The genetic history of Portugal over the past 5,000 years

Background: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present the most comprehensive collection of ancient Portuguese genomes (n = 67), spanning 5,000 years of human history, from the Neolithic to the 19th century. Results: We identify early admixture between local hunter-gatherers and Anatolian-related farmers in Neolithic Portugal, with a north-south gradient of Magdalenian ancestry persistence. This profile continues into the Chalcolithic, though Bell Beaker-associated sites reveal Portugal's first evidence of Steppe-related ancestry. Such ancestry has a broader demographic impact during the Bronze Age, despite continuity of local Chalcolithic genetic ancestry and limited Mediterranean connections. The village of Idanha-a-Velha emerges as a major Roman migration and interaction hub, presenting a notably diverse genetic profile that includes north African and eastern Mediterranean ancestries. The Early Medieval period is marked by the arrival of central European genetic diversity (Suebi/Visigoth-related), adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant additional African admixture in the south. The latter remains stable during the post-Islamic period, suggesting enduring African influences. Conclusions: We reveal dynamic patterns of migration in line with cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archaeological data, enhancing our understanding of Iberia's biological and cultural heritage.