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.

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.

Archaeological evidence points to substantial changes in Bronze Age societies in the European-Mediterranean region. Isotope geochemical proxies have been compiled to provide independent ancillary data to improve the paleoenvironmental history for the period of interest and support the interpretation of the archaeological observations. In addition to published compositions, in this study we gathered new H isotope data from fluid inclusion hosted water from a stalagmite of the Trió Cave, Southern Hungary, and compared http://www.sciencedirect.com/science/article/pii/S1040618217309448 the H isotope data with existing stable isotope and trace element compositions reported for the stalagmite. Additionally, animal bones and freshwater bivalve shells (Unio sp.) were collected from Bronze Age archaeological excavations around Lake Balaton and their stable C and O isotope compositions were measured in order to investigate climate changes and lake evolution processes during this period. The data indicate warm and humid conditions with elevated summer precipitation around 3.7 cal ka BP (Before Present, where present is AD 1950), followed by a short-term deterioration in environmental conditions at about 3.5 cal ka BP. The environment became humid and cold with winter precipitation dominance around 3.5 to 3.4 cal ka BP, then gradually changed to drier conditions at ~3.2 cal ka BP. Significant cultural changes have been inferred for this period on the basis of observations during archaeological excavations. The most straightforward consequences of environmental variations have been found in changes of settlement structure. The paleoclimatological picture is well in line with other East-Central European climate records, indicating that the climate fluctuations took place on a regional scale.