Neandertal ancestry influences our immune system in more ways than previously recognized

 Researchers find surprising links which show that Neandertal ancestry influences our immune system today in ways more nuanced than previously recognised. 

Viruses account for an estimated 10-20% of the global disease burden. Many DNA viruses can persist in the body for a lifetime, and virus load varies greatly even among people without symptoms. Throughout human history, they have posed persistent and rapidly evolving threats, placing strong adaptive pressure on our immune system. Previous research has shown that many genetic variants involved in immunity bear the marks of these evolutionary battles - including signatures of natural selection and contributions from interbreeding with archaic humans. While Neandertal ancestry has previously been associated with beneficial effects in RNA virus defence, the new study highlights a contrasting trend for DNA viruses.

Because of past admixture with archaic humans, around 2% of the genomes of present-day non-Africans is composed of Neandertals DNA and an additional 2-4% of people in Oceania of Denisovan ancestry These introgressed sequences have shaped many biological traits, including immunity. But their role in defences against DNA viruses has remained largely unexplored.

Modern disadvantages don’t imply ancient harm

RNA and DNA viruses differ fundamentally in their biology - including infection strategies, tissue tropism, and the pace at which they evolve. These differences raise the possibility that the effects of archaic genetic variants on DNA and RNA virus response might differ. To investigate this, the team explored the contribution of archaic DNA - primarily Neandertal ancestry - to the DNA viral load of participants in the UK Biobank. By analysing viral sequences detected in large-scale genomic data, the researchers asked whether archaic variants correlate with the presence or quantity of common DNA viruses.

The study uncovered multiple associations between archaic DNA and the loads of Epstein-Barr virus (EBV), Human Herpesvirus 7 (HHV‑7), and anelloviruses of the Teno family. These viruses are widespread in humans and often persist as chronic infections. Overall, archaic DNA was disproportionally often associated with higher virus loads. These viruses often cause no symptoms, but the amount of viral DNA can reflect how effectively the immune system keeps them in check.

“Our results suggest that Neandertal-derived variants may not provide effective defense against several DNA viruses in people today,” said Michael Dannemann, a co-author of this study. “This stands in striking contrast to their previously reported beneficial effects on RNA virus immunity.” However, the researchers emphasise that these negative effects in present-day populations do not mean that the same variants were harmful to Neandertals themselves. “Viruses evolve extremely quickly,” noted Dannemann.

“The pathogenic landscape faced by Neandertals tens of thousands of years ago would have been vastly different from the one we face today. A variant that reduced viral burden in the past may increase it now.” Supporting this idea, the team identified genomic regions carrying archaic variants that show shifts in selective pressure over time, including signatures of more recent negative selection. These evolutionary signals align with the possibility that once-beneficial archaic alleles have become disadvantageous in today’s environments.

The findings highlight that archaic DNA in people today interacts with modern pathogens in distinct ways - and that its effects can differ sharply between virus classes. The work underscores that archaic genetic ancestry still influences our immune system today - but in ways more nuanced than previously recognised.

Read more: https://academic.oup.com/gbe/article/18/5/evag110/8664352 

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Journal

Genome Biology and Evolution

DOI

10.1093/gbe/evag110 

South American Indigenous peoples are diverse and descend from a third wave of migration

 The Indigenous peoples of South America are descended from three waves of migration. According to a study conducted exclusively by researchers from the continent, one of these waves, which is most represented in the current population, came from Mesoamerica around 1,300 years ago. This finding reveals the greater complexity of the history of Indigenous peoples and their greater genetic diversity than previously anticipated. The research is featured on the cover of the May 7 issue of the scientific journal Nature. “We reached these conclusions through very intensive collaborative work,” says Tábita Hünemeier, a geneticist at the Institute of Biosciences at the University of São Paulo (IB-USP) in Brazil. She coordinated the study, on which she has been working for over a decade, and was surprised by the higher-than-expected genetic diversity.

A total of 128 genomes were fully sequenced and compared to 71 other sequences available in databases. The genomes represented 45 Indigenous groups from eight Latin American countries: Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru. The goal was to estimate the genetic affinities among all Indigenous American groups by taking ancient genomes into account. The researcher celebrates the inclusion of biomedical scientist Putira Sacuena from the Federal University of Pará (UFPA), among the authors. “She was the first Indigenous woman to work in genetic anthropology,” Hünemeier states. The researchers consider Indigenous collaboration in studies concerning native peoples to be a welcome development in the quest to understand their history.

