Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1–8 who received a limited amount of admixture from resident hunter-gatherers3–5,9. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 180 samples, 130 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE, n = 100), Germany (5500–3000 BCE, n = 42), and Spain (5500–2200 BCE, n = 38)—we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

Perhaps nowhere in European prehistory does the idea of clearly-defined cultural boundaries remain more current than in the initial Neolithic, where the southeast–northwest trend of the spread of farming crosses what is perceived as a sharp divide between the Balkans and central Europe. This corresponds to a distinction between the Vinča culture package, named for a classic site in Serbia, with its characteristic pottery assemblage and absence of longhouses, and the Linearbandkeramik (LBK), with equally diagnostic but different pottery, and its apparently culturally-diagnostic longhouses, extending in a more northerly belt through central Europe westward to the Dutch coast. In this paper we question the concept of such a clear division through a presentation of new data from the site of Szederkény-Kukorica-dűlő. A large settlement in southeast Transdanubia, Hungary, excavated in advance of road construction, Szederkény is notable for its combination of pottery styles, variously including Vinča A, Ražište and LBK, and longhouses of a kind otherwise familiar from the LBK world. Formal modelling of its date establishes that the site probably began in the later 54th century cal BC, lasting until the first decades of the 52nd century cal BC. Occupation, featuring longhouses, pits and graves, probably began at the same time in the eastern and western parts of the settlement, starting a decade or two later in the central part; the western part was probably the last to be abandoned. Vinča pottery is predominantly associated with the eastern and central parts of the site, and Ražište pottery with the west. Formal modelling of the early history of longhouses in the LBK world suggests their emergence in the Formative LBK of Transdanubia c. 5500 cal BC followed by rapid dispersal in the middle of the 54th century cal BC, associated with the ‘earliest’ (älteste) LBK. The adoption of longhouses at Szederkény thus appears to come a few generations after the start of this ‘diaspora’. Rather than explaining the mixture of things, practices and perhaps people at Szederkény with reference to problematic notions such as hybridity, we propose instead a more fluid and varied vocabulary, encompassing combination and amalgamation, relationships and performance in the flow of social life, and networks; this makes greater allowance for diversity and interleaving in a context of rapid change.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth-fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.

In European and many African, Middle Eastern and Southern Asian populations lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the last 10,000 years 1 . While LP selection and prehistoric milk consumption must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions 2,3 . We provide detailed distributions of milk exploitation across Europe over the last 9k years using c. 7,000 pottery fat residues from >550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Surprisingly, comparison of model likelihoods indicates that LP selection varying with levels of prehistoric milk exploitation provides no better explanation of LP allele frequency trajectories than uniform selection since the Neolithic. In the UK Biobank 4,5 cohort of ~500K contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests other hypotheses on the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available, but that under particular conditions and microbiological milieux this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitationproxies for these driversprovide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today’s Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers. Author Summary We report an exceptional large Neolithic DNA dataset from the Carpathian Basin, which was the cradle of the first Central European farming culture, the so called Linearbandkeramik culture. We generated 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic and Neolithic specimens from western Hungary and Croatia, attributed to the hunter-gatherers, Starčevo and LBK cultures (7th/6th millennium BC). We observe genetic discontinuity between Mesolithic foragers and early farmers, and genetic continuity between farming populations of the 6th-4th millennium BC across a vast territory of southeastern and Central Europe. Nine novel Y chromosome DNA profiles offer first insights into the Y chromosome diversity of the earliest European farmers, and further support the migration (demic diffusion) from the Near East into Central Europe along the Continental route of Neolithisation. The joint analyses of the two uniparental genetic systems let us conclude that men and women had a similar roles in the Early Neolithic migration process but their dispersal patterns were determined by sex-specific rules.

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Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE, n = 98), Germany (5500–3000 BCE, n = 42), and Spain (5500–2200 BCE, n = 37)—we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ances try among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

IntroductionGreat timber longhouses are a defining feature of the first Neolithic communities in central and western Europe, belonging to the Linearbandkeramik (LBK) culture of the later sixth millennium cal BC (Coudart 1998). Even in the first recorded phase of longhouse construction (belonging to the LBK 'formative' phase), many elements of this architecture, such as longpits, side ditches and internal post rows, were already present (Bánffy 2013).During the succeeding (or earliest) LBK, buildings could be substantial, up to 20m long or so by 6m wide (Stäuble 2005). From the later LBK onwards, in the Flomborn, Ačkovy, Notenkopf and Keszthely phases, which began c. 5300 cal BC, some longhouses reach over 30m in length and become more elaborate internally, the typical internal cross-rows of three posts changing to any number of combinations and layouts (Modderman 1970; Coudart 1998). Many settlements have been found, each characterised by larger and smaller groupings of long houses.Despite their high archaeological visibility, wide distribution, and thousands of excavated examples, many questions remain about these iconic structures. Where did this architecture first emerge? In the virtual absence of preserved floors, what can be said about the use of the interiors? How long did these buildings last, given the substantial oak posts with which the majority of them were framed? How did houses relate to their neighbours?What did variation in house size mean in terms of household composition? Should each house be considered an independent unit, or was household membership distributed across more than one building? Consideration of such questions was long framed by the Hofplatzmodell, or independent homestead model. This model emerged from pioneering, large-scale rescue excavations on the Aldenhovener Platte in north-western Germany (Boelicke et al. 1988), and is based on a complex set of arguments built upon a combination of site layouts, horizontal stratigraphy, ceramic sequence constructed through correspondence analysis of decorative motifs on fineware pottery, and an inferred house duration of some 25-30 years (summarised in Zimmermann 2012). The model posits that each longhouse existed in its own space-or yard in Dutch terminology (van de Velde 1979)-and is separated from irregularly spaced neighbours by a wider area that includes an activity zone spanning approximately 25m (in the case of Langweiler 8: Boelicke et al. 1988). With each succeeding generation, these loose 3 house clusters shifted slightly. Community thus comprised a combination of independent households, or groupings of such households, as seen at Vaihingen, south-western Germany, or Cuiry-lès-Chaudardes, northern France (Bogaard et al. 2011; Hachem 2011); wards are a useful term in this context (van de Velde 1979).More recently, the Hofplatzmodell has been strongly criticised (Rück 2009(Rück , 2012 Versend-GilencsaThe large archaeological rescue excavation at Versend-Gilencsa ( The western part of the site is more densely packed with feature...