100 ancient genomes show repeated population turnovers in Neolithic Denmark.

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

Wild cereal grain consumption among Early Holocene foragers of the Balkans predates the arrival of agriculture.

Forager focus on wild cereal plants has been documented in the core zone of domestication in southwestern Asia, while evidence for forager use of wild grass grains remains sporadic elsewhere. In this paper, we present starch grain and phytolith analyses of dental calculus from 60 Mesolithic and Early Neolithic individuals from five sites in the Danube Gorges of the central Balkans. This zone was inhabited by likely complex Holocene foragers for several millennia before the appearance of the first farmers ~6200 cal BC. We also analyzed forager ground stone tools (GSTs) for evidence of plant processing. Our results based on the study of dental calculus show that certain species of Poaceae (species of the genus Aegilops) were used since the Early Mesolithic, while GSTs exhibit traces of a developed grass grain processing technology. The adoption of domesticated plants in this region after ~6500 cal BC might have been eased by the existing familiarity with wild cereals.

Before humans invented agriculture and the first farmers appeared in southwestern Asia, other ancient foragers (also known as hunter-gatherers) in southeastern Europe had already developed a taste for consuming wild plants. There is evidence to suggest that these foragers were intensely gathering wild cereal grains before the arrival of agriculture. However, until now, the only place outside southwestern Asia this has been shown to have occurred is in Greece, and is dated around 20,000 years ago. In the past, researchers proposed that forager societies in the Balkans also consumed wild cereals before transitioning to agriculture. But this has been difficult to prove because plant foods are less likely to preserve than animal bones and teeth, making them harder to detect in prehistoric contexts. To overcome this, Cristiani et al. studied teeth from 60 individuals found in archaeological sites between Serbia and Romania, which are attributed to the Mesolithic and Early Neolithic periods. Food particles extracted from crusty deposits on the teeth (called the dental calculus) were found to contain structures typically found in plants. In addition, Cristiani et al. discovered similar plant food residues on ground stone tools which also contained traces of wear associated with the processing of wild cereals. These findings suggest that foragers in the central Balkans were already consuming certain species of wild cereal grains 11,500 years ago, before agriculture arrived in Europe. It is possible that sharing knowledge about plant resources may have helped introduce domesticated plant species in to this region as early as 6500 BC. This work challenges the deep-rooted idea that the diet of hunter-gatherers during the Palaeolithic and Mesolithic periods primarily consisted of animal proteins. In addition, it highlights the active role the eating habits of foragers might have played in introducing certain domesticated plant species that have become primary staples of our diet today.

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

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.

The exceptional finding of Locus 2 at Dehesilla Cave and the Middle Neolithic ritual funerary practices of the Iberian Peninsula.

There is a significant number of funerary contexts for the Early Neolithic in the Iberian Peninsula, and the body of information is much larger for the Late Neolithic. In contrast, the archaeological information available for the period in between (ca. 4800-4400/4200 cal BC) is scarce. This period, generally called Middle Neolithic, is the least well-known of the peninsular Neolithic sequence, and at present there is no specific synthesis on this topic at the peninsular scale. In 2017, an exceptional funerary context was discovered at Dehesilla Cave (Sierra de Cádiz, Southern Iberian Peninsula), providing radiocarbon dates which place it at the beginning of this little-known Middle Neolithic period, specifically between ca. 4800-4550 cal BC. Locus 2 is a deposition constituted by two adult human skulls and the skeleton of a very young sheep/goat, associated with stone structures and a hearth, and a number of pots, stone and bone tools and charred plant remains. The objectives of this paper are, firstly, to present the new archaeological context documented at Dehesilla Cave, supported by a wide range of data provided by interdisciplinary methods. The dataset is diverse in nature: stratigraphic, osteological, isotopic, zoological, artifactual, botanical and radiocarbon results are presented together. Secondly, to place this finding within the general context of the contemporaneous sites known in the Iberian Peninsula through a systematic review of the available evidence. This enables not only the formulation of explanations of the singular new context, but also to infer the possible ritual funerary behaviours and practices in the 5th millennium cal BC in the Iberian Peninsula.

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.

Diet and Mobility in the Corded Ware of Central Europe.

Isotopic investigations of two cemetery populations from the Corded Ware Culture in southern Germany reveal new information on the dating of these graves, human diet during this period, and individual mobility. Corded Ware Culture was present across much of temperate Europe ca. 2800-2200 cal. BC and is represented by distinctive artifacts and burial practices. Corded Ware was strongly influenced by the Yamnaya Culture that arose in the steppes of eastern Europe and western Eurasia after 3000 BC, as indicated by recent aDNA research. However, the development of CW on different chronological and spatial scales has to be evaluated. Examination of the CW burials from southern Germany supports an argument for substantial human mobility in this period. Several burials from gravefields and larger samples from two large cemeteries at Lauda-Königshofen "Wöllerspfad" and at Bergheinfeld "Hühnerberg" contributed the human remains for our study of bone and tooth enamel from the Corded Ware Culture. Our results suggest that Corded Ware groups in this region at least were subsisting on a mix of plant and animal foods and were highly mobile, especially the women. We interpret this as indicating a pattern of female exogamy, involving different groups with differing economic strategies.

Population genomics of Bronze Age Eurasia.

The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Local and foreign males in a late Bronze Age cemetery at Neckarsulm, south-western Germany: strontium isotope investigations.

The cemetery of Neckarsulm in southwestern Germany was discovered in 2001 and contained the inhumation graves of 50 individuals in 32 graves. The cemetery was in use for about 50 years during the Late Bronze Age (Urnfield culture, Hallstatt A1 period). The individuals who could confidently be identified were almost exclusively adult males. The majority of the skeletal remains exhibit specialized facets that most likely resulting from horseback riding. Several characteristics make this cemetery very unusual: The inhumations in contrast to normal cremation in this time period, the large number of multiple burials, the uniform sex and age of the deceased. There is no information concerning the cause of death of the individuals from the cemetery. Isotopic analysis was used for diet and mobility investigation. Diet for these individuals was relatively homogeneous and included both terrestrial and freshwater species. Tooth enamel from 37 individuals was analysed for strontium and oxygen isotopes. Almost one-third of the individuals in the sample exhibited non-local strontium isotope ratios and likely came from different areas in southwest Germany.