Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west–east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

Human bones from single inhumation burials and artifacts made from terrestrial mammal (ungulate) bone found in direct association with the skeletons were obtained from the Stone Age site of Schela Cladovei situated just below the Iron Gates Gorge of the River Danube. The results of stable isotope analyses of the human bone collagen are consistent with a heavy dependence on aquatic protein while radiocarbon dating of the samples reveals an offset of 300–500 years between the two sample types, indicating a freshwater reservoir effect in the human bone samples. Since protein consumption is by far the major source of nitrogen in the human diet we have assumed a linear relationship between δ¹⁵N and the level of aquatic protein in each individual's diet and derived a calibration for ¹⁴C age offset versus δ¹⁵N which has been applied to a series of results from the site at Lepenski Vir within the gorge. The corrected ¹⁴C ages (7310-6720 BP) are now consistent with the previous ¹⁴C age measurements made on charcoal from related contexts (7360–6560 BP). In addition, the data indicate a change from a primarily aquatic to a mixed terrestrial/aquatic diet around 7100 BP and this may be argued as supporting a shift from Mesolithic to Neolithic. This study also has wider implications for the accurate dating of human bone samples when the possibility exists of an aquatic component in the dietary protein and strongly implies that δ¹⁵N analysis should be undertaken routinely when dating human bones.

Over the past 50 years the most enigmatic feature of pollen diagrams from northwest Europe has been the mid-Holocene ‘elm decline’, and there has been much speculation as to the origin(s) and cause(s) of this event. A total of 150 radiocarbon dates from 139 sites spanning the elm decline in Britain and Ireland have been collated and scrutinized. Statistical analyses on 138 dates show that the event has a mean date of 5036 ¹⁴C yr BP with a standard deviation of ± 247. Calibration of the dates and combining the sum probabilities yielded a range spanning 6347-5281 cal yr BP (1s), covering 1066 years. The start of the elm decline event lies between 6343 and 6307 cal yr BP (1s), a period of 36 years, indicating that the onset was rapid. The end of the event lies between 5290 and 5420 cal yr BP (1s), a period of 130 years. The probability distribution indicates that the elm decline was a uniform phased event across the British Isles. It appears that the elm decline can be explained to a large extent by the outbreak of disease. However, recent research on palaeoclimatic change and the nature of the transition from the Mesolithic to Neolithic in the British Isles suggests that both climatic change and human activities were implicated. It was probably the interplay between these factors, rather than any in isolation, that catalyzed the widespread, catastrophic decline of elm populations during the mid-Holocene.

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.