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It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to 6,500 years old. Despite the high genetic diversity of S. enterica all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of five thousand years. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential, and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human adapted S. enterica is linked to human cultural transformations.

Excavation of the Late Neolithic dolmen of Oberbipp BE, Steingasse in the Swiss Central Plateau provided a unique opportunity for a comprehensive study of the archaeological and anthropological evidence. In multidisciplinary studies, we investigated the processes at work during construction, use, and abandonment of the megalithic structure, as well as the dietary habits, subsistence strategy, and possible mobility of the Neolithic population. Archaeological methods included micromorphology, archaeobiology, typology, use-wear analysis, and geology. The anthropological investigation was complemented by an analysis of stable isotope ratios and palaeogenetics. Local topography and the cover of alluvial sediments ensured an extraordinary conservation of the monument. It allowed the preservation of the human remains of at least 42 individuals of both sexes and all ages. The observation of the sedimentary and post-depositional processes, supplemented by an extensive series of radiocarbon dates, allowed us to reconstruct the history of the dolmen in its environment and the definition of at least two deposition phases. We found genetic evidence of lactase intolerance, a local population with a mixed ancestry of early Anatolian farmers and Western hunter-gatherers, and a crop-based diet. Sparse remains of a nearby Late Neolithic settlement sustain the interpretation that this is the burial site of a local farming community. Evidence of higher mobility of females and kinship over three generations solely in the paternal line suggests a virilocal community. Bone-altering pathologies support the assumption of a caring society. 1. Introduction 1.1. Context 1.2. Discovery and excavation 1.3. Topography and geology 1.4. Aim of the study 2. Materials and methods 2.1. Archaeology 2.2. Soil micromorphology and geology 2.3. Archaeobotany and archaeozoology 2.4. Anthropology and molecular genetics 2.5. Radiocarbon dating 3. Results 3.1. Site occupation 3.2. The monument 3.3. The burials 3.4. Associated artefacts 3.5. Archaeozoology and archaeobotany 4. Discussion 4.1. Limitations of the study 4.2. Landscape history 4.3. The regional burial tradition in the late fourth millennium 4.4. Construction and use of the monument 4.5. Standing stones and further monuments 4.6. Animal activity, human disturbances, erosion, and destruction 4.7. Population and mobility 4.8. Conclusions

Nowadays, the discovery and excavation of an almost intact Late Neolithic dolmen is rare, as those monuments were often visible in the landscape and have been investigated or destroyed in earlier times; therefore, information about the buried individuals has often been lost. The excavation of the dolmen, a stone grave chamber, from Oberbipp, Switzerland, in 2012 provided a unique opportunity to study human skeletal remains from a Late Neolithic collective burial (3350–2650 BCE). Over 2,000 fragmented and commingled skeletal elements were recovered and form the basis of this morphological study. Established morphological methods were employed to evaluate the minimum number of individuals, age at death, sex, stature, and the presence of pathological alterations and trauma. Sex was determined additionally by aDNA analysis. Elements of the entire human skeleton were recovered indicating a primary burial site. At least 42 individuals (femora) from all age classes (57%:43% adults to subadults) were buried in the dolmen. Based on aDNA analysis (n = 23, partes petrosae) slightly more males than females (44%:35% males to females, 22% indeterminate) were recovered. Stature was estimated from complete femora (n = 3) indicating an average body height between 154–157 cm. Pathological alterations and trauma could be observed on several bones, however, without indications for major interpersonal violence. The caries intensity of Swiss samples seems to be higher compared with other Neolithic European sites. A possible separation of burial areas for males and females based on the recovery of skeletal elements within the dolmen along with aDNA results is postulated. In addition, this article contributes to a better understanding of Late Neolithic populations in Central Europe.

Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860–2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region., European populations underwent strong genetic changes during the Neolithic. Here, Furtwängler et al. provide ancient nuclear and mitochondrial genomic data from the region of Switzerland during the end of the Neolithic and the Early Bronze Age that reveal a complex genetic turnover during the arrival of steppe ancestry.

The Neolithic period is archaeologically well documented in Central Europe, and several studies considered dietary habits and migration patterns. However, even though Switzerland and the alpine region are well known for Neolithic cultures, most of today’s knowledge about the population comes from organic materials such as wood, faunal, or botanic remains and not from the human remains themselves. This comprehensive study presents dietary reconstructions from stable isotope data (δ13C, δ15N, δ34S) of humans (n = 88) and fauna (n = 60) dating to the Neolithic from 21 sites that cluster in three main Swiss regions (Jura, Midland, Eastern Switzerland). The general data show a terrestrial C3 plant–based diet, and the δ15N values indicate regional differences between the groups, while males and females consumed similar proportions of animal proteins. It is assumed that freshwater fish was part of the diet at least in some regions. The data indicate that different subsistence strategies were practiced (animal husbandry/pastoralism vs. agriculture) possibly in relation to cultural influences. The δ34S values suggest some mobility in general, while indications for patrilocal societies are seen as females exhibit greater δ34S ranges. Overall, we conclude that most likely different subsistence strategies were practised, while no social stratigraphy based on nutritional access could be observed for the studied populations.

Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860–2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region. European populations underwent strong genetic changes during the Neolithic. Here, Furtwangler et al. provide ancient nuclear and mitochondrial genomic data from the region of Switzerland during the end of the Neolithic and the Early Bronze Age that reveal a complex genetic turnover during the arrival of steppe ancestry.

In Early Middle Ages (sixth–eleventh centuries AD), South Tyrol (Italian Alps) played a key role for geographical and military reasons. Historical sources document that allochthonous groups (germani) entered the territory, and the material culture shows mutual cultural exchanges between autochthonous andgermani. Besides the nature of the migration, the demographic and socio-cultural impacts on the local population are still unknown. Stable isotope analyses were performed to provide insights into dietary patterns, subsistence strategies, changes in socio-economic structures, and mobility, according to spatial (e.g. valleys, altitudes) and chronological (centuries) parameters. Bone collagen of 32 faunal and 91 human bone samples from nine sites, located at different altitudes, was extracted for stable carbon, nitrogen, and sulphur isotope analyses. In total, 94% (30/32) of the faunal remains were of good quality, while the humans displayed 93% (85/91) of good quality samples for δ13C and δ15N and 44% (40/91) for δ34S stable isotopes. The isotopic results of the animals reflected a terrestrial-based diet. Statistical differences were observed within and among the humans of the different valleys. The δ13C values of individuals sampled from higher altitudes indicated a mainly C3plant-based diet compared to areas at lower altitudes, where more positive δ13C values showed an intake of C4plants. The δ15N values suggested a terrestrial-based diet with a greater consumption of animal proteins at higher altitudes. The data revealed higher variability in δ34S values in the Adige valley, with individuals probably migrating and/or changing dietary habits.

Objectives Stable isotope analysis has often been used in neonatal remains from archeological contexts to investigate the presence of a signal of breastfeeding and weaning in past populations. Tooth histology on the other hand might be used as an indicator of birth survival. This pilot study aimed to investigate the feasibility of using stable nitrogen (δ15 N) and carbon (δ13 C) isotope values from neonatal bone collagen to elucidate if values deviating from the adult female average could indicate breastfeeding and co-occur with the presence of a neonatal line (NNL). The combination of these independent indicators might be useful in clarifying the fate of individuals who died around birth. Materials and methods Bone collagen from 21 archeological human and animal specimens was extracted and analyzed via mass-spectrometry for δ15 N and δ13 C. A verification of the stable isotope results was undertaken using tooth histology on three individuals who were investigated for the presence of a NNL as an indicator of live birth and short survival. Results The biological age of the human samples varied between 8.5 lunar months (Lm) and 2 postnatal months (Pm) of age. All except one individual exhibited elevated δ15 N values compared to the female average. The histological analyses revealed no NNL for this and two further individuals (n = 3). Discussion The results indicate that elevated nitrogen values of very young infants relative to a female average in archeological contexts are not necessarily associated with a breastfeeding onset signal, and therefore cannot be used exclusively as a proxy of birth survival. The elevation might be possible due to various reasons; one could be nutritional, in particular maternal stress during pregnancy or a metabolic disorder of mother and/or her child. In those cases, the evaluation of a NNL might reveal a false breastfeeding signal as seen for two individuals in our sample who have elevated nitrogen values despite the fact no NNL could be observed. Overall, our data support the growing awareness that bone collagen δ15 N values of neonates/infants should not be used as a proxy for breastfeeding or birth survival on its own.

Stable isotope analysis has often been used in neonatal remains from archeological contexts to investigate the presence of a signal of breastfeeding and weaning in past populations. Tooth histology on the other hand might be used as an indicator of birth survival. This pilot study aimed to investigate the feasibility of using stable nitrogen (δBone collagen from 21 archeological human and animal specimens was extracted and analyzed via mass-spectrometry for δThe biological age of the human samples varied between 8.5 lunar months (Lm) and 2 postnatal months (Pm) of age. All except one individual exhibited elevated δThe results indicate that elevated nitrogen values of very young infants relative to a female average in archeological contexts are not necessarily associated with a breastfeeding onset signal, and therefore cannot be used exclusively as a proxy of birth survival. The elevation might be possible due to various reasons; one could be nutritional, in particular maternal stress during pregnancy or a metabolic disorder of mother and/or her child. In those cases, the evaluation of a NNL might reveal a false breastfeeding signal as seen for two individuals in our sample who have elevated nitrogen values despite the fact no NNL could be observed. Overall, our data support the growing awareness that bone collagen δ

In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.

The discovery of a Neolithic dolmen in Switzerland with inhumations, dating between 3500 and 3000 BCE, was an exceptional finding. To provide best conditions for subsequent studies on the archaeological remains our interdisciplinary team decided to apply 3D documentation. Depending on different factors, two scanning systems with four scanners and photogrammetry were applied and the obtained data was combined. Detailed excavation plans and simultaneously a reduction of excavation time without loss of information were the result. A virtual animation of the dolmen in its reconstructed ancient appearance combined with the context of the grave goods was created. The 3D documentation provided initial data for anthropological and paleogenetic analyses. The individuals buried in the dolmen might provide novel information to the Neolithic research of central Europe. Additionally, with the help of the 3D data, the dolmen was rebuilt to make this archaeological heritage accessible to the public.