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.

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.