Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

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.

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 population history of northeastern Siberia since the Pleistocene.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Author Correction: Ancient hepatitis B viruses from the Bronze Age to the Medieval period.

In Fig. 2 of this Letter, the 'E' and 'G' clade labels were inadvertently reversed, and in Table 2 the genotype of DA27 was 'D1' instead of 'D5'. These have been corrected online.

Ancient hepatitis B viruses from the Bronze Age to the Medieval period.

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

The Beaker phenomenon and the genomic transformation of northwest Europe.

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.

Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe.

This corrects the article DOI: 10.1038/nature25738.

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.

Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.

The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans.

Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

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.

Geometric singular perturbation analysis of a dynamical target mediated drug disposition model.

In this paper we present a mathematical analysis of a pharmacological ODE model for target mediated drug disposition (TMDD). It is known that solutions of this model undergo four qualitatively different phases. In this paper we provide a mathematical identification of these separate phases by viewing the TMDD model as a singular perturbed system. Our analysis is based on geometric singular perturbation theory and we believe that this approach systemizes-and sheds further light on-the scalings arguments used by previous authors. In particular, we present a novel description of the third phase through a distinguished solution of a nonlinear differential equation. We also describe the solution curve for large values of initial drug doses and recover, en route, a result by Aston et al. (J Math Biol 68(6):1453-1478, 2014) on rebounding using our alternative perturbation approach. Finally, from our main result we derive a new method for estimating the parameters of the system in the event that detailed data is available. Ideally our approach to the TMDD model should stimulate further research into applications of these methods to more complicated models in pharmacology.

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.

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.

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.

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.

A strontium isotope baseline of Cyprus. Assessing the use of soil leachates, plants, groundwater and surface water as proxies for the local range of bioavailable strontium isotope composition.

In this study, a strontium isotope baseline for Cyprus is presented. The aim of the study was two-fold; first to provide an environmental multi-proxy-based baseline (water/plants/soil leachates) suitable for archaeological provenance and mobility studies, food source authentication, and forensic investigations; and second, to contribute to the debate around which proxy (or combination of proxies) might be most suitable to define bioavailable fractions of strontium in geologically complex areas also exposed to sea-spray and other Sr-bearing aerosols. Lowest bioavailable strontium isotope signatures range is found within terranes dominated by ophiolites, where 87Sr/86Sr ratios range from 0.7055 to 0.7081, however, results reveal a high degree of variability in bioavailable 87Sr/86Sr ratios, both spatially, along depth profiles and amongst the different proxies. A narrower range of bioavailable Sr isotope signatures is observed within the Circum Troodos Sedimentary Successions (C.T.S.S.), both in spatial distribution and between different proxies. Observed range is 87Sr/86Sr = 0.7079 to 0.7089 in areas dominated by pre-Quaternary C.T.S.S., and 87Sr/86Sr ratios = 0.7076 to 0.7086 in areas covered by Quaternary C.T.S.S., revealing the lithologies to be very homogenous with respect to bioavailable strontium ratios. Intra-site variations in three archaeological sites (multiple samples from each site from within a 500 m radius) within the pre-Quaternary and Quaternary C.T.S.S. are smaller than inter-site variations, suggesting that tracing studies inferred from baselines sampled within a limited spatial area could lead to erroneous conclusions regarding provenance. The study points to the necessity for conducting multi-proxy, spatially extensive sampling to adequately characterize complex geological areas, if these should serve as reliable reference areas in provenance studies.