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 

What animal bones reveal about life on the medieval Liao frontier

 

Peer-Reviewed Publication

The Hebrew University of Jerusalem

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Photographs of the Site 23 midden with some of the faunal assemblage and the whistling arrow 

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Credit: (Photo Credit - Tal Rogovski)

In the windswept steppe of northeastern Mongolia, archaeologists have unearthed a rare window into daily life along the medieval frontier of the Liao Empire. Excavations at a remote garrison site revealed thousands of animal bones—evidence of herding, hunting, fishing, and a harsh environment—offering a ground-level view of survival far from the imperial centers recorded in history books. The findings challenge traditional accounts by illuminating the lives of soldiers and civilians who lived not in palaces, but along the empire’s long and lonely wall.

In the remote steppe of northeastern Mongolia, far from the opulent courts and bustling cities of medieval East Asia, a buried trash heap is telling a different story of empire—one of survival, adaptation, and forgotten lives on the edge.

A new study led by doctoral candidate Tikvah Steiner of the Institute of Archaeology at the Hebrew University of Jerusalem, under the supervision of Prof. Gideon Shelach-Lavi and Prof. Rivka Rabinovich, has unearthed an unusually rich zooarchaeological deposit at Site 23—a garrison outpost along the 4,000-kilometer-long medieval wall system that once marked the shifting frontiers of the Liao Empire (916–1125 CE). The research is part of the ERC funded project “The Wall- people and ecology in medieval China and Mongolia”, led by Prof. Shelach-Lavi from the Dept. of Asian Studies at Hebrew University. The results, published in Archaeological Research in Asia, reveal a compelling portrait of life on the margins of empire: not just soldiers, but possibly their families and support staff raising livestock, supplemented by hunting and fishing, and enduring harsh climatic conditions—all in near-total absence from historical record.

Built by the semi-nomadic Kitan rulers of the Liao dynasty to secure their northern borders, the function and use of the long-wall system in present-day Mongolia and northern China is little understood. Despite its’ monumental scale, the wall and the people who lived along it are scarcely mentioned in the many historical texts of the period.But the trash heap—or midden—analyzed by Steiner’s team offers a more intimate glimpse into the empire’s outer defenses. Dated to around 1050 CE, the deposit contains over 7,000 animal bones, many of them remarkably well preserved. Sheep, goats, horses, dogs, gazelles, and even catfish—each bone, burn mark, and butchery cut opens a window into how this garrison survived.

“What we found was not just a military checkpoint supplied by a central power,” says Steiner. “This was a self- sufficient group—perhaps of soldiers, perhaps of civilians—managing livestock, crafting implements from bone, hunting and fishing in the local environment, possibly receiving some sort of supplies from the central power, and making choices about which animals to slaughter and when, all in a challenging and isolated environment.”

The analysis suggests a largely self-sufficient pastoral economy, with evidence of sheep and goat herding, horse breeding, some hunting of wild gazelle and mustelids, and seasonal fishing. The high number of neonatal animal remains—especially of lambs and puppies—suggests that this community may have suffered a devastating climatic event such as a late spring freeze, echoing historical accounts of environmental crises that strained the Liao Empire in its final decades.

Unlike the sweeping imperial chronicles of the Liaoshi, which glorify courtly hunting expeditions and tribute missions, the bones from Site 23 reveal the quiet, daily negotiations of life and death in the hinterlands. The presence of cattle phalanges split for marrow extraction, worked bones used as tools or ornaments, and even a rare whistling arrow carved from bone—all point to a resourceful, resilient population adapting imperial policy to local conditions.

“The historical texts focus on emperors, not outposts,” adds Prof. Rabinovich. “But archaeology lets us hear the voices of those who lived, worked, and died far from the palace. These bones are a form of testimony.”

The research marks a significant contribution to the interdisciplinary study of medieval Inner Asia, bridging the often-separate worlds of historical texts and material culture. It also provides an important comparative dataset for understanding frontier life across empires, from the Roman limes to the Great Wall of China.

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Journal

Archaeological Research in Asia

DOI

10.1016/j.ara.2025.100639 

New light on the stone alignments in the Carnac region

 

Peer-Reviewed Publication

University of Gothenburg

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Alignments of Carnac

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Credit: Bettina Schultz Paulsson

The enigmatic stone alignments in the Carnac region of Brittany, France, are among the most famous megalithic monuments in Europe – alongside Stonehenge, Menga, and the megalithic temples of Malta. For the first time, it has now been possible to date parts of these alignments with a higher precision and gain new insights into their function.

This breakthrough results from a French–Swedish collaboration within the framework of the ERC-funded research project NEOSEA, led by the University of Gothenburg in partnership with the French excavation company Archeodunum and the University of Nantes.

“The alignments in the Carnac region now appear to be among the earliest megalithic monuments in Europe, with this section constructed between 4600 and 4300 cal BC. We have also confirmed the Bay of Morbihan as the earliest megalithic region in Europe”,
says archaeologist Bettina Schulz Paulsson at the University of Gothenburg, who leads the NEOSEA project and is one of the researchers behind the new study published in Antiquity.

