A ritual murder shaped the Early and Middle Neolithic across Central and Southern Europe.

In the Rhône Valley's Middle Neolithic gathering site of Saint-Paul-Trois-Châteaux (France), the positioning of two females within a structure aligned with the solstices is atypical. Their placement (back and prone) under the overhang of a silo in front of a third in a central position suggests a ritualized form of homicidal ligature strangulation. The first occurrence dates back to the Mesolithic, and it is from the Early Neolithic of Central Europe that the practice expands, becoming a sacrificial rite associated with an agricultural context in the Middle Neolithic. Examining 20 cases from 14 sites spanning nearly two millennia from Eastern Europe to Catalonia reveals the evolution of this ritual murder practice.

At the Origins of Tobacco-Smoking and Tea Consumption in a Virgin Population (Yakutia, 1650-1900 A.D.): Comparison of Pharmacological, Histological, Economic and Cultural Data.

(1) Background: The way tobacco and tea spread among virgin populations is of major interest our understanding of how ancient economic and cultural practices could have influenced current habits. (2) Methods: hair concentrations of theobromine, theophylline, caffeine, nicotine, and cotinine were measured in hair samples from 47 frozen bodies of people from eastern Siberia, dated from the contact with Europeans to the assimilation of people into Russian society. (3) Results: hair concentration of theobromine, theophylline, and caffeine vary with the type of beverage consumed: green, black, or local herbal teas. Shortly after the first contacts, a few heavy consumers of tobacco were found among light or passive consumers. Tobacco-related co-morbidities began to be recorded one century after and heavy tea users were only found from the 19th century (4) Conclusions: Economic factors and social and family contacts seem to have played a decisive role in tobacco consumption very early on. Behavioral evolution governed the process of substance integration into Siberian culture and was a determinant for the continuity of its use across long periods of time. Analyzing the respective contributions of social and economic processes in the use of these substances opens avenues of investigation for today's public health.

Sucrose Is Not the Whole Story: Risk Factors and Oral Health at the Contact (Yakutia, Siberia-16th/19th).

(1) Background: contact between indigenous and European populations has often resulted in changes in oral health attributed to the introduction of sucrose. Most studies are per tooth over considerable periods and with few ethnological references. (2) Aim: dental epidemiology of 96 autochthonous frozen bodies from Yakutia between the early 17th century and the late 19th century; comparisons with historical texts and ethnographic data. (3) Material and methods: we use descriptive statistics and discriminant factorial analyses to identify dominant variables in the dataset and compare periods and subjects, considering all variables. (4) Results: the peculiarities of the population are the rarity of cavities and the relative frequency of dental pathologies leading to death. Assimilation into the Russian Orthodox culture has led to decreased tooth wear and an increase in tooth loss. Dental health evolves only two centuries after the contact. (5) Conclusions: the confrontation with historical data suggests that changes are not related to the growing importance of sucrose but to a combined action: the substitution of dendrophagy by cereal flour; the decrease in immunity linked to the development of chronic infectious diseases; tobacco addiction and the mandibular torus: a risk factor promoting apical cysts.

The last battle of Anne of Brittany: Solving mass grave through an interdisciplinary approach (paleopathology, biological anthropology, history, multiple isotopes and radiocarbon dating).

Mass graves are usually key historical markers with strong incentive for archeological investigations. The identification of individuals buried in mass graves has long benefitted from traditional historical, archaeological, anthropological and paleopathological techniques. The addition of novel methods including genetic, genomic and isotopic geochemistry have renewed interest in solving unidentified mass graves. In this study, we demonstrate that the combined use of these techniques allows the identification of the individuals found in two Breton historical mass graves, where one method alone would not have revealed the importance of this discovery. The skeletons likely belong to soldiers from the two enemy armies who fought during a major event of Breton history: the siege of Rennes in 1491, which ended by the wedding of the Duchess of Brittany with the King of France and signaled the end of the independence of the region. Our study highlights the value of interdisciplinary approaches with a particular emphasis on increasingly accurate isotopic markers. The development of the sulfur isoscape and testing of the triple isotope geographic assignment are detailed in a companion paper [13].