This work adds important information to what is known about the human colonization of South America. The first wave of migration left records dating back up to 12,000 years ago at Lapa do Santo (read more at revistapesquisa.fapesp.br/en/the-peoples-of-lagoa-santa/) and in the Sumidouro cave in the Lagoa Santa region of Minas Gerais state in Brazil, as well as in Chile. Around 9,000 years ago, another migration left distinct marks in the genetic and archaeological record in Peru and Argentina. However, the Middle Holocene period, between 8,000 and 4,200 years ago, brought environmental changes that damaged ecosystems and reduced the availability of resources, affecting human populations as well.

The Indigenous peoples inhabiting the continent today are partly descended from individuals who arrived from what is now Mexico about 1,300 years ago. This third wave had not been documented until now and is a major new finding. DNA analyses also suggest that Indigenous groups became less populous and more isolated from one another after the arrival of Europeans in the 16th century. The study detected signs of inbreeding – which occurs when reproduction happens among small groups with no possibility of migration – among the Sirionó, Suruí, and Karitiana peoples within the Tupi lineage. This indicates a population collapse, which was likely caused by epidemics, enslavement, and disruptions to subsistence and traditional knowledge. A recent recovery can be observed in some regions of western South America. Genetic diversity is higher in Central America and the Southern Cone.

A puzzling discovery was the presence of ancient genomic segments characteristic of Australasians (people from Australia and surrounding islands), Neanderthals (from Europe), and Denisovans (from East Asia) in South American DNA. The hypothesis is that these ancient genes play a beneficial, as yet unknown, role and were maintained by natural selection. While the article focused on diversity and population trajectories rather than functional aspects, the identification of regions associated with immune response, cardiometabolic traits, fertility, and anthropometric traits suggests that future studies may explore the role of human evolution on the continent in greater depth. According to Hünemeier, genetic markers used in previous studies were designed based on European and African populations, making them unsuitable for understanding the Americas. “Now we have parameters”.

Importantly, the study documented the prolonged presence of human groups with marked genetic diversity in many areas, which contradicts some views about Indigenous groups. This underscores the need for more comprehensive representation of these peoples in global genomic databases. “The whole world had genomic data to tell the story of its population; only Brazil didn’t,” says André Strauss, an archaeologist at the Museum of Archaeology and Ethnology (MAE) at USP who did not participate in the study. He refers to an article he published in 2018 in the journal Cell on the ancient history of the South American population (read more at revistapesquisa.fapesp.br/en/when-indigenous-people-occupied-lagoa-santa/). The article left a mystery hanging: If the people of Lagoa Santa were not the direct ancestors of today’s Indigenous peoples, who are their ancestors? “The current article confirms the two previous migratory waves and characterizes the third.”

Strauss aims to identify this wave in the archaeogenetic record. “Most of the skeletons we have are older. There are very few from pottery-making groups,” he explains. One reason for this is that caves and sambaquis are environments that are more conducive to the preservation of skeletons. In places like the Amazon, however, they decompose. Based on the available molecular data, more information is on the way. “We already have over a thousand more sequenced samples,” says Hünemeier. “We understand that to grasp the diversity and complexity of the Americas, it’s best to have a few individuals from many populations.

Ancient DNA reveals web of marriage and migration in Peru

 

Long-distance movement, intermarriage and kinship shaped ancient Andean coastal networks before the Inca Empire, new research finds

Peer-Reviewed Publication

University of Sydney

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image: 

Fig. 1 | Map of the study area. A. Locations of the Chincha Valley and other Andean sites referenced in this study that yielded ancient DNA data. B. The archaeological sites under investigation for this study. Basemaps for panels A and B were obtained from the World Imagery dataset (https://www.arcgis.com/home/item.html?id=10df2279f9684e4a9f6a7f08febac2a9) and created with ArcGIS Pro v3.6.2. Sources: ESRI, Michael Bauer Research GmbH 2022, Instituto Nacional de Estadística e Informática (INEI), Earthstar Geographics, Vantor. 

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Credit: Basemaps for panels A and B were obtained from the World Imagery dataset (https://www.arcgis.com/home/item.html?id=10df2279f9684e4a9f6a7f08febac2a9) and created with ArcGIS Pro v3.6.2. Sources: ESRI, Michael Bauer Research GmbH 2022, Instituto Nacional de Estadística e Informática (INEI), Earthstar Geographics, Vantor.

 

Long-distance migration along Peru’s Pacific coast began at least 800 years ago, centuries before the rise of the Inca Empire and much earlier than previously thought, a new international study reveals. 

