Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France.

The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.

Landscape of fear: indirect effects of conflict can account for large-scale population declines in non-state societies.

The impact of inter-group conflict on population dynamics has long been debated, especially for prehistoric and non-state societies. In this work, we consider that beyond direct battle casualties, conflicts can also create a 'landscape of fear' in which many non-combatants near theatres of conflict abandon their homes and migrate away. This process causes population decline in the abandoned regions and increased stress on local resources in better-protected areas that are targeted by refugees. By applying analytical and computational modelling, we demonstrate that these indirect effects of conflict are sufficient to produce substantial, long-term population boom-and-bust patterns in non-state societies, such as the case of Mid-Holocene Europe. We also demonstrate that greater availability of defensible locations act to protect and maintain the supply of combatants, increasing the permanence of the landscape of fear and the likelihood of endemic warfare.

Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic.

The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.

Radiocarbon dataset for the TRB central-place at Kaldus, Poland.

This dataset compiles radiocarbon dates received for botanical macroremains and animal bones from domestic and ritual pits and human graves unearthed during excavations at the archaeological site of Kaldus (Poland) that can be related to the Funnel Beaker culture (TRB). Prior to radiocarbon dating by accelerator mass spectrometry (AMS), plant macroremains were checked against diagnostic attributes of species identification by standard paleobotanical analysis. The dataset contains already published (n = 4) and new (n = 10) radiocarbon dates that were used to establish the absolute chronology of the TRB habitus at Kaldus and its diachronic spatial organization. This dataset serves as an archive for future studies focusing on the TRB settlement pattern and organization in the region of modern Poland. It also has a utility to be reused in archaeological and chronological research on the movement of copper metalwork and the gradual spread of human cremation rite in the region.

Cranial Surgery in Antiquity: The Size of Trepanations During the Neolithic Period in France.

The trepanation, a surgical procedure performed on the skull, finds its roots in prehistoric times. This investigation delves into the analysis of the trepanned skulls housed at the Musée de l'Homme in Paris, focusing on those found in France, a region abundant in archaeological evidence of early neurosurgical techniques. With the opportunity to scrutinize these human remains, our study aimed to analyze the dimensions of Neolithic trepanations across 41 skulls. We particularly explored the relationships between minimum and maximum hole diameters, revealing a strong interrelation. Additionally, we successfully applied a straightforward protocol to determine the perforation area in ten Neolithic trepanations. These findings shed light on the medical practices of ancient civilizations, particularly in France during the Neolithic era. Moreover, this study underscores the significance of museum collections as valuable resources for scientific inquiry and the historical understanding of medicine.

Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise.

The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.

Isotope and morphometrical evidence reveals the technological package associated with agriculture adoption in western Europe.

This study aimed to reconstruct the environmental conditions and the crop management practices and plant characteristics when agriculture appeared in western Europe. We analyzed oak charcoal and a large number of cereal caryopsides recovered from La Draga (Girona, Spain), an early (5300 to 4800 cal. BC) agricultural site from the Iberian Peninsula. The carbon isotope discrimination (Δ13C) values of oak, the dominant forest species in the region, indicates prevalence of a wet climate at the site. Further, we reconstructed crop management conditions, achievable yield, and crop characteristics through the analysis of Δ13C, nitrogen isotope composition (δ15N), nitrogen content, and the reconstructed weight of wheat and barley caryopsides, following protocols developed by our team [Araus et al., Nat. Commun. 5, 3953 (2014)] and comparison of these parameters with present-day organic agriculture in the region. In parallel, a regional perspective was achieved through the study of wheat and barley grains of seventeen Neolithic sites from the western Mediterranean. The results suggest that rather than small-garden cultivation, a more extensive agriculture was practiced under good water availability and moderate manuring. Moreover, results from La Draga evidence that grain weight and spike morphology were comparable to contemporary cereals. Growing conditions and the prevalence of improved crop traits indicate that agriculture was fairly consolidated at the time it reached the western edge of Europe.

From hunter-gatherers to food producers: New dental insights into the Nile Valley population history (Late Paleolithic-Neolithic).

OBJECTIVES: This study presents biological affinities between the last hunter-fisher-gatherers and first food-producing societies from the Nile Valley. We investigate odontometric and dental tissue proportion changes between these populations from the Middle Nile Valley and acknowledge the biological processes behind them. MATERIALS AND METHODS: Dental remains of 329 individuals from Nubia and Central Sudan that date from the Late Pleistocene to the mid-Holocene are studied. Using 3D imaging techniques, we investigated outer and inner metric aspects of upper central incisors, and first and second upper molars. RESULTS: Late Paleolithic and Mesolithic foragers display homogeneous crown dimensions, dental tissue proportions, and enamel thickness distribution. This contrasts with Neolithic trends for significant differences from earlier samples on inner and outer aspects. Finally, within the Neolithic sample differences are found between Nubian and Central Sudanese sites. DISCUSSION: Substantial dental variation appears to have occurred around 6000 bce in the Nile Valley, coinciding with the emergence of food-producing societies in the region. Archeological and biological records suggest little differences in dietary habits and dental health during this transition. Furthermore, the substantial variations identified here would have happened in an extremely short time, a few centuries at most. This does not support in situ diet-related adaptation. Rather, we suggest these data are consistent with some level of population discontinuity between the Mesolithic and Neolithic samples considered here. Complex settlement processes could also explain the differences between Nubia and Central Sudan, and with previous results based on nonmetric traits.

Exploring the complex pre-adaptations of invasive plants to anthropogenic disturbance: a call for integration of archaeobotanical approaches.

Pre-adaptation to anthropogenic disturbance is broadly considered key for plant invasion success. Nevertheless, empirical evidence remains scarce and fragmentary, given the multifaceted nature of anthropogenic disturbance itself and the complexity of other evolutionary forces shaping the (epi)-genomes of recent native and invasive plant populations. Here, we review and critically revisit the existing theory and empirical evidence in the field of evolutionary ecology and highlight novel integrative research avenues that work at the interface with archaeology to solve open questions. The approaches suggested so far focus on contemporary plant populations, although their genomes have rapidly changed since their initial introduction in response to numerous selective and stochastic forces. We elaborate that a role of pre-adaptation to anthropogenic disturbance in plant invasion success should thus additionally be validated based on the analyses of archaeobotanical remains. Such materials, in the light of detailed knowledge on past human societies could highlight fine-scale differences in the type and timing of past disturbances. We propose a combination of archaeobotanical, ancient DNA and morphometric analyses of plant macro- and microremains to assess past community composition, and species' functional traits to unravel the timing of adaptation processes, their drivers and their long-term consequences for invasive species. Although such methodologies have proven to be feasible for numerous crop plants, they have not been yet applied to wild invasive species, which opens a wide array of insights into their evolution.

Evolutionary Trends of Polygenic Scores in European Populations From the Paleolithic to Modern Times.

This study examines the temporal and geographical evolution of polygenic scores (PGSs) across cognitive measures (Educational Attainment [EA], Intelligence Quotient [IQ]), Socioeconomic Status (SES), and psychiatric conditions (Autism Spectrum Disorder [ASD], schizophrenia [SCZ]) in various populations. Our findings indicate positive directional selection for EA, IQ, and SES traits over the past 12,000 years. Schizophrenia and autism, while similar, showed different temporal patterns, aligning with theories suggesting they are psychological opposites. We observed a decline in PGS for neuroticism and depression, likely due to their genetic correlations and pleiotropic effects on intelligence. Significant PGS shifts from the Upper Paleolithic to the Neolithic periods suggest lifestyle and cognitive demand changes, particularly during the Neolithic Revolution. The study supports a mild hypothesis of Gregory Clark's model, showing a noticeable rise in genetic propensities for intelligence, academic achievement and professional status across Europe from the Middle Ages to the present. While latitude strongly influenced height, its impact on schizophrenia and autism was smaller and varied. Contrary to the cold winters theory, the study found no significant correlation between latitude and intelligence.

An archaeobotanical and stable isotope approach to changing agricultural practices in the NW Mediterranean region around 4000 BC.

It has recently been observed, that a change in the crop spectrum happened during the so-called Middle Neolithic in France at ca. 4000 BC. An agricultural system based on free-threshing cereals (naked wheat and naked barley) seems to shift to one based on glume wheats. This is a major change for traditional farmers and this paper aims to shed light on its possible causes. Here we describe the results of new investigations in a key area for the understanding of this process: the NW Mediterranean arch, where free-threshing cereals are the main cultivars since ca. 5100 BC. New data confirm that the shift towards glume wheats is also observed in some sites of the NE of the Iberian Peninsula and that among the glume wheats that spread at ca. 4000 BC we should not only consider emmer and einkorn but also Timopheevi's wheat. Stable isotope analyses indicate no major decrease in soil fertility or alterations in local precipitation regimes. The agricultural change may be the result of a combination of the spread of damaging pests for free-threshing cereals and presumably new networks being developed with the North-eastern part of Italy and the Balkans.

The paleopathology and paleoepidemiology of Upper paleolithic tuberculosis: Review of evidence and hypotheses.

Molecular phylogeny work has shown that tuberculosis is ancient human-adapted infection predating the Neolithic period. They also show that the Upper Paleolithic is a key period of emergence of the MTB complex strains, contemporary with the exit of modern man from Africa. Despite the richness of Upper Paleolithic sites in Eurasia and the relative abundance of human remains, the only proven case of Paleolithic tuberculosis has been described so far date from the Azilian, a culture of the European Final Paleolithic, which is more recent than the ancient Neolithic sites of the Near East, area that currently hold the record for the oldest paleopathological evidence of tuberculosis. The purpose of this review is to present evidence for the existence of tuberculosis in the Paleolithic and to list hypotheses explaining the weak demonstrative contribution of paleopathology for pre-Neolithic periods.

Oldest evidence of tuberculosis in the Mediterranean islands: From the mainland to Cyprus.

Recent studies combining macroscopical observations and microCT analysis strongly suggested the diagnosis of tuberculosis for a child from the site of Khirokitia (Cyprus, 7th - early 6th millennium cal. BC), whose age at death is between 5 and 7 years. Many single primary burials were discovered at the site where the dead (MNI = 243) are buried in the same way, whatever their age. Nevertheless, the burial of this child presents a unique feature on the site (a male Ovis trophy marking the limit of the burial pit), probably indicating specific attention for this young deceased. This case is the oldest known in the Mediterranean islands and presents a particular interest from a paleoepidemiological point of view. Indeed, considering, on the one hand, the settlement pattern of the island of Cyprus by migrants from the Near East, and on the other hand, the presence of human tuberculosis in the Near East as early as about 10,500 years BP, it is very likely that the prehistoric migrants brought the disease from mainland to Cyprus.

Tuberculosis in prehistory in Eastern Central Europe (Hungary) - Chronological and geographical distribution.

Tuberculosis (TB) has long been a major scourge of humankind. Paleopathological and paleomicrobiological studies have revealed the past presence of the disease on a large spatial and temporal scale. The antiquity of the disease has extensively been studied in the Carpathian Basin, given its dynamic population and cultural changes since prehistory. These studies, however, have mainly focused on the populations living during the Common Era. The aim of this paper is to present the published and the recently discovered cases of prehistoric TB, from the Neolithic (6000-4500/4400 BCE) to the Bronze Age (2600/2500-800 BCE) Central Carpathian Basin (Hungary). We summarize 18 published cases and present new cases dating to the Neolithic period and introduce 3 newly discovered Bronze Age cases of TB. Despite extensive research, TB has not yet been identified from the Copper and Iron Ages in the Carpathian Basin. Considering the state of TB research, and supplemented by our prehistoric dataset, the spatio-temporal pattern of the disease can be further elucidated, thus advancing future molecular and paleopathological studies. Our dataset offers comprehensive spatial and temporal information on the spread of the disease in the Carpathian Basin, along with a detailed biological profile of the demonstrated cases and extensive paleopathological descriptions of the observed lesions, complemented by photographic evidence. This invaluable resource paves the way for enhanced understanding and progress in the field.

The firing temperatures of burnt clay from the Chinese neolithic cultural relics and its paleoenvironmental imprints.

The impact of human-induced fires on the surrounding environment has been particularly significant during the Anthropocene epoch. Neolithic burnt clay, which is widely distributed in the archaeological relics of ancient civilizations across the Eurasian continent, provides pivotal information about the ancient firing stories. However, understanding of the paleoenvironmental imprints of fire in burnt clay has been largely limited by the lack of sufficient analytical data on comprehensive knowledge of ancient firing conditions. In this study, a detailed magnetic analysis was conducted on burnt clay materials from a Neolithic site in Fujian, southeastern China, which presented a burnt clay-based record of the Neolithic firing temperature in relation to paleoenvironmental conditions. Based on magnetic analysis, the ancient firing temperature was determined to be approximately 620 °C, which is comparable with other records from Eurasian Neolithic sites. Frequency-dependent magnetic susceptibility provides alternative indicative information for ancient firing conditions in addition to conventional magnetic susceptibility. Furthermore, magnetic properties of burnt clay may decode the in-situ source characteristics with respect to geological background. In addition, a potential link between temporal variations in ancient firing temperatures in burnt clay and surrounding paleoenvironmental changes is tentatively interpreted by local environmental feedback of temperature-moisture conditions and anthropogenic activity. This study further confirms the archaeological potential of thermomagnetic properties as useful indicators in paleoenvironmental studies. More work combining paleoenvironmental and archaeological archives is critically essential to understand ancient firing history in the context of environmental conditions.

Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China.

The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.1,2 However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China.

Parallel worlds and mixed economies: multi-proxy analysis reveals complex subsistence systems at the dawn of early farming in the northeast Baltic.

The transition from foraging to farming was a key turning point in ancient socio-economies. Yet, the complexities and regional variations of this transformation are still poorly understood. This multi-proxy study provides a new understanding of the introduction and spread of early farming, challenging the notions of hierarchical economies. The most extensive biological and biomolecular dietary overview, combining zooarchaeological, archaeobotanical, dietary stable isotope and pottery lipid residue analyses is presented, to unravel the nature and extent of early farming in the 3rd millennium cal BCE in the northeast Baltic. Farming was introduced by incoming Corded Ware cultural groups (CWC), but some dietary segregation existed within these communities, with some having more access to domesticates, others incorporating more wild resources into their diet. The CWC groups coexisted in parallel with local hunter-fisher-gatherers (HFG) without any indication of the adoption of domesticates. There was no transition from foraging to farming in the 3rd millennium cal BCE in the NE Baltic. Instead, we see a complex system of parallel worlds with local HFGs continuing forager lifeways, and incoming farmers practising mixed economies, with the continuation of these subsistence strategies for at least a millennium after the first encounter with domesticated animals.

High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry.

The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.

The making of the oral microbiome in Agta hunter-gatherers.

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter-gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

The first maternal genetic study of hunter-gatherers from Vietnam.

The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.