Early Neolithic Farmers Research Articles

Future-Proofing Agriculture: De Novo Domestication for Sustainable and Resilient Crops.

The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This challenge is exacerbated by a reduction in cultivable land and the adverse effects of climate change on crop yield quantity and quality. Breeders actively embrace cutting-edge omics technologies to pursue resilient genotypes in response to these pressing issues. In this global context, new breeding techniques (NBTs) are emerging as the future of agriculture, offering a solution to introduce resilient crops that can ensure food security, particularly against challenging climate events. Indeed, the search for domestication genes as well as the genetic modification of these loci in wild species using genome editing tools are crucial steps in carrying out de novo domestication of wild plants without compromising their genetic background. Current knowledge allows us to take different paths from those taken by early Neolithic farmers, where crop domestication has opposed natural selection. In this process traits and alleles negatively correlated with high resource environment performance are probably eradicated through artificial selection, while others may have been lost randomly due to domestication and genetic bottlenecks. Thus, domestication led to highly productive plants with little genetic diversity, owing to the loss of valuable alleles that had evolved to tolerate biotic and abiotic stresses. Recent technological advances have increased the feasibility of de novo domestication of wild plants as a promising approach for crafting optimal crops while ensuring food security and using a more sustainable, low-input agriculture. Here, we explore what crucial domestication genes are, coupled with the advancement of technologies enabling the precise manipulation of target sequences, pointing out de novo domestication as a promising application for future crop development.

Past human expansions shaped the spatial pattern of Neanderthal ancestry.

The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.

A multi-method approach with machine learning to evaluating the distribution and intensity of prehistoric land use in Eastern Iberia

The present study seeks to better understand the coupling of social and biophysical systems during the late Pleistocene and Holocene, a period characterized by changing interglacial conditions as well as human population expansion and intensified ecosystem management. The approach consists of a combination of patch-based archaeological survey methods, sediment column sampling for paleoenvironmental data, geospatial analysis, and machine learning for chronological unmixing, allowing the systematic evaluation of the distribution and intensity of prehistoric land use in the study area of eastern Mediterranean Iberia. Occupational and Land Use Intensity maps developed from continuous distributions of surface artifacts as well as a summed probability density curve developed from 14C dates indicate low but steady human presence in the study area during the Middle Paleolithic and Upper Paleolithic with a marked decrease of human presence across the Pleistocene/Holocene boundary. The Early (and Middle) Neolithic saw the most ubiquitous and intensive occupation of the study area followed by a significant decline during the Late Neolithic/Chalcolithic. The charcoal analysis also supports this pattern. Early Neolithic farming strategies may not have been damaging initially during the climatic regime of the Early Holocene but exacerbated the impacts of higher temperatures and summer droughts, with a loss of the most productive farmland, seen at the onset of the Late Neolithic. Similar boom-bust population trends have been documented throughout Europe during these same time spans and may indicate a recursive interaction or “coupling” between global and regional climate events and human land use strategies.

Reassessing Neolithic Diets in Western Scotland

Although marine resources are known to have been exploited by both foragers and early farmers in Scotland, the importance of seafood to the diets of Neolithic groups has been widely debated. Here we present paired stable isotope (δ13C and δ15N) and radiocarbon measurements on Early Neolithic human remains from Raschoille Cave in Oban. These are compared with published data for other sites in western Scotland and used to re-evaluate the use of marine resources by the first farmers. The diets of Late Mesolithic foragers and Early Neolithic farmers were modelled from stable isotope data using both Linear and Bayesian (FRUITS) mixing models. Our FRUITS dietary models indicate that Mesolithic foragers obtained much of their dietary protein and calories from marine resources, consistent with the predominance of shellfish, fish and sea mammal remains in their shell middens. Of note is the large proportion of dietary calories obtained from plant foods, which is like that of the early farming groups. The diets of Early Neolithic farmers appear relatively homogeneous across Scotland. Plant foods were the primary source of calories. Meat and/or dairy from terrestrial mammals were the most important source of dietary protein. Marine resources were, at most, a minor component of the ‘lifetime’ diet.

A Healthier Smile in the Past? Dental Caries and Diet in Early Neolithic Farming Communities from Central Germany.

Dental health is closely linked to an individual’s health and diet. This bioarcheological study presents dental caries and stable isotope data obtained from prehistoric individuals (n = 101) from three Early Neolithic sites (c. 5500-4800 BCE) in central Germany. Dental caries and ante-mortem tooth loss (AMTL) were recorded and related to life history traits such as biological sex and age at death. Further, we correlate evidence on caries to carbon and nitrogen isotope data obtained from 83 individuals to assess the relationship between diet and caries. In 68.3% of the adults, carious lesions were present, with 10.3% of teeth affected. If AMTL is considered, the values increase by about 3%. The prevalence of subadults (18.4%) was significantly lower, with 1.8% carious teeth. The number of carious teeth correlated significantly with age but not sex. The isotopic data indicated an omnivorous terrestrial diet composed of domestic plants and animal derived protein but did not correlate with the prevalence of carious lesions. The combined evidence from caries and isotope analysis suggests a prevalence of starchy foods such as cereals in the diet of these early farmers, which aligns well with observations from other Early Neolithic sites but contrasts to Late Neolithic and Early Bronze Age populations in Germany.

Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily

SummarySicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.

Food practices of the first farmers of Europe: Combined use-wear and microbotanical studies of Early Neolithic grinding tools from the Paris Basin

Food practices have always been a key issue to reconstruct part of the cultural identities of past and present societies. In archaeology, the question of vegetal processing and consumption has generally been discussed through different, yet complementary lenses that include botanical remains and cooking pots. However, it has seldom been integrated in a combined approach. Our paper explores the characteristics and role of plant transformation in Early Neolithic contexts from the Paris Basin (5100–4900 BCE), by combining use-wear analysis of grinding tools and the study of microbotanical remains (starch grains and phytoliths). Our integrated approach reinforces the interpretations and reduces the methodological limitations that arise when each analysis is considered separately. It also proposes a more complex vision than initially expected regarding the uses and lifecycles of grinding tools in daily plant preparation. Together with the dominant processing of cereals and legumes, tubers and rhizomes appear to have been regularly ground on querns. Different steps in plants processing are also evident, such as dehusking, heating, and sprouting. Other clues point towards the transformation of bark and ferns, known for their varied medicinal properties. These results and related methodological issues support discussions regarding the possible conservatism or innovations in vegetal food practices of Early Neolithic farmers inhabiting a region located at the most westerly point of the Linearbandkeramik expansion during the final centuries of this first wave of Neolithic dispersal throughout the European continent.

A brief history of plants in north-eastern France: 6,000 years of crop introduction in the Plain of Troyes, Champagne

The amount and strength of archaeobotanical and archaeological data available for the territory of the Plain of Troyes, in Champagne (north-eastern France), make it possible to write a local history of domestic plants. The story begins with the arrival of the early Neolithic farmers (5200 bc), introducing agriculture with the first staple crops, the hulled wheats emmer and einkorn, pea, lentil, and possibly opium poppy. Their descendants left few traces, but from the very beginning of the Late Bronze Age (14th century bc), human expansion quickly resumed, supported by a completely remodelled farming system. Many new plants (spelt, millets, pulses…), introduced from far-off countries were cultivated, securing production, and decreasing gathering. This apparently successful agriculture lasted for one millennium till the middle of the Late Iron Age (2nd century bc). Technical innovations in agricultural tools then triggered new changes in production systems, evidenced by a sharp decline in millets and a more modest rise in naked wheats. This trend continued during the Roman era, a time where many agricultural innovations took place, especially concerning fruticulture and possibly viticulture. The true development of the latter occurred during Early Middle Ages. At that time hulled six-row barley and naked wheats were well established as the main crops, while two more species, cultivated oat and rye, were added to the already large panel of cereals. Our investigations do not go further than the 10th century ad, but despite the large gap till today, some legacies of the past are still perceptible in the contemporary agricultural heritage.

Palynomorphs in surface sediments of the North-Western Black Sea as indicators of environmental conditions

Most previous Black Sea palynology studies have used pollen-spore assemblages as proxies for climate and landscape changes, and dinocyst assemblages as proxies for surface water salinity. However, there are few data on within-region variations in these assemblages using large sets of surface samples and a full suite of palynomorphs, including terrigenous pollen + spores, freshwater algal spores, and organic remains of marine microplankton, micro- and meiobenthos. Here we fill this knowledge gap, using results from a palynological study of 43 surface samples from water depths of 71–905 mbsl on the Ukrainian Shelf and adjoining continental slope, NW Black Sea. The palynology samples were collected in conjunction with water and sediment chemistry data, grain-size, micropaleontological and meiobenthos data from the EU-FP6 project HERMES “Hotspot Ecosystems Research on the Margins of European Seas”. This dataset uniquely covers shelf and upper slope areas east and west of the Odessa-Sinop Fault Zone (OSFZ) that delimits areas of lower and higher hydrocarbon gas contents, respectively.The new data show that on the wide shelf with a shallow (ca. 80 m) oxycline, pollen assemblages differ from classical models for marine pollen transport. On the Ukrainian Shelf, pollen concentrations are extraordinarily high far offshore and the grains are often pyrite-infilled. These features apparently reflect high pollen preservation potential in low oxygen sediments, probably enhanced by cross-shelf transport of land-derived particulate organic matter. The new data have important consequences for accurate modelling of carbon burial and storage in epicontinental seas, and they provide a baseline for evaluating marine pollen concentrations expected to reflect the early Neolithic farming on the Ukrainian shelf. Furthermore, although large concentrations of dinocysts comprise more than half of the total Non-Pollen Palynomorphs (NPP), the high pollen concentrations skew the P:D index (pollen:dinocyst ratio) commonly used to evaluate changes in paleo-shoreline (proxy sea-level) positions. Despite the discharge of several large rivers to the Ukrainian Shelf, there are negligible traces of freshwater algae in the HERMES samples except at Sta. 15 where Pediastrum is abundant. Overall, palynomorphs of terrestrial origin make up about half (52%) of the acid-resistant organic-walled particles on the outer NW Black Sea Shelf and adjacent slope.The abundances of the major micro- and meiobenthic palynomorph groups show the same trends east and west of the OSFZ as the micropaleontological data reported for the HERMES samples taken at the same sites. The combined microzooplankton and zoobenthos surface assemblage data provide an important new baseline for evaluating historical and past changes in biodiversity and aquatic foodweb structure in the now polluted NW Black Sea. Comparison can also be made with foodweb reconstructions for Permian black shales.

Furness’s First Farmers: Evidence of Early Neolithic Settlement and Dairying in Cumbria

In 2015, excavations at Stainton Quarry, Furness, Cumbria, recovered remains that provide a unique insight into Early Neolithic farming in the vicinity. Five pits, a post-hole, and deposits within a tree-throw and three crevices in a limestone outcrop were investigated. The latter deposits yielded potentially the largest assemblage of Carinated Bowl fragments yet recovered in Cumbria. Lipid analysis identified dairy fats within nine of these sherds. This was consistent with previous larger studies but represents the first evidence that dairying was an important component of Early Neolithic subsistence strategies in Cumbria. In addition, two deliberately broken polished stone axes, an Arran pitchstone core, a small number of flint tools and debitage, and a tuff flake were retrieved. The site also produced moderate amounts of charred grain, hazelnut shell, charcoal, and burnt bone. Most of the charred grain came from an Early Neolithic pit and potentially comprises the largest assemblage of such material recovered from Cumbria to date. Radiocarbon dating indicated activity sometime during the 40th–35th centuries calbcas well as an earlier presence during the 46th–45th centuries. Later activity during the Chalcolithic and the Early Bronze Age was also demonstrated. The dense concentration of material and the fragmentary and abraded nature of the pottery suggested redeposition from an above-ground midden. Furthermore, the data recovered during the investigation has wider implications regarding the nature and use of the surrounding landscape during the Early Neolithic and suggests higher levels of settlement permanence, greater reliance on domesticated resources, and a possible different topographical focus for settlement than currently proposed.

A massacre of early Neolithic farmers in the high Pyrenees at Els Trocs, Spain

Violence seems deeply rooted in human nature and an endemic potential for such is today frequently associated with differing ethnic, religious or socio-economic backgrounds. Ethnic nepotism is believed to be one of the main causes of inter-group violence in multi-ethnic societies. At the site of Els Trocs in the Spanish Pyrenees, rivalling groups of either migrating early farmers or farmers and indigenous hunter-gatherers collided violently around 5300 BCE. This clash apparently resulted in a massacre of the Els Trocs farmers. The overkill reaction was possibly triggered by xenophobia or massive disputes over resources or privileges. In the present, violence and xenophobia are controlled and sanctioned through social codes of conduct and institutions. So that, rather than representing an insurmountable evolutionary inheritance, violence and ethnic nepotism can be overcome and a sustainable future achieved through mutual respect, tolerance and openness to multi-ethnic societies.

The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.

The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330–1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26–3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial ‘Bergsgraven’. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic–Caspian steppe herders, as well as smaller components originating from hunter–gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

River Valleys Shaped the Maternal Genetic Landscape of Han Chinese.

A general south-north genetic divergence has been observed among Han Chinese in previous studies. However, these studies, especially those on mitochondrial DNA (mtDNA), are based either on partial mtDNA sequences or on limited samples. Given that Han Chinese comprise the world's largest population and reside around the whole China, whether the north-south divergence can be observed after all regional populations are considered remains unknown. Moreover, factors involved in shaping the genetic landscape of Han Chinese need further investigation. In this study, we dissected the matrilineal landscape of Han Chinese by studying 4,004 mtDNA haplogroup-defining variants in 21,668 Han samples from virtually all provinces in China. Our results confirmed the genetic divergence between southern and northern Han populations. However, we found a significant genetic divergence among populations from the three main river systems, that is, the Yangtze, the Yellow, and the Zhujiang (Pearl) rivers, which largely attributed to the prevalent distribution of haplogroups D4, B4, and M7 in these river valleys. Further analyses based on 4,986 mitogenomes, including 218 newly generated sequences, indicated that this divergence was already established during the early Holocene and may have resulted from population expansion facilitated by ancient agricultures along these rivers. These results imply that the maternal gene pools of the contemporary Han populations have retained the genetic imprint of early Neolithic farmers from different river basins, or that river valleys represented relative migration barriers that facilitated genetic differentiation, thus highlighting the importance of the three ancient agricultures in shaping the genetic landscape of the Han Chinese.

Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians

One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria – Shekerdja mogila, Gabrova mogila and Bereketska mogila – dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe.

Neolithic Explanations Revisited: Modelling the Arrival and Spread of Domesticated Cattle into Neolithic Britain

ABSTRACT Set against the new chronological framework for the introduction and spread of the Neolithic into Britain this paper considers the logistics of introducing domestic cattle from continental Europe. Cattle were the most extensively utilised domestic animal at the start of the Neolithic and understanding the processes behind their introduction is critical for exploring early Neolithic farming systems. We begin by exploring the realities of creating a viable new animal population and then moving that population to Britain across the water from Continental Europe. Using a series of simulated models we demonstrate that only a very small number of cattle need to have been introduced into Britain in order to enable the uptake and spread of domestic cattle across the whole island. This, in turn, may effect how we consider the mechanisms involved in the adoption of the Neolithic, and can better inform our understanding of the kinds of processes involved in the transition to the Neolithic.

FADS1 and the Timing of Human Adaptation to Agriculture.

Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced ∼8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet, or efficiency of selection due to increases in effective population size.

Symbols in motion: Flexible cultural boundaries and the fast spread of the Neolithic in the western Mediterranean.

The rapid diffusion of farming technologies in the western Mediterranean raises questions about the mechanisms that drove the development of intensive contact networks and circulation routes between incoming Neolithic communities. Using a statistical method to analyze a brand-new set of cultural and chronological data, we document the large-scale processes that led to variations between Mediterranean archaeological cultures, and micro-scale processes responsible for the transmission of cultural practices within farming communities. The analysis of two symbolic productions, pottery decorations and personal ornaments, shed light on the complex interactions developed by Early Neolithic farmers in the western Mediterranean area. Pottery decoration diversity correlates with local processes of circulation and exchange, resulting in the emergence and the persistence of stylistic and symbolic boundaries between groups, while personal ornaments reflect extensive networks and the high level of mobility of Early Neolithic farmers. The two symbolic productions express different degrees of cultural interaction that may have facilitated the successful and rapid expansion of early farming societies in the western Mediterranean.

The beginning of the Neolithic in the Po Plain (northern Italy): Problems and perspectives

The Po Valley is one of the major physiographic units of northern Italy. It can be considered as a key area for the interpretation of long-term historical events and processes because of its location midway between the Mediterranean world and continental Europe. This paper is an updated summary of our knowledge of the Early Neolithic farming communities of the region. In particular it discusses data derived from radiocarbon dated sites. Its aim is to provide the international audience with an updated view of the topic, based on the discussion of a new series of AMS radiocarbon results, to frame the earliest producing communities of the Po Valley into the more general picture of the Neolithization of Italy. To achieve the goal, apart from radiocarbon assays, we have taken into consideration material culture remains, subsistence economy, environmental resources, and data gathered from archaeometric analyses and technology.

Immigration and admixture in Europe

Paleogenomics![Figure][1] Early Neolithic farmers moved through the Aegean region as they traveled from Asia to Europe. PHOTO ©ROBERTHARDING/ALAMY STOCK PHOTO The Neolithic transition in Europe marked the shift from hunting-gathering societies to sedentary farming societies. Evidence has