and human-targeted fish have become 22% smaller. But the real surprise came from the prey fish species — those eaten by predators like sharks. These have doubled in abundance and grown 17% larger on modern reefs. This study provides the first historical evidence for the "predator release effect" — where removing top predators allows their prey to flourish. Whilst scientists have long predicted such an effect, evidence for it was scarce without knowing what reefs looked like before human impact. Remarkably, the tiniest reef fish that shelter in coral crevices, showed no change in size or abundance over millennia. Their stability suggests a remarkable resilience to the multitude of changes occurring on reefs at higher layers of the food chain.

To compare fossilized and modern reefs, scientists collected, quantified and measured thousands of skeletal remains, including the tiny tooth-like scales that give shark skin a sandpapery texture, called dermal denticles.

To study the abundance and size of prey fish and small coral reef-sheltered fish (also known as cryptobenthic fishes), they also examined fish otoliths — the calcium carbonate structures found in fishes' inner ears. Because otoliths grow in layers, scientists can estimate a fish’s size at death. In total, the team examined 807 denticles and 5,724 otoliths.

The behavior of some organisms can also leave a fossil record. In this study, scientists measured the frequency and size of damselfish bite marks on coral branches from both fossilized and modern reefs. They found that the number of bites has increased in modern reefs — also indicating the rise in prey fish populations.

These results illustrate an important change in food webs of modern Caribbean reefs: with fewer sharks and other predatory fish to control the population of exposed prey fishes, they have become bigger and more abundant, reflecting release from predation. On the other hand, small reef-sheltered fish remained unchanged in size and abundance over thousands of years, suggesting that the degradation of water quality and habitat in the region did not drive the changes in community structure.

This study demonstrates the power of the fossil record for future conservation. By revealing what reefs looked like before intensive human fishing, these 7,000-year-old fossils provide the missing baseline critical to understand the food webs of pre-human coral reefs, and document which elements of reefs changed and which are resilient.

This research, published in the Proceedings of the National Academy of Sciences, PNAS, was a collaboration among scientists from the Smithsonian Tropical Research Institute (STRI), the Sistema Nacional de Investigación (SENACYT) in Panama, the Marine Science Institute at the University of Texas at Austin, the Center for Biodiversity Outcomes at Arizona State University, the Graduate School of Oceanography at the University of Rhode Island, The Nature Conservancy, the Biodiversity Research Center at Academia Sinica in Taiwan, the Department of Earth & Environmental Sciences at Boston College, and the Cotsen Institute of Archaeology and Department of Anthropology at the University of California, Los Angeles.

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Journal

India: 50,000 years of evolutionary history

 India’s population is genetically one of the most diverse in the world, yet it remains underrepresented in global datasets. In a study publishing in the Cell Press journal Cell, researchers analyzed genomic data from more than 2,700 people from across India, capturing genetic variation from most geographic regions, linguistic groups, and communities. They found that most modern-day Indian people’s ancestry can be traced back to Neolithic Iranian farmers, Eurasian Steppe pastoralists, and South Asian hunter-gatherers. 

“This study fills a critical gap and reshapes our understanding of how ancient migrations, archaic admixture, and social structures have shaped Indian genetic variation,” says senior author Priya Moorjani of the University of California, Berkeley. “Studying these subpopulations allows us to explore how ancient ancestry, geography, language, and social practices interacted to shape genetic variation. We hope our study will provide a deeper understanding of the origin of functional variation and inform precision health strategies in India.” 

The researchers used data from the Longitudinal Aging Study in India, Diagnostic Assessment of Dementia (LASI-DAD) and generated whole-genome sequences from 2,762 individuals in India, including people who spoke a range of different languages. They used these data to reconstruct the evolutionary history of India over the past 50,000 years at fine scale, showing how history impacts adaptation and disease in present-day Indians. They showed that most Indians derive ancestry from populations related to three ancestral groups: Neolithic Iranian farmers, Eurasian Steppe pastoralists, and South Asian hunter-gatherers. 

“In India, genetic and linguistic variation often go hand in hand, shaped by ancient migrations and social practices,” says lead author Elise Kerdoncuff of UC-Berkeley. “Ensuring linguistic variation among the people whose genomes we include helps prevent biased interpretations of genetic patterns and uncover functional variation related to all major communities to inform both evolutionary research and future biomedical surveys.”  

One of the key goals of the study was to understand how India’s complex population history has shaped genetic variation related to disease. In India, many subpopulations have an increased risk of recessive genetic disorders, which is due largely to historical isolation and marrying within communities.  

Another focus was on the impact of archaic hominin ancestry—specifically, Neanderthal and Denisovan—on disease susceptibility. For example, some of the genes inherited from these archaic groups have an impact on immune functions. 

“One of the most striking and unexpected findings was that India harbors the highest variation in Neanderthal ancestry among non-Africans,” says co-lead author Laurits Skov, also of UC-Berkeley. “This allowed us to reconstruct around 50% of the Neanderthal genome and 20% of the Denisovan genome from Indian individuals, more than any other previous archaic ancestry study.” 

One constraint of this work was the limited availability of ancient DNA from South and Central Asia. As more ancient genomes become available, the researchers will be able to refine this work and identify the source of Neolithic Iranian farmer and Steppe pastoralist-related ancestry in contemporary Indians. They also plan to continue studying the LASI-DAD cohort to enable a closer look at the source of the genetic adaptations and disease variants across India.  