By analysing ancient DNA (aDNA) alongside archaeological and historical data, the study provides some of the strongest evidence to date of population movement along the Pacific coast prior to Inca rule (AD 1400 to 1532), demonstrating that pre-Inca coastal communities were far more mobile and connected at local and interregional scales than historically believed. 

Published in Nature Communications, it suggests people travelled more than 700 kilometres from Peru’s north coast to the Chincha Valley in the south. Here, they settled and intermarried with neighbouring populations, while maintaining distinctive cultural traditions – such as cranial modification and painting the dead with red pigment – for generations. The study also identified a single grave containing relatives who engaged in endogamy, or close-kin procreation.  

“Migration and kinship have long been part of the human story and the development of powerful societies,” said co-lead author Dr Jacob Bongers, digital archaeologist and member of the Vere Gordon Childe Centre at the University of Sydney, and Visiting Research Fellow at the Australian Museum Research Institute.  

“What’s most interesting about this research is that it shows the close-knit and far-reaching social networks of pre-Inca coastal communities, as well as how people maintained cultural traditions of marking group identities for centuries, even as they intermarried with distinct groups,” he said. 

Tracing ancient movement and mating patterns through aDNA  

The research team analysed aDNA samples of 21 individuals recovered from burial sites in the Chincha Valley to reconstruct family relationships and explore genetic diversity over time.  

“The genome-wide data and radiocarbon dates suggest migrants arrived in the Chincha Valley by at least the thirteenth century AD, well before Inca expansion,” Dr Bongers said. “Their ancestry traced back to the Peruvian north coast, more than 700 kilometres away, and the aDNA of these early migrants revealed no evidence of mixing with local populations.” 

Genetic evidence revealed mixed ancestry between people from the north, central and south coasts over subsequent generations. “This likely means that, after northerners migrated to Chincha, they intermarried with groups from neighbouring coastal areas, a practice that continued during the Spanish Colonial Period (AD 1532-1825),” Dr Bongers said.  

Genetic and bioarchaeological data from the aDNA samples also indicated close-kin procreation.  

“The burial of family members together and the evidence for close-kin unions in the lower Chincha Valley highlights the importance of the familial unit for ancient Andeans,” said co-lead author Assistant Professor Jordan Dalton from the State University of New York, Oswego. 

“The close biological relationships suggest the sampled individuals were members of an ayllu or parcialidad, a traditional, kin-based group that shares common territory, resources and ancestry. Close-kin unions may have served as a strategic means of retaining control over resources within the group,” she said.  

Cultural traditions endured across centuries    

All sampled individuals had some north coast ancestry, demonstrating population continuity for at least 200 years. This coincides with persistent cultural traditions maintained in Chincha from at least the thirteenth to fifteenth centuries. 

“In the sampled individuals from the lower and middle valley we observed practices such as cranial modification, a process carried out in infancy to shape the head using boards and bindings, human vertebrae strung on reed sticks, and the postmortem application of red pigment to the skull,” Dr Bongers said.  

“Postmortem red pigment application and cranial modification are cultural traditions that have long been documented on Peru’s north coast, so this evidence shows migrants may have brought their body modification traditions south to mark group identities." 

The timing of migration from northern Peru aligned with major social and political changes along Peru’s coast, yet the precise reasons for population movement remain uncertain, Dr Bongers said. 

“Climate hazards, the expansion of powerful northern polities such as the Chimú, and access to valuable resources including seabird guano, are all possible drivers of ancient Andean migration,” he said. 

"Importantly, this research expands our understanding of how and when interregional interaction occurred along the Andean Pacific coast and makes it clear the Inca incorporated highly mobile and deeply connected coastal communities into their empire." 

Close genetic relatedness between distant European megalithic societies

 

Despite distinct archaeological differences, the people from the Western Funnel Beaker culture were more closely related to neighboring Wartberg communities than previously understood, according to a genomic study of German burial sites. The findings reveal surprisingly long-distance family ties – including a father/son pair buried over 200 kilometers apart – suggesting that kinship, mobility, and social exchange connected megalithic populations across great distances. During the Late Neolithic (~4500 to 2800 BCE), megalithic monuments – large stone structures – emerged across Europe. These architectural works reflected local traditions while also hinting at far-reaching social, cultural, or ancestral ties between distant populations. 

