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The increase of brain dimensions and complexity has characterized the evolution of the genus Homo. According to the available fossil and genetic evidence, a crucial stage came before the divergence of Neanderthals, Denisovans and Homo sapiens, during the Middle Pleistocene. We consider a specimen of about 400 ka, whose phenotype is at the roots of this divergence: Ceprano calvarium (Italy). Here, we show a derived cerebrovascular organization with a mosaic of modern human and primitive features characteristics. Computed microtomography shows vascular variation and ontogenetic defects associated with ventricular and lymphatic involvement while phylogenetic analyzes highlight a dysregulation of the Tet1 gene that shows an accelerated mutation rate between 1.2 Ma and 466 ka, in contrast with the expected neutral evolution of the human genome. These results shed light on the dynamics of cranio-cerebral growth during the encephalization process and on the cerebral vascular and lymphatic system involved in this process. The results of this study could have implications for the research of many of the diseases of the central nervous system that have become predominant in an increasingly structured and long-lived brain system such as that of modern Homo sapiens. One-Sentence Summary: Genetic mutation, anatomical variations and glymphatic system in the process of encephalization towards Homo sapiens.

SUMMARYMultiple sclerosis (MS) is a modern neuro-inflammatory and -degenerative disease, which is most prevalent in Northern Europe. Whilst it is known that inherited risk to MS is located within or within close proximity to immune genes it is unknown when, where and how this genetic risk originated. By using the largest ancient genome dataset from the Stone Age, along with new Medieval and post-Medieval genomes, we show that many of the genetic risk variants for MS rose to higher frequency among pastoralists located on the Pontic Steppe, and were 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, likely driven by pathogenic challenges coinciding with dietary and lifestyle environmental changes. This study highlights the critical importance of this period as a determinant of modern immune responses and its subsequent impact on the risk of developing MS in a changing environment.

Summary The Eurasian Holocene (beginning c. 12 thousand 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 an imputed dataset of >1600 complete ancient genome sequences, and new computational methods for locating selection in time and space, we reconstructed the selection landscape of the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, possibly associated with the dietary shift occurring in this period. We show that the selection on loci such as the FADS cluster, associated with fatty acid metabolism, and the lactase persistence locus, began earlier than previously thought. A substantial amount of selection is also found in the HLA region and other loci associated with immunity, possibly due to the increased exposure to pathogens during the Neolithic, which may explain the current high prevalence of auto-immune disease, such as psoriasis, due to genetic trade-offs. By using ancient populations to infer local ancestry tracks in hundreds of thousands of samples from the UK Biobank, we find strong genetic differentiation among ancient Europeans in loci associated with anthropometric traits and susceptibility to several diseases that contribute to present-day disease burden. These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago. Alleles associated with increased risk of some mood-related phenotypes are overrepresented in the farmer ancestry component entering Europe from Anatolia around 11,000 years ago, while western hunter-gatherers show a strikingly high contribution of alleles conferring risk of traits related to diabetes. Our results paint a picture of the combined contributions of migration and selection in shaping the phenotypic landscape of present-day Europeans that suggests a combination of ancient selection and migration, rather than recent local selection, is the primary driver of present-day phenotypic differences in Europe.

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.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.To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA andThe 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.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.

Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.

Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and past genetic diversity of our species. Here we present a “multi-omics” study, integrating genomic and proteomic analyses of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified “Villabruna cluster”. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Multi-omics analysis of dental calculus showed a diet rich of animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.

The Medieval period in Europe was a time of unprecedented social complexity and significant social and political change that had an impact on human diets. The present study aims to use stable isotope analysis from bone proteins to explore the diets of humans (n = 76) and fauna (n = 5) from the Medieval town of Leopoli-Cencelle (VT, Italy). The town was occupied between the 9th–15th centuries CE, however, the analysed remains date to the Late Medieval period (12th–15th centuries CE). Historical sources provide some information about the inhabitants of this community: the majority of the population was represented by craftsmen and traders, but farmers and shepherds were also present. To date, no biomolecular data regarding this community have been published. The results indicated an increase of 3–5‰ in δ15N values of humans compared to animals, reflecting a high trophic-level. The δ13C results indicated that animal and human diet was mainly based on C3 terrestrial resources, although three humans possessed an isotopic signature indicative of C4 plant consumption. No statistically significant differences between sexes or age groups (adults vs juveniles) were detected. The isotopic results were further placed in their regional and chronological context, adding valuable data to our understanding of diet and food distribution during the Medieval period in Italy.