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This research was supported by the National Institute on Aging and the University of Southern California. 

Cell, Kerdoncuff et al. “50,000 years of evolutionary history of India: Impact on health and disease variation” https://www.cell.com/cell/fulltext/S0092-8674(25)00462-3

The transition to agriculture and a sedentary lifestyle: How this Neolithic way of life spread from the Fertile Crescent to Anatolia

 The transition to agriculture and a sedentary lifestyle is one of the great turning points in human history. Yet how this Neolithic way of life spread from the Fertile Crescent across Anatolia and into the Aegean has been hotly debated. A Turkish-Swiss team offers important new insights, by combining archaeology and genetics in an innovative way.

How open are people to experimenting with new ways of life? Did farming spread from its origins in Anatolia to neighboring regions by farmers migrating? Or was it rather local hunter-gatherers adopting their neighbors’ ways of life? A new study, published in Science, now reconciles these opposing views. The authors find that this massive cultural change occurred through both phenomena – depending on the region and the period.

The research, led by geneticists and archaeologists at Middle East Technical University (METU) and Hacettepe University in Ankara (Turkey), and the University of Lausanne (UNIL, Switzerland), sheds light on a major turning point in human history. The team’s work shows that cultural changes took place not only due to the movement of people, but also through spread of ideas. “In some regions of West Anatolia, we see the first transitions to village life nearly 10,000 years ago. However, we also observe thousands of years of genetic continuity, which means that populations did not migrate or mix massively, even though cultural transition was definitely happening,” explains Dilek Koptekin, the study’s first author. 

A missing chapter in the Neolithic story

Previous research had already shown how agriculture gradually replaced hunting and gathering in Europe after 6,000 BCE, through the movement of farmers out of Anatolia (modern-day Turkey). But what happened before this tipping point, especially in Anatolia, remained unclear. “Our study allows us to go back in time – to events that were mainly a matter of speculation up to now,” says Koptekin.

This advancement was possible by sequencing the genome of a 9,000-year-old individual from West Anatolia, the oldest yet in the region. Combining this genome with 29 new paleogenomes as well as published data, the researchers found surprising genetic continuity in West Anatolia across seven millennia. “Genetically speaking, these people were mainly locals, meaning that their ancestors had not recently arrived from elsewhere. Yet their material culture evolved rapidly: they moved from caves to houses, and adopted new tools and rituals from afar. This suggests that these communities adopted Neolithic practices by cultural exchange rather than population replacement,” says computational biologist Anna-Sapfo Malaspinas from UNIL. 

How exactly did that happen? “The answer lies in what we call ‘background mobility’,” explains geneticist Mehmet Somel from METU. “This means a low but steady movement of individuals around different regions, perhaps linked to exchange, finding partners, or other motivations. These encounters then led to the sharing of material and ideas.” Such movement is illustrated by traces of obsidian, a volcanic glass used for tools, found in western Anatolia but sourced from central Anatolian volcanoes hundreds of kilometers away. Materials, and with them ideas, were apparently on the move. 

Ideas move further than people

Seeking deeper insights into this mobility, the team used an innovative approach, combining ancient DNA with archaeological material data. The researchers scoured hundreds of articles and quantified archaeological features such as pottery types, tools, and architectural remains. This allowed them to systematically compare materials with the genetic profiles of individuals buried at the same sites. “By giving quantitative values to the archaeological data, we were able to directly compare large amounts of data across different sites for the first time,” specifies archaeologist Çiğdem Atakuman from METU. The team thereby traced not only who moved where, but also how ideas and practices circulated.

The scientists’ findings challenge previous assumptions that new tools or objects necessarily indicate the arrival of a new population. “Archaeologists have this proverb, ‘Pots don’t equal people’. Our study confirms this notion,” comments Dilek Koptekin. 

An evolving mosaic

But this is not the whole story. In some areas of Anatolia, genetic data revealed both mobility and admixture of populations around 7,000 BCE. Here, new groups moved in, bringing both different genes and different practices. In the Aegean region, too, a later wave of population movement introduced further cultural elements that would eventually spread into Europe. 

“These types of migration events, which leave genetically visible shifts, probably comprised a small fraction of movement happening compared to background mobility,” says Füsun Özer from Hacettepe University. “The Neolithic, in this view, was not a single process, but a patchwork of transformations, combining cultural adoption, mobility, and at times, migration.” Koptekin adds, “Humans have always been adaptive and inclined to change their way of living. We don’t need crises or big migration events to bring about change.”

Conceptualized and led primarily by researchers based in Turkey, the study underscores the importance of supporting research in regions directly connected to the questions under investigation. For Anna-Sapfo Malaspinas, it is a valuable example of how extending large-scale funding opportunities beyond established scientific hubs strengthens underrepresented research communities. “Our collaboration shows how we, as a scientific community, should move forward to create a more inclusive and globally balanced research landscape,” concludes the biologist.

The methodological leap achieved in this study, integrating genomic and archaeological data at large scale for the first time, marks a turning point for prehistoric research. It allows future research to move beyond simple models and embrace more complex realities of human history.

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Journal

Science

DOI

10.1126/science.adr3326