One megalithic society, the Western Funnel Beaker culture (TRB-west) of north-central Europe, is known for its elaborate stone burial chambers and other distinct traditions. However, there has been little genetic evidence available that helps clarify how TRB-West people were related to neighboring megalithic communities. The only TRB-West site where well-preserved human remains have been recovered to date is Sorsum, located in present-day Germany. This site has megalithic features that resemble the nearby Wartberg culture (WBC).

To investigate whether the archaeological similarities also reflect kinship between these groups, Nicolas Antonio da Silva and colleagues analyzed the genomes of 203 individuals (including 129 newly generated genomes) from the Sorsum site and five WBC sites. The results revealed that the people buried at Sorsum were genetically far more closely related with WBC groups than other TRB-west groups, despite their differing archaeological labels. Both Sorsum and WBC individuals also shared unusually high levels of ancestry from western hunter-gatherers, particularly through male lineages, suggesting deep and sustained biological connections. 

Notably, de Silva et al. discovered striking evidence of long-distance kinship networks, including a biological father and son buried at sites separated by 225 kilometers (the WBC site of Niedertiefenbach and Sorsum, respectively). Other second-degree biological relationships were also identified between Sorsum and distant WBC sites, suggesting occasional movement, intermarriage, or social and cultural exchange across large geographic areas for the time. Yet both regions lack close genetic ties with more distant megalithic populations in the British Isles or Scandinavia to the north. This indicates that megalithic traditions likely spread culturally, rather than through biological networks. 

The authors argue that Sorsum and the WBC communities formed a genetically continuous population, despite some marked differences in material culture. Sorsum may have represented a northern branch of the WBC world that adopted certain TRB-west traditions while remaining biologically and socially connected to the neighboring WBC groups.

 

People’s consumption of plants began increasing thousands of years before the introduction of agriculture

 A new study published in Nature Ecology and Evolution examining human populations in Sri Lankan tropical rainforests shows that people’s consumption of plants began increasing thousands of years before the introduction of agriculture. The research focuses on human and animal remains dating from approximately 20,000 to 3,000 years ago and uses zinc isotope analysis of tooth enamel to reconstruct an organism’s position in the food web – known as a trophic position – and dietary composition.

The results show that humans consistently occupied an intermediate, omnivorous position in the food web, with diets including both animal and plant resources. However, over time, the isotope data reveal a gradual shift toward values associated with greater plant consumption. This trend begins in the Late Pleistocene and continues into the Holocene, far earlier than the first confirmed evidence for domesticated crops in the region. Rather than reflecting a sudden agricultural ‘revolution’, the findings point to a long-term process of plant engagement among rainforest hunter-gatherers.

“Our results show that plant use was not a late development linked to farming, but part of a much longer trajectory,” said Dr. Nicolas Bourgon, lead author of the study and postdoctoral researcher in the Department of Coevolution of Land Use and Urbanisation at the Max Planck Institute of Geoanthropology. “These rainforest populations were already intensifying their use of plant resources thousands of years before agriculture appears in the archaeological record.”

The study builds on decades of archaeological work at key cave sites, including Fa-Hien Lena, Batadomba-lena, and Balangoda Kuragala, which have produced evidence for sustained human occupation of tropical rainforest environments over tens of thousands of years. While previous interpretations have often emphasized hunting, largely due to the preservation of animal remains and tools, direct evidence for plant consumption has remained limited because organic materials rarely survive in such settings.

To address this gap, the researchers applied state-of-the-art zinc isotope analysis (δ⁶⁶Zn) to tooth enamel from 24 human individuals and 57 faunal samples. This method that reflects an individual’s trophic level and is particularly suited to tropical contexts.

The geochemical data indicate suggest that plant foods were consistently a substantial part of human diets, but became increasingly important over time. This suggests a gradual shift in how rainforest resources were used and managed, rather than a simple response to the later introduction of agriculture.

“The Sri Lankan archaeological record provides a rare opportunity to examine long-term human–environment interactions in a tropical setting,” says Dr. Oshan Wedage, from the Department of History and Archaeology at the University of Sri Jayewardenepura. “These results highlight how local populations adapted their resource use over time, particularly in relation to plant exploitation.”

“This study contributes to a growing body of evidence that tropical rainforests were not barriers to human occupation,” says Prof. Patrick Roberts, director of the Department of Coevolution of Land Use and Urbanisation at the Max Planck Institute of Geoanthropology. “Instead, they were environments where people developed dynamic subsistence strategies and interacted with their surroundings over very long timescales.”

Beyond its regional implications, the study contributes to broader discussions about the origins of agriculture, land use, and the role of plant use in human evolution. The findings support models in which agriculture emerges from long-standing foraging practices rather than abrupt subsistence shifts.

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Journal

Nature Ecology & Evolution

DOI

10.1038/s41559-026-03082-6 

Study reveals one of world’s first cities prospered as wealth-gap shrank

New research reveals that the 4,000-year-old city of Mohenjo-daro defied the ‘rules’ of history by becoming more equal as it became more successful.

For decades, historians have generally agreed that the progress of small villages as they evolved into cities came at the price of widening inequality.  A small group of leaders, Kings and priests, would inevitably seize control of the wealth and the gap between rich and poor would grow.

But a new study at the University of York delves into the archaeology of Mohenjo-daro, the Indus civilisation’s largest city, and shows the opposite was true. By analysing house sizes across the ancient city, researchers found that Mohenjo-daro was not only more equal than its neighbours in Mesopotamia and Greece, but it actually became more egalitarian over time.

The lead author, Dr Adam Green from the University of York’s Department of Archaeology and Department of Environment and Geography, said: “Legacy data from the ancient city shows that as the city matured, the gap between the largest and smallest homes narrowed. In fact by its later years, the wealth gap in this massive urban centre had dropped to levels typical of the first farming villages.

“While ancient Egyptians were building pyramids for god-kings, and the Greeks were constructing massive palaces at Knossos, the people of the Indus were building something entirely different.

“Instead of gold-filled tombs and huge temples, Mohenjo-daro focused on sophisticated brick-lined drains and organised street layouts. Instead of allowing the perks of society to accumulate with a tiny elite, the city’s amenities were widely distributed amongst the everyday households.”

This was particularly true with regard to the distribution of the famous Indus seals, which were tools of business and trade. Indus seals were typically found in ordinary homes and not in public buildings, with no palaces to monopolise these tools of government. 

It was evident that rather than a single ruler hoarding resources, the city’s inhabitants worked together to ensure fair access to a good standard of life.

Investment in very practical things, like drainage and street maintenance, was also a sign of working collectively for the public good. The use of a standardized system of weights and measures across the region ensured that exchange remained fair for all citizens.

The findings, published in the journal Antiquity, challenge the modern assumption that rising inequality is an unavoidable side effect of economic growth. Mohenjo-daro, the researchers say, stands as proof that a society can be technologically advanced and highly productive whilst also ensuring its prosperity is shared by the many, rather than the few.

Dr Green said: “Mohenjo-daro is often cited as being famous for what it doesn't have, such as the absence of palaces for kings, gold-filled tombs, and no statues of rulers. But what it does have is so important. 

“In the period when inequality appears to be lowest, productivity appears to rise. It challenges the idea that prosperity requires us to concentrate decision-making powers in the hands of the few. 

“It is quite an interesting lesson for modern societies, as the Indus civilisation demonstrates clearly that an urban society can be highly productive and inventive at scale, whilst also ensuring that resources and power are shared equitably. In fact, doing so may even have been essential to sustaining prosperity over the centuries.”

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Journal

Antiquity

Butchering marks on ancient bones tell when Bronze Age people started using more efficient metal tools

 

Recent zooarchaeological research suggests that the transition from stone to metal butchering tools in the southern Levant occurred during or after the Middle Bronze Age and was accompanied by changes in butchering practices. However, few large and well-dated zooarchaeological assemblages that span the Bronze Ages have been systematically analyzed, limiting our understanding of when and how this technological transition occurred. 

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Caption

A chop mark by a metal axe on a goat or sheep vertebra. These chops were performed for dismemberment. 

Credit

Haskel J Greenfield and Jeremy A Beller

This study investigates the evolution of butchering technology using newly analyzed zooarchaeological data from Bronze Age Tell Aphek (Antipatris), Israel. Tell Aphek, a prominent urban settlement continuously inhabited since the Early Bronze Age, is an ideal site for examining long-term technological change. Microscopic analysis of butchery marks on faunal remains, including scanning electron microscopy, was utilized to distinguish marks produced by stone tools from those produced by metal tools. 

The results show that stone tools dominate in the earliest periods (e.g., the Early Bronze Age) and a dramatic and sudden shift toward metal butchering tools occurs with the onset of the Middle Bronze Age occupation. By the end of the Late Bronze Age, metal tools had almost completely replaced stone tools as the main butchering implements. This transition is also associated with observable changes in butchering efficiency. 

These findings demonstrate that the microscopic analysis of butchering marks provides a valuable perspective on technoeconomic transformations occurring between the Early Bronze Age and later periods in the southern Levant.