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.

As a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (δ18Oca and δ13Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured δ18Oca values suggest a significant role of local sources in the water inputs to the body water, whereas δ13Cca values indicate food resources, principally based on C3 plants. Both δ13Cca and δ18Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas.

The present research, an integrative study combining archeology, skeletal biology, and molecular anthropology, deals with skeletal remains recovered in Mora Cavorso Cave (Jenne, Rome, Italy). Burial activity there dates to 6275 ± 45 BP (5322-5084 cal.) and 6405 ± 35 BP (5472-5314 cal.), according to C analyses of a charcoal fragment and a human bone, respectively. This range of dates ascribes the human remains and the archeological materials to a late phase of the Early Neolithic of Central Italy. The human skeletal remains were scattered throughout the cave. We performed morphological examinations and carbon and nitrogen isotope analyses--using bone collagen--to reconstruct the paleobiology and the paleodiet of the community. The complex comprised at least 28 individuals, including adult males and females and sub-adults. The skeletal remains exhibited a high degree of biomechanical stress and several cases of degenerative and infectious diseases; one of them showed a sclerosing mastoiditis. The stable isotope analyses suggested a diet rich in terrestrial food sources in particular sheep and goat livestock. These results seem to point out that no dietary shift occurred during the Neolithic period in this community, suggesting the maximum use of the environmental resources that these early Neolithic had available. It is worth noting that two individuals showed high nitrogen values, likely the result of nutritional stress brought on by limited protein intake or metabolic diseases.

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

The paper aims to point out the subsistence in Eneolithic Central Italian communities by Stable Isotope Analysis. This period marked a tipping point in the food strategies because it was characterized by economic changes and several technological improvements leading to enhance land exploitation and livestock breeding. Carbon and nitrogen stable isotope analysis has been used to analyze the food consumption of 54 people belonging to 5 Eneolithic communities scattered throughout Central Italy, where no data have yet been published. The estimation of the main protein intake has been achieved in order to quantify the differences among these communities. The results are consistent with a diet mainly based on terrestrial resources, with no exclusive marine sources consumption, although their occasional usage cannot be ruled out, especially for selected funerary contexts. The data suggest an overall subsistence based on greater local resource procurement, supported by regional productivity maximization. A roughly homogeneous landscape could be outlined in Tuscany and Marche communities witnessing a shared diet preference that could be modified by local preferences. The fully developed trade routes between the two sides of the Apennines could address the overall dietary homogeneity of the studied communities, especially between Fontenoce di Recanati and the southern Tuscan human groups such as Grotta del Fontino and Buca di Spaccasasso, with lesser influence for Le Lellere and Podere Cucule that seem to suggest a more locally based subsistence, even though the funerary affinities do not match this overall diet homogeneity.

Objectives The aim of this study was to explore the mitochondrial variability in the Yanomami population to reconstruct its demographic history and explore its genetic composition in relation to its cultural and linguistic features. Methods A total of 174 human head hair shafts -collected in 1958- belonging to individuals from a Yanomami group living in Santa Isabel, Brazil, were analyzed. Automated extraction of the hairs was performed, and several methods were applied to optimize the analysis of the degraded DNA. The mtDNA hypervariable segments I–II, along with the 9-bp COII-tRNALys deletion, were investigated. Using published data from the Yanomami and other Amazonian populations, several statistical analyses were carried out to explore the genetic variability within the study population. Results Ninety eight percent of the mitochondrial DNA (mtDNA) sequences analyzed belonged to Native American haplogroups, while 2% belonged to African haplogroups. Compared with the Yanomami groups previously studied, the Santa Isabel sample seemed more genetically similar to other Amazonian populations. Conclusions Among the Yanomami samples studied to date, the Santa Isabel Yanomami show a higher genetic heterogeneity. This could be due to gene flow with non-Yanomami populations, as well as to the introduction of new mitochondrial haplotypes by gold miners. In both cases, the geographic location of Santa Isabel might have made this Yanomami village less isolated than the others, suggesting that the Rio Negro played a central role in increasing its genetic variability. On the whole, the Yanomami were quite genetically diversified, probably mirroring their great linguistic heterogeneity. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc.

