A study of 100 ancient genomes from Denmark reveals repeated population turnovers during the Mesolithic, Neolithic, and Early Bronze Age. The Mesolithic individuals from the Maglemose, Kongemose, and Ertebølle cultures form a distinct genetic cluster related to Western European hunter-gatherers, showing genetic homogeneity from 10,500 to 5,900 years before present. The Neolithic transition, delayed by over a millennium compared to Central Europe, was abrupt, leading to a population replacement with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for about 1,000 years before being replaced by immigrants with Steppe-derived ancestry, giving rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. The study combines genetic data with proxies for diet, mobility, and vegetation to show parallel shifts in genotype, phenotype, diet, and land use during these demographic events. The Mesolithic and Neolithic periods in southern Scandinavia are marked by cultural transitions, but genetic and demographic impacts remain largely uncharacterized. The Neolithic transition in Denmark was delayed, with hunter-gatherer societies flourishing until around 5,900 years before present. The study also shows that the Neolithic transition in Denmark involved a mix of Anatolian farmer ancestry and non-local hunter-gatherer ancestry, with a later influx of Steppe-related ancestry. The results highlight the role of both cultural diffusion and demic diffusion in shaping the genetic landscape of Denmark. The study provides insights into the complex genetic history of Denmark, showing how population turnovers and cultural changes were interconnected. The findings suggest that the Neolithic transition in Denmark was driven by new people arriving and rapidly taking over the territory, leading to significant changes in the local landscape and culture. The study also highlights the environmental impact of these population changes, with shifts in land use and vegetation patterns. The research underscores the importance of high-resolution genetic data in understanding the demographic and cultural dynamics of prehistoric societies.A study of 100 ancient genomes from Denmark reveals repeated population turnovers during the Mesolithic, Neolithic, and Early Bronze Age. The Mesolithic individuals from the Maglemose, Kongemose, and Ertebølle cultures form a distinct genetic cluster related to Western European hunter-gatherers, showing genetic homogeneity from 10,500 to 5,900 years before present. The Neolithic transition, delayed by over a millennium compared to Central Europe, was abrupt, leading to a population replacement with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for about 1,000 years before being replaced by immigrants with Steppe-derived ancestry, giving rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. The study combines genetic data with proxies for diet, mobility, and vegetation to show parallel shifts in genotype, phenotype, diet, and land use during these demographic events. The Mesolithic and Neolithic periods in southern Scandinavia are marked by cultural transitions, but genetic and demographic impacts remain largely uncharacterized. The Neolithic transition in Denmark was delayed, with hunter-gatherer societies flourishing until around 5,900 years before present. The study also shows that the Neolithic transition in Denmark involved a mix of Anatolian farmer ancestry and non-local hunter-gatherer ancestry, with a later influx of Steppe-related ancestry. The results highlight the role of both cultural diffusion and demic diffusion in shaping the genetic landscape of Denmark. The study provides insights into the complex genetic history of Denmark, showing how population turnovers and cultural changes were interconnected. The findings suggest that the Neolithic transition in Denmark was driven by new people arriving and rapidly taking over the territory, leading to significant changes in the local landscape and culture. The study also highlights the environmental impact of these population changes, with shifts in land use and vegetation patterns. The research underscores the importance of high-resolution genetic data in understanding the demographic and cultural dynamics of prehistoric societies.