More than 3,000 standing stones stretch over 10 km in the region, from Carnac/La Trinité-sur-Mer to Erdeven, forming a unique concentration of megalithic alignments in a coastal landscape.

The archaeologists have excavated a previously unknown area, Le Plasker, bordering Carnac. In connection with this, they were able to carry out advanced analyses of the material, including radiocarbon dating – and statistical analyses of large series of radiocarbon dates, as well as sediment and charcoal analysis.

The rescue excavation at Le Plasker, located in the centre of Plouharnel, was conducted by the excavation company Archeodunum under the leadership of Audrey Blanchard, excavation director and researcher on the NEOSEA-project at University of Gothenburg, ahead of the development of a 7,000 m² business park. Better modern excavation technique combined with systematic sampling revealed numerous archaeological features.

“Thanks to nearly 50 radiocarbon dates and the application of Bayesian statistical modelling, we were able to reconstruct the site’s history with unprecedented chronological precision”, says Bettina Schulz Paulsson.

Bayesian modelling
Due to the acidic soils of the Morbihan, organic material – especially bone – rarely survives, which has long limited opportunities for radiocarbon dating in the region. Moreover, it is often impossible to confirm a connection between the dated charcoal samples and the erection of the standing stones and other methods, such as OSL dating (optically stimulated luminescence), often yield results that are too imprecise to support clear conclusions.

“However, with a sufficiently large dataset and Bayesian modelling, this challenge was overcome”, Schulz Paulsson explains.

Several alignments of standing stones were dated to between 4600 and 4300 cal BC. While the stones themselves have been removed – either in historical times or prehistory – their foundation pits remain. These pits were aligned alongside hearths or cooking pits, suggesting that the stone lines may have been constructed in association with fire-related features. Whether these hearths were used for lighting, cooking, or feasting during the erection of the stones remains unclear. Further analyses of sediments and stone fragments are ongoing.

The site also revealed a monumental early tomb, constructed around 4700 cal BC directly above the remains of a Mesolithic hunter-gatherer hut.

The study is published in Antiquity as open access: “Le Plasker in Plouharnel (fifth millennium cal BC): a newly discovered section of the megalithic complex of Carnac”
https://doi.org/10.15184/aqy.2025.10123

Early farmers in the Andes were doing just fine, challenging popular theory

 

Diet data shows consistent food resources during the transition from foraging to farming

Peer-Reviewed Publication

PLOS

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View of the Aymara community of Jachacachi, home to the archaeological sites of Kaillachuro and Jiskairumoko, which offer insights into the transition to agriculture in the Andean Altiplano.

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Credit: Luis Flores-Blanco, CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

In the Andes, the rise of agriculture to replace foraging was not the result of hardship and resource scarcity, but instead a time of economic resilience and innovation, according to a study published June 25, 2025 in the open-access journal PLOS One by Luis Flores-Blanco of the University of California Davis and Arizona State University, U.S., and colleagues.

The transition from foraging to farming was a major shift in human history that laid the foundations for the expansion of modern civilization. The current prevailing view is that this transition was a time of hardship, with communities forced to rely on crops due to growing human populations and dwindling wild food resources. In this study, Flores-Blanco and colleagues examine the diet of people living in the Andes throughout this transitional period.

The researchers interpreted ancient diets by measuring ratios of Carbon and Nitrogen isotopes from the bones of 16 individuals buried at the sites of Kaillachuro and Jiskairumoko in the Lake Titicaca Basin. Both sites were inhabited from approximately 5,000 to 3,000 years ago, during the transition from foraging to farming. Isotope signatures indicate a high proportion (84%) of plant material in the diet, supplemented by a smaller proportion of meat from large mammals. These proportions are not only consistent throughout this transitional time period at both sites, they are also identical to those of earlier foraging communities and later farming communities.

Altogether, these results contradict the image of an agricultural shift driven by hardship, and instead reveal that food resources remained consistent for thousands of years. Wild foods were increasingly managed and domesticated, creating mixed foraging-farming economies. The authors propose that this economic resilience was likely aided by certain cultural advances happening at this time, including expanding trade networks and innovations in ceramic and archery technologies.

Luis Flores-Blanco adds: "Our research shows that the origin of agriculture in the Titicaca Basin was a resilient process. Ancient Andean peoples relied on their deep knowledge of harvesting wild plants like potatoes and quinoa, as well as hunting camelids. With this understanding of their environment, they effectively managed their resources—domesticating both plants and animals—and gradually incorporated these domesticated species into their diet. So, the first Altiplano farmers continued to rely on the same foods consumed by Archaic foragers. In this research, we show that this Andean economy path made this transition both beneficial and stable."

"These discoveries come from integrating contributions from different specialized fields, from extracting dietary information from bones, analyzing macrobotanical remains, and running statistical analyses."