The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations.This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time.Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories.The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations.Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.

Stable isotope analysis in the reconstruction of human palaeodiets can yield clues to early human subsistence strategies, origins and history of farming and pastoralist societies, and intra- and intergroup social differentiation. In the last 10 years, the method has been extended to the pathological investigation. Stable isotope analysis to better understand a diet-related disease: celiac disease in ancient human bones was carried out. To do this, we analyzed the nitrogen and carbon isotopic composition of human (n = 37) and faunal (n = 8) bone remains from the archaeological site of Cosa at Ansedonia, on the Tyrrhenian coast near Orbetello (Tuscany), including the skeletal remains of a young woman (late 1st century–early 2nd century Common Era [CE]) with morphological and genetic features suggestive of celiac disease. We compared the young woman's isotopic data with those of other individuals recovered at the same site but from two later time periods (6th century CE; 11–12th century CE) and with literature data from other Italian archaeological sites dating to the same period. Her collagen δ13C and δ15N values differed from those of the samples at the same site, and from most but not all of the contemporary sites. Although the woman's diet appears distinct, chronic malnutrition resulting from severe malabsorption of essential nutrients due to celiac disease may have affected the isotopic composition of her bone collagen. Am J Phys Anthropol 154:349–356, 2014. © 2014 Wiley Periodicals, Inc.

The most abundant of the collagen protein family, type I collagen is encoded by the COL1A2 gene. The COL1A2 restriction fragment length polymorphisms (RFLPs) EcoRI, RsaI and MspI in samples from several different central-eastern Mediterranean populations were analysed and found to be potentially informative anthropogenetic markers.The objective was to define the genetic variability of COL1A2 in the central-eastern Mediterranean and to shed light on its genetic distribution in human groups over a wide geographic area.PCR-RFLP analysis of EcoRI, RsaI and MspI polymorphisms of the COL1A2 gene was performed on oral swab and blood samples from 308 individuals from the central-eastern Mediterranean Basin. The genetic similarities among these groups and other populations described in the literature were investigated through correspondence analysis.Single-marker data and haplotype frequencies seemed to suggest a genetic homogeneity within the European populations, whereas a certain degree of differentiation was noted for the Egyptians and the Turks.The genetic variability in the central-eastern Mediterranean area is probably a result of the geographical barrier of the Mediterranean Sea, which separated European and African populations over time.

The genetic variation in Italy is the result of ancient population movement, demographic change, and geography. The increasing possibility of studying the maternal genetic structure of selected Italian population samples at a high level of phylogenetic resolution provides a particularly useful model to assess the presence of genetic traces of the ancient people who lived in Italy in pre-Roman times in present populationsIn this study we reconstructed the genetic maternal history of Jenne and Vallepietra, two mountain communities in the Aniene Valley in the Simbruini Mountains near Rome. Both communities have been spared external invasion due to their geographic location, which very likely preserved the genetic pool of these autochthonous populations.The study population (124 individuals from Jenne and Vallepietra) were investigated for D-loop mtDNA hypervariable segments I (HVS-I) and II (HVS-II) and for informative single nucleotide polymorphisms (SNPs) within the coding region. The detected haplotypes were then compared with those of other Italian, European and Mediterranean populations.The distribution of mtDNA diversity in Jenne and Vallepietra, although similar to that found in other European populations, shows a basic variability and the typical signs of a certain degree of isolation between them and other populations analysed; in particular, the Vallepietra sample showed an unusually high frequency (71.3%) of mtDNA haplogroups which are typical of Near Eastern and South-Western Asian populations.The high degree of differentiation between the two villages is intriguing, since it suggests a low level of gene flow between them, despite their close geographic proximity and shared linguistic features. The degree of their genetic isolation, also in comparison to other Italian, European and Mediterranean populations, is consistent with isolation among geographically separated populations.

Paleogenetics is providing increasing evidence about the biological characteristics of ancient populations. This paper examines the guiding principles and methodologies to the study of ancient DNA with constant references to the state of the art in this fascinating disciplin.

Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation.The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis.Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components.As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA.Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis.

Stable isotope analysis in the reconstruction of human palaeodiets can yield clues to early human subsistence strategies, origins and history of farming and pastoralist societies, and intra- and intergroup social differentiation. In the last 10 years, the method has been extended to the pathological investigation. Stable isotope analysis to better understand a diet-related disease: celiac disease in ancient human bones was carried out. To do this, we analyzed the nitrogen and carbon isotopic composition of human (n = 37) and faunal (n = 8) bone remains from the archaeological site of Cosa at Ansedonia, on the Tyrrhenian coast near Orbetello (Tuscany), including the skeletal remains of a young woman (late 1st century-early 2nd century Common Era [CE]) with morphological and genetic features suggestive of celiac disease. We compared the young woman's isotopic data with those of other individuals recovered at the same site but from two later time periods (6th century CE; 11-12th century CE) and with literature data from other Italian archaeological sites dating to the same period. Her collagen δ(13) C and δ(15) N values differed from those of the samples at the same site, and from most but not all of the contemporary sites. Although the woman's diet appears distinct, chronic malnutrition resulting from severe malabsorption of essential nutrients due to celiac disease may have affected the isotopic composition of her bone collagen.

SummarySeveral major migrations and population turnover events during the later Stone Age (after c. 11,000 cal. BP) are believed to have shaped the contemporary population genetic diversity in Eurasia. While the genetic impacts of these migrations have been investigated on regional scales, a detailed understanding of their spatiotemporal dynamics both within and between major geographic regions across Northern Eurasia remains largely elusive. Here, we present the largest shotgun-sequenced genomic dataset from the Stone Age to date, representing 317 primarily Mesolithic and Neolithic individuals from across Eurasia, with associated radiocarbon dates, stable isotope data, and pollen records. Using recent advances, we imputed >1,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences. We show that 1) Eurasian Mesolitic hunter-gatherers were more genetically diverse than previously known, and deeply divergent between the west and the east; 2) Hitherto genetically undescribed hunter-gatherers from the Middle Don region contributed significant ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the transition from Mesolithic hunter-gatherers to Neolithic farmers was highly distinct, east and west of a “Great Divide” boundary zone extending from the Black Sea to the Baltic, with large-scale shifts in genetic ancestry to the west. This include an almost complete replacement of hunter-gatherers in Denmark, but no substantial shifts during the same period further to the east; 4) Within-group relatedness changes substantially during the Neolithic transition in the west, where clusters of Neolithic farmer-associated individuals show overall reduced relatedness, while genetic relatedness remains high until ~4,000 BP in the east, consistent with a much longer persistence of smaller localised hunter-gatherer groups; 5) A fast-paced second major genetic transformation beginning around 5,000 BP, with Steppe-related ancestry reaching most parts of Europe within a 1,000 years span. Local Neolithic farmers admixed with incoming pastoralists in most parts of Europe, whereas Scandinavia experienced another near-complete population replacement, with similar dramatic turnover-patterns also evident in western Siberia; 6) Extensive regional differences in the ancestry components related to these early events remain visible to this day, even within countries (research conducted using the UK Biobank resource). Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall. Overall, our findings show that although the Stone-Age migrations have been important in shaping contemporary genetic diversity in Eurasia, their dynamics and impact were geographically highly heterogeneous.