Triple sulfur-oxygen-strontium isotopes probabilistic geographic assignment of archaeological remains using a novel sulfur isoscape of western Europe.

Sulfur isotope composition of organic tissues is a commonly used tool for gathering information about provenance and diet in archaeology and paleoecology. However, the lack of maps predicting sulfur isotope variations on the landscape limits the possibility to use this isotopic system in quantitative geographic assignments. We compiled a database of 2,680 sulfur isotope analyses in the collagen of archaeological human and animal teeth from 221 individual locations across Western Europe. We used this isotopic compilation and remote sensing data to apply a multivariate machine-learning regression, and to predict sulfur isotope variations across Western Europe. The resulting model shows that sulfur isotope patterns are highly predictable, with 65% of sulfur isotope variations explained using only 4 variables representing marine sulfate deposition and local geological conditions. We used this novel sulfur isoscape and existing strontium and oxygen isoscapes of Western Europe to apply triple isotopes continuous-surface probabilistic geographic assignments to assess the origin of a series of teeth from local animals and humans from Brittany. We accurately and precisely constrained the origin of these individuals to limited regions of Brittany. This approach is broadly transferable to studies in archaeology and paleoecology as illustrated in a companion paper (Colleter et al. 2021).

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.

Genetic evidence suggests a sense of family, parity and conquest in the Xiongnu Iron Age nomads of Mongolia.

In an effort to characterize the people who composed the groups known as the Xiongnu, nuclear and whole mitochondrial DNA data were generated from the skeletal remains of 52 individuals excavated from the Tamir Ulaan Khoshuu (TUK) cemetery in Central Mongolia. This burial site, attributed to the Xiongnu period, was used from the first century BC to the first century AD. Kinship analyses were conducted using autosomal and Y-chromosomal DNA markers along with complete sequences of the mitochondrial genome. These analyses suggested close kin relationships between many individuals. Nineteen such individuals composed a large family spanning five generations. Within this family, we determined that a woman was of especially high status; this is a novel insight into the structure and hierarchy of societies from the Xiongnu period. Moreover, our findings confirmed that the Xiongnu had a strongly admixed mitochondrial and Y-chromosome gene pools and revealed a significant western component in the Xiongnu group studied. Using a fine-scale approach (haplotype instead of haplogroup-level information), we propose Scytho-Siberians as ancestors of the Xiongnu and Huns as their descendants.

The genetic legacy of legendary and historical Siberian chieftains.

Seventeen years of archaeological and anthropological expeditions in North-Eastern Siberia (in the Sakha Republic, Yakutia) have permitted the genetic analysis of 150 ancient (15th-19th century) and 510 modern individuals. Almost all males were successfully analysed (Y-STR) and this allowed us to identify paternal lineages and their geographical expansion through time. This genetic data was confronted with mythological, historical and material evidence to establish the sequence of events that built the modern Yakut genetic diversity. We show that the ancient Yakuts recovered from this large collection of graves are not representative of an ancient population. Uncommonly, we were also able to demonstrate that the funerary preference observed here involved three specific male lineages, especially in the 18th century. Moreover, this dominance was likely caused by the Russian conquest of Siberia which allowed some male clans to rise to new levels of power. Finally, we give indications that some mythical and historical figures might have been the actors of those genetic changes. These results help us reconsider the genetic dynamics of colonization in some regions, question the distinction between fact and myth in national histories and provide a rare insight into a funerary ensemble by revealing the biased process of its composition.

The limitations of kinship determinations using STR data in ill-defined populations.

The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing).

A serological survey of echinococcosis, toxocariasis and trichinellosis among rural inhabitants of Central Yakutia.

In 2018, a seroepidemiological survey was carried out in 3 ulus, or districts (Churapchinsky, Megino-Kangalassky and Ust-Aldansky) in Central Yakutia (Sakha Republic, Russian Federation) about 3 helminth zoonoses, namely, echinococcosis (alveolar or cystic), toxocariasis and trichinellosis. Ninety rural volunteers agreed to answer a questionnaire that inquired about demographic and environmental parameters along with food habits. Then they were asked to provide a venous blood sample. Serological investigations were carried out by enzyme-linked immunosorbent assay. Four subjects tested positive for echinococcosis, 1 for toxocariasis and 2 for trichinellosis. No demographic or environmental or dietary possible risk factor was found to be associated with these positive results. In conclusion, only echinococcosis and trichinellosis appeared to be in Yakutia as health threats among the 3 investigated zoonoses.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

Genetic kinship and admixture in Iron Age Scytho-Siberians.

Scythians are known from written sources as horse-riding nomadic peoples who dominated the Eurasian steppe throughout the Iron Age. However, their origins and the exact nature of their social organization remain debated. Three hypotheses prevail regarding their origins that can be summarized as a "western origin", an "eastern origin" and a "multi-regional origin". In this work, we first aimed to address the question of the familial and social organization of some Scythian groups (Scytho-Siberians) by testing genetic kinship and, second, to add new elements on their origins through phylogeographical analyses. Twenty-eight Scythian individuals from 5 archeological sites in the Tuva Republic (Russia) were analyzed using autosomal Short Tandem Repeats (STR), Y-STR and Y-SNP typing as well as whole mitochondrial (mtDNA) genome sequencing. Familial relationships were assessed using the Likelihood Ratio (LR) method. Thirteen of the 28 individuals tested were linked by first-degree relationships. When related, the individuals were buried together, except for one adult woman, buried separately from her mother and young sister. Y-chromosome analysis revealed a burial pattern linked to paternal lineages, with men bearing closely related Y-haplotypes buried on the same sites. Inversely, various mtDNA lineages can be found on each site. Y-chromosomal and mtDNA haplogroups were almost equally distributed between Western and Eastern Eurasian haplogroups. These results suggest that Siberian Scythians were organized in patrilocal and patrilineal societies with burial practices linked to both kinship and paternal lineages. It also appears that the group analyzed shared a greater genetic link with Asian populations than Western Scythians did.

The antiquity of the spondyloarthritides: Presentation of one of the oldest Neolithic cases in Western Europe.

In humans, little is yet known about the origins of the inflammatory rheumatisms of the spondyloarthritides group, especially regarding the period of their emergence. However, a better knowledge of their history would help to clarify their aetiology. We report a paleopathological case of European origin, dated from the late Neolithic (3621-3023 cal BC), consisting of an isolated vertebral block combining erosion, ossification and severe anterior and posterior ankylosis. The lesional presentation is very suggestive of a severe form of axial spondyloarthritis. This specimen and some other rare cases from the same period found in Western Europe suggest that these diseases appeared, in this geographical region, in evolving groups of humans as part of the demographic and epidemiological transition that constituted the Neolithic period. The emergence of infectious agents and the profound dietary changes that occurred during this period of human history may have favoured the appearance of the spondyloarthritides.

New genetic evidence of affinities and discontinuities between bronze age Siberian populations.

OBJECTIVES: This work focuses on the populations of South Siberia during the Eneolithic and Bronze Age and specifically on the contribution of uniparental lineage and phenotypical data to the question of the genetic affinities and discontinuities between western and eastern populations. MATERIALS AND METHODS: We performed molecular analyses on the remains of 28 ancient humans (10 Afanasievo (3600-2500 BC) and 18 Okunevo (2500-1800 BC) individuals). For each sample, two uniparentally inherited systems (mitochondrial DNA and Y-chromosome DNA) were studied, in order to trace back maternal and paternal lineages. Phenotype-informative SNPs (Single Nucleotide Polymorphisms) were also analyzed, along with autosomal STRs (Short Tandem Repeats). RESULTS: Most of the Afanasievo men submitted to analysis belonged to a single sub-haplogroup, R1b1a1a, which reveals the predominance of this haplogroup in these early Bronze Age populations. Conversely, Okunevo individuals carried more diverse paternal lineages that mostly belonged to Asian/Siberian haplogroups. These differences are also apparent, although less strongly, in mitochondrial lineage composition and phenotype marker variant frequencies. DISCUSSION: This study provides new elements that contribute to our understanding of the genetic interactions between populations in Eneolithic and Bronze Age southern Siberia. Our results support the hypothesis of a genetic link between Afanasievo and Yamnaya (in western Eurasia), as suggested by previous studies of other markers. However, we found no Y-chromosome lineage evidence of a possible Afanasievo migration to the Tarim Basin. Moreover, the presence of Y-haplogroup Q in Okunevo individuals links them to Native American populations, as was suggested by whole-genome sequencing.

Oral health status in historic population: Macroscopic and metagenomic evidence.

Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.

Tracing intensive fish and meat consumption using Zn isotope ratios: evidence from a historical Breton population (Rennes, France).

Here we report Sr and Zn isotope ratios of teeth of medieval to early modern Breton people a population whose diet is known from historical, archeological and collagen isotope data. Most of the population, buried in the Dominican convent of Rennes, France, consists of parliamentary nobles, wealthy commoners and ecclesiastics, who had a diet rich in animal products. Our aim is to assess how the Zn isotope ratios of their teeth compare to those of other French historical populations previously studied, which were characterized by cereal-based diets, and those of modern French individuals, who daily eat animal products. We describe a clear offset (∼0.35‰) between local and non-local human individuals in Zn isotope ratios. The δ66Zntooth values of local individuals overlap that of modern French people, and are lower than those of local carnivores. Non-local δ66Zn values are similar to those of historical individuals analyzed previously. We conclude the lower Zn isotope ratios of local humans relative to the associated fauna can be explained by the consumption of carnivorous fish and pork, in agreement with historical, zooarchaeological and collagen (C, N, S) isotope data. Zn isotopes could therefore be a tracer of fish and/or substantial meat consumption in ancient populations.

Study of a seventeenth-century French artificial mummy: autopsical, native, and contrast-injected CT investigations.

BACKGROUND: A lead coffin was fortuitously discovered in a church called "Eglise des Toussaints" in Rennes (French Brittany). A collaborative taskforce investigated this extraordinary discovery. A multi-disciplinary team of experts from the National Institute for Preventive Archeological Research (INRAP) and Rangueil University Hospital of Toulouse was created, including anthropologists, archeologists, forensic pathologists, radiologists, and pathologists. The inscription on the lead coffin specified that the body belonged to "Messer Louys de Bruslon, Lord of Plessis," a nobleman who died on November 1, 1661. Multiple holes were visible in the lead coffin, and deterioration threatened the mummy. We opened the lead coffin and discovered an excellently preserved mummy, except for mostly skeletonized upper and lower limbs. The mummy was conserved in several layers of shrouds. Vegetal embalming material covered the head and filled the face, the thorax, and the abdomen. The embalmers had removed all thoracic and abdominal organs and conserved some pelvic organs (e.g., the bladder). METHODS: Multi-slice computed tomography (MSCT) scanner evaluated the mummy, at each step of our analysis. The excellent preservation of abdominal vascular axes led us to perform a CT angiography using Angiofil®, an oily contrast agent developed for postmortem imaging, before an autopsy. RESULTS: Sub-diaphragmatic arteries, including the abdominal aorta and iliac arteries, were excellently preserved. The vascular contrast agent filled all arteries. The native CT, CT angiography, and autopsy did not detect any vascular lesion. CONCLUSION: Our study, based on rare archeological material, allowed a complete examination of an excellently preserved seventeenth-century mummy, using MSCT, angiography, and an autopsy. We did not detect any arterial lesion and proposed a comprehensive description of the embalmment process.

Ancient genomes revisit the ancestry of domestic and Przewalski's horses.

The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski's horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.