Luisa Hinostroza adds: "This article challenges the traditional idea that the transition to agriculture occurred out of necessity or periods of crisis. Our findings demonstrate, instead, that in the Altiplano, it was a process marked by stability and food sufficiency sustained for thousands of years. These results constitute crucial evidence revealing the capacity of Andean societies to efficiently manage their resources, such as tubers and grains, and maintain long-term stability."

 The freely available article in PLOS One: https://plos.io/44gu6Xe

Ancient canoe replica tests Paleolithic migration theory

 

Long-standing questions about migration of early modern humans in East Asia may finally be answered thanks to a rare and exciting voyage in a dugout canoe.

Peer-Reviewed Publication

University of Tokyo

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The team set out in their handmade canoe, making the entire experience as authentic as possible. ©2025 Kaifu et al. CC-By-ND

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Credit: ©2025 Kaifu et al. CC-By-ND

When and where the earliest modern human populations migrated and settled in East Asia are relatively well known. However, how these populations moved between islands on treacherous stretches of sea is still shrouded in mystery. In two new papers, researchers from Japan and Taiwan led by Professor Yousuke Kaifu from the University of Tokyo simulated methods ancient peoples would have needed to accomplish these journeys, and they used period-accurate tools to create the canoes to make the journey themselves.

Evidence suggests that around 30,000 years ago, humans made a sea crossing — without maps, metal tools or modern boats — from what is now called Taiwan to some of the islands in southern Japan, including Okinawa. To find out exactly how this crossing was made, a team led by Kaifu performed various simulations and experiments, including the use of physical recreations, to learn the most plausible way this crossing was achieved. Of the two newly published papers, one used numerical simulations to cross one of the strongest currents in the world called the Kuroshio. The simulation showed that a boat made using tools of the time, and the right know-how, could have navigated the Kuroshio. The other paper detailed the construction and testing of a real boat which the team successfully used to paddle between islands over 100 kilometers apart.

“We initiated this project with simple questions: ‘How did Paleolithic people arrive at such remote islands as Okinawa?’ ‘How difficult was their journey?’ ‘And what tools and strategies did they use?’” said Kaifu. “Archaeological evidence such as remains and artifacts can’t paint a full picture as the nature of the sea is that it washes such things away. So, we turned to the idea of experimental archaeology, in a similar vein to the Kon-Tiki expedition of 1947 by Norwegian explorer Thor Heyerdahl.”

In 2019, the team constructed a 7.5-meter dugout canoe called Sugime, built from a single Japanese cedar trunk, using replicas of 30,000-year-old stone tools. They paddled it 225 kilometers from eastern Taiwan to Yonaguni Island in the Ryukyu group, which includes Okinawa, navigating only by the sun, stars, swells and their instincts. They paddled for over 45 hours across the open sea, mostly without any visibility of the island they were targeting. Several years later, the team is still unpicking some of the data they created during the experiment, and use what they find to inform or test models about various aspects of sea crossings in that region so long ago.

“A dugout canoe was our last candidate among the possible Paleolithic seagoing crafts for the region. We first hypothesized that Paleolithic people used rafts, but after a series of experiments, we learned that these rafts are too slow to cross the Kuroshio and are not durable enough,” said Kaifu. “We now know that these canoes are fast and durable enough to make the crossing, but that’s only half the story. Those male and female pioneers must have all been experienced paddlers with effective strategies and a strong will to explore the unknown. We do not think a return journey was possible. If you have a map and know the flow pattern of the Kuroshio, you can plan a return journey, but such things probably did not take place until much later in history.”

To understand whether such a journey could have been made in different circumstances, the team also used advanced ocean models to simulate hundreds of virtual voyages. These simulations tested different starting points, seasons and paddling strategies under both modern and ancient ocean conditions.

“I major in oceanography and use numerical methods and particle tracking techniques to research things like eel and salmon migrations, pumice drift after volcanic eruptions, and oil spills in the Gulf of Mexico,” said Yu-Lin Chang from the Japan Agency for Marine-Earth Science and Technology, and a visiting researcher at UTokyo and lead author of one of the papers in this study. “The Kuroshio Current is generally considered dangerous to navigate. I thought if you entered it, you could only drift aimlessly. But the results of our simulations went far beyond what I had imagined. I’m pleased this work helped illuminate how ocean voyages may have occurred 30,000 years ago.”

The simulations helped fill gaps that a one-time experiment could not. They revealed that launching from northern Taiwan offered a better chance of success than from further south, and that paddling slightly southeast rather than directly at the destination was essential for compensating against the powerful current. These findings suggest a high level of strategic seafaring knowledge among early modern humans.

“Scientists try to reconstruct the processes of past human migrations, but it is often difficult to examine how challenging they really were. One important message from the whole project was that our Paleolithic ancestors were real challengers. Like us today, they had to undertake strategic challenges to advance,” said Kaifu. “For example, the ancient Polynesian people had no maps, but they could travel almost the entire Pacific. There are a variety of signs on the ocean to know the right direction, such as visible land masses, heavenly bodies, swells and winds. We learned parts of such techniques ourselves along the way.”