100 ancient genomes show repeated population turnovers in Neolithic Denmark

Abstract

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

Population genomics of post-glacial western Eurasia

“…Adding extra proximate sources allowed us to further refine the ancestry composition of northern European HGs. In Denmark, our 28 sequenced and imputed HG genomes derived almost exclusively from a southern European source (Italy_15000BP_9000), with notable homogeneity across a 5,000-year transect 34 (Extended Data Fig. 4a and Supplementary Data 12).…”

“…bp, steppe-related ancestry was already dominant in individuals from Britain, France and the Iberian Peninsula 12,51 . Notably, because of the delayed neolithization in southern Scandinavