We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by~2500 BCE and, by~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The forces propelling its expansion are a matter of long-standing debate, with support for both cultural diffusion and migration. We present new genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 Beaker-associated individuals. We detected limited genetic affinity between Iberian and central European Beaker-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, migration played a key role in the further dissemination of the Beaker Complex, a phenomenon we document most clearly in Britain, where the spread of the Beaker Complex introduced high levels of Steppe-related ancestry and was associated with a replacement of ~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 400 years earlier.

Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focus on the maternal genetic makeup of the Neolithic (~ 5500–3000 BCE), Chalcolithic (~ 3000–2200 BCE) and Early Bronze Age (~ 2200–1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.

Significance Subsistence shifts from hunting and gathering to agriculture over the last 12,000 y have impacted human culture, biology, and health. Although past human health cannot be assessed directly, adult stature variation and skeletal indicators of nonspecific stress can serve as proxies for health during growth and development. By integrating paleogenomic genotype and osteological stature data on a per-individual basis for 167 prehistoric Europeans, we observe relatively shorter than expected statures among early farmers after correcting for individual genetic contributions to stature. Poorer nutrition and/or increased disease burdens for early agriculturalists may partly underscore this result. Our integrated osteological–genetic model has exciting potential for studies of past human health and expansion into various other contexts.

This corrects the article DOI: 10.1038/nature25738.