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Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N  = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1 , HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR , NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia. [ABSTRACT FROM AUTHOR]

The Middle Neolithic in western Europe is characterized by monumental funerary structures, known as megaliths, along the Atlantic façade. The first manifestations of this phenomenon occurred in modern-day France with the long mounds of the Cerny culture. Here, we present genome-wide data from the fifth-millennium BCE site of Fleury-sur-Orne in Normandy (France), famous for its impressively long monuments built for selected individuals. The site encompasses 32 monuments of variable sizes, containing the burials of 19 individuals from the Neolithic period. To address who was buried at the site, we generated genome-wide data for 14 individuals, of whom 13 are males, completing previously published data [M. Rivollat et al., Sci. Adv. 6, eaaz5344 (2020)]. Population genetic and Y chromosome analyses show that the Fleury-sur-Orne group fits within western European Neolithic genetic diversity and that the arrival of a new group is detected after 4,000 calibrated BCE. The results of analyzing uniparentally inherited markers and an overall low number of long runs of homozygosity suggest a patrilineal group practicing female exogamy. We find two pairs of individuals to be father and son, buried together in the same monument/grave. No other biological relationship can link monuments together, suggesting that each monument was dedicated to a genetically independent lineage. The combined data and documented father–son line of descent suggest a male-mediated transmission of sociopolitical authority. However, a single female buried with an arrowhead, otherwise considered a symbol of power of the male elite of the Cerny culture, questions a strictly biological sex bias in the burial rites of this otherwise “masculine” monumental cemetery. [ABSTRACT FROM AUTHOR]

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe. [ABSTRACT FROM AUTHOR]

The expansion of Neolithic stable isotope studies in France now allows distinct regional population-scale food patterns to be linked to both local environment influences and specific economic choices. Carbon and nitrogen isotope values of more than 500 humans and of animal samples also permit hypotheses on sex-biased human provenance. To advance population scale research, we here present the first study that draws together carbon (C), nitrogen (N), sulphur (S) and strontium (Sr), dental calculus, aDNA, and palaeoparasitology analysis to infer intra-population patterns of diet and provenance in a Middle Neolithic population from Le Vigneau 2 (human = 40; fauna = 12; 4720–4350 cal. BC) from north-western France. The data of the different studies, such as palaeoparasitology to detect diet and hygiene, CNS isotopes and dental calculus analysis to examine dietary staples, Sr and S isotopes to discriminate non-locals, and aDNA to detect maternal (mtDNA) versus paternal lineages (Y chromosome), were compared to anthropological information of sex and age. Collagen isotope data suggest a similar diet for all individuals except for one child. The provenance isotopic studies suggest no clear differences between sexes, suggesting both males and females used the territory in a similar pattern and had access to foods from the same environments. [ABSTRACT FROM AUTHOR]

Objectives The arrival of Neolithic farmers in Europe was the source of major cultural and genetic transitions. Neolithic settlers brought a new set of maternal lineages (mitochondrial DNA), recently well-characterized on the continental road, from the Balkans to West Germany (Rhine River). In the present study, the first mitochondrial DNA data from groups associated with this continental expansion wave located west of the Rhine River has been provided and their genetic affinities with contemporary groups have been discussed. Material and methods The mitochondrial DNA analysis of 27 human remains originating from Obernai (5,000-4,400 cal. BC), a necropolis located in French Alsace Region and attributed to Grossgartach, Planig-Friedberg, and Roessen cultures was conducted. Results and discussion Among the 27 individuals studied, 15 HVR-I sequences and 17 mitochondrial haplogroups could be determined. The analysis of the Obernai gene pool clearly confirmed the genetic homogeneity of Linearbandkeramik (LBK) groups on both sides of the Rhine River. Notably, one N1a sequence found in Obernai is shared with LBK farmers from Central Europe, including one individual from the Flomborn site located approximately 200 km north-east of Obernai. On the whole, data gathered so far showed major genetic influence of the Danubian wave from Transdanubia to Atlantic French Coast, going by Alsace Region. However, the genetic influence of descendants from the Mediterranean Neolithic expansion and the significant hunter-gatherer admixture detected further west in the Paris Basin were not perceived in the Obernai necropolis. Conclusions Genetic homogeneity and continuity within LBK groups can be proposed on both sides of the Rhine River for the middle Neolithic groups. Nevertheless, mitochondrial data gathered so far for Neolithic groups from the entire extant French Territory clearly point out the complexity and the variability of Neolithic communities interactions that is worthy of further investigation. [ABSTRACT FROM AUTHOR]

Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices. [ABSTRACT FROM AUTHOR]

The French Paris Basin is well known as a complex cultural area of the Early/Middle Neolithic, particularly with respect to funerary practices. Gurgy “Les Noisats”, which is an important necropolis in the southern Paris basin, is a burial site (N = 128) associated with the first Neolithic groups established in that area. The understanding of the necropolis composition and organization is complicated given the substantial homogeneity of the site's spatial organization in relation to a great diversity of characterized funerary traits. The unprecedented quantity of genetic (mitochondrial DNA), osteological (sex, age), and archaeological (funerary) data obtained for the Gurgy necropolis facilitates the search for potential correlations between cultural and biological (i.e. genetic and osteological) diversity at the site level. Despite the application of the powerful geographic information system, no correlation could be detected (i) between individual maternal lineages and specific bioarchaeological profiles (ii) or between maternal lineages and spatially identified bio-archaeological clusters. Therefore, analyses were performed to test for a correlation between the maternal ancestries of the individuals (i.e., hunter-gatherer/Central European farmer and Southern European farmer ancestries) and specific funerary traits. Again, the homogeneity of the funerary treatment of all of the individuals regardless of their potential maternal ancestries is striking. Taken together, our results regarding the way in which the Gurgy necropolis functioned provide strong evidence for the acculturation of all maternal ancestries groups, at least in terms of funerary practice. In addition, the demonstration of a recurrent association of adult men and immature individuals suggests a patrilocal system, which could be consistent with the detected acculturation of women who present a hunter-gatherer ancestry. [ABSTRACT FROM AUTHOR]