Repeated plague infections across six generations of Neolithic Farmers.

In the period between 5,300 and 4,900 calibrated years before present (cal. BP), populations across large parts of Europe underwent a period of demographic decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.

Vittrup Man-The life-history of a genetic foreigner in Neolithic Denmark.

The lethally maltreated body of Vittrup Man was deposited in a Danish bog, probably as part of a ritualised sacrifice. It happened between c. 3300 and 3100 cal years BC, i.e., during the period of the local farming-based Funnel Beaker Culture. In terms of skull morphological features, he differs from the majority of the contemporaneous farmers found in Denmark, and associates with hunter-gatherers, who inhabited Scandinavia during the previous millennia. His skeletal remains were selected for transdisciplinary analysis to reveal his life-history in terms of a population historical perspective. We report the combined results of an integrated set of genetic, isotopic, physical anthropological and archaeological analytical approaches. Strontium signature suggests a foreign birthplace that could be in Norway or Sweden. In addition, enamel oxygen isotope values indicate that as a child he lived in a colder climate, i.e., to the north of the regions inhabited by farmers. Genomic data in fact demonstrates that he is closely related to Mesolithic humans known from Norway and Sweden. Moreover, dietary stable isotope analyses on enamel and bone collagen demonstrate a fisher-hunter way of life in his childhood and a diet typical of farmers later on. Such a variable life-history is also reflected by proteomic analysis of hardened organic deposits on his teeth, indicating the consumption of forager food (seal, whale and marine fish) as well as farmer food (sheep/goat). From a dietary isotopic transect of one of his teeth it is shown that his transfer between societies of foragers and farmers took place near to the end of his teenage years.

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations.

Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.

The selection landscape and genetic legacy of ancient Eurasians.

The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.

The genetic and cultural impact of the Steppe migration into Europe.

BACKGROUND: During the early 3rd millennium BCE migration from Pontic Steppe, mainly related to Yamnaya culture, has affected European populations both culturally and genetically, however, it has long been debated to what extent this migration was male-driven, and how this replacement process took place which eliminated partially/largely Neolithic male lines over time. AIM: This paper aims to evaluate the influence of the Steppe migration on European Bronze Age populations by calculating both male and female genetic contributions of the Steppe-related ancestry to the European Bronze Age populations. With this approach, we will be able to clarify the hypotheses on whether it was male-biased migration or not. SUBJECTS AND METHODS: To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA and qpAdm analyses by using published genome-wide data. In addition, we quantified male and female genetic contribution into Europe by using the analysis of uniparental markers and the X-chromosome. RESULTS: The Steppe migration had a considerable impact on the genetic makeup of the Bronze Age European populations. The data suggest that the Steppe-related ancestry arriving into Central Europe was male-driven, dominantly in the Corded Ware culture populations and lesser in the Bell Beaker populations. In fact, there is no evidence that this migration had a significant input on the mitochondrial genetic pool of all European Bronze Age populations. CONCLUSIONS: Our analyses suggest that the Steppe-related ancestry had genetic impact on mainly Central-Eastern Europe. Moreover, this migration was male-driven for most of the Central European populations belonging to the Corded Ware groups, and to a lesser extent for the Bell Beaker groups.

The geographic distribution of bioavailable strontium isotopes in Greece - A base for provenance studies in archaeology.

Sr isotopes are a powerful tool used to reconstruct human mobility in archaeology. This requires extensive bioavailable 87Sr/86Sr baselines used as reference for deciphering potential areas of origin. We define the first extensive bioavailable Sr isotope baselines for the different geographical regions and surface lithologies of Greece by combining new Sr data with previously published bioavailable 87Sr/86Sr data. We present 82 new Sr concentrations and 87Sr/86Sr signatures of plants, soil leachates, surface waters and spring waters from Central Greece and combine these with published baseline values from all over Greece. We define individual baselines for ten of the thirteen geographical regions of Greece. We also provide soil leachate 87Sr/86Sr ratios from the two archaeological Bronze Age sites of Kirrha and Ayios Vasileios in Central and Southern Greece and demonstrate the validity and applicability of the new baselines for these sites. The bioavailable 87Sr/86Sr compositions of Central Greece define a narrow range of 87Sr/86Sr values between 0.70768 - 0.71021, with the widest range observed for the soil leachates. Sr derived from carbonate weathering appears to be the most important Sr source sampled by the proxies. There is an overall larger variability in baseline ranges of the different geographical regions, the narrowest is that for West Greece and the widest that for West Macedonia. In addition, we computed statistical Sr isotope ranges for the five main surface lithological groups characterising the sampling sites of the various proxies. Narrowly ranged, unradiogenic bioavailable Sr isotope signatures are typical of areas characterised by igneous outcrops as well as by Cenozoic and Mesozoic sediments. Areas, where Palaeozoic and Precambrian bedrock outcrops dominate, produce significantly wider ranges. Our study promotes the usefulness of multi-proxy baselines for geographical reference purposes and thus their promising applicability for future human mobility studies.

Testing Late Bronze Age mobility in southern Sweden in the light of a new multi-proxy strontium isotope baseline of Scania.

The Bronze Age of Sweden's southernmost region, Scania, is complex and intriguing. One could say that Scania represented in many ways a gateway for people, ideas and material culture connecting continental Europe with Sweden. Shedding light on the dynamics of human mobility in this region requires an in depth understanding of the local archaeological contexts across time. In this study, we present new archaeological human data from the Late Bronze Age Simris II site, located in an area of Scania showing a dynamic environment throughout the Late Bronze Age, thus likely involving various forms of mobility. Because the characterization of solid strontium isotope baselines is vital for delineating human mobility in prehistory using the strontium isotope methodology, we introduce the first environmentally based multi-proxy (surface water-, plant- and soil leachates) strontium isotope baselines for sub-regions of Scania. Our results show, that the highly complex and spatially scattered lithologies characterising Scania does not allow for a spatially meaningful, geology-based grouping of multi-proxy data that could be beneficial for provenance studies. Instead, we propose sub-regional baselines for areas that don't necessarily fully correspond and reflect the immediate distribution of bedrock lithologies. Rather than working with a Scania-wide multi-proxy baseline, which we define as 87Sr/86Sr = 0.7133 ± 0.0059 (n = 102, 2σ), we propose sub-regional, multi-proxy baselines as follows: Area 1, farthest to the north, by 87Sr/86Sr = 0.7184 ± 0.0061 (n = 16, 2σ); Area 2, comprising the mid and western part of Scania, with 87Sr/86Sr = 0.7140 ± 0.0043 (n = 48, 2σ); Area 3-4, roughly corresponding to a NW-SE trending zone dominated by horst-graben tectonics across Scania, plus the carbonate dominated south western part of Scania with 87Sr/86Sr = 0.7110 ± 0.0030 (n = 39, 2σ). Our results also reflect that the complexity of the geology of Scania requires systematic, high density, statistically sound sampling of multiple proxies to adequately constrain the baseline ranges, particularly of those areas dominated by Precambrian lithologies. The averaging effect of biosphere Sr in surface water might be beneficial for the characterization of baselines in such terranes. Our sub-regional, area-specific baselines allow for a first comparison of different baseline construction strategies (single-proxy versus multi-proxy; Scania-wide versus sub-regional). From the Late Bronze Age Simris II site, we identified six individuals that could be analysed for Sr isotopes, to allow for an interpretation of their provenance using the newly established, environmental strontium isotope baselines. All but one signature agrees with the local baselines, including the 87Sr/86Sr value we measured for a young individual buried in a house urn, typically interpreted as evidence for long distance contacts. The results are somewhat unexpected and provides new aspects into the complexity of Scandinavian Bronze Age societies.

Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.

The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.

Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries.

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.

The spatiotemporal spread of human migrations during the European Holocene.

The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora.