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.

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.

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.

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 and germani. 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 δ 13 C and δ 15 N and 44% (40/91) for δ 34 S 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 δ 13 C values of individuals sampled from higher altitudes indicated a mainly C 3 plant-based diet compared to areas at lower altitudes, where more positive δ 13 C values showed an intake of C 4 plants. The δ 15 N values suggested a terrestrial-based diet with a greater consumption of animal proteins at higher altitudes. The data revealed higher variability in δ 34 S values in the Adige valley, with individuals probably migrating and/or changing dietary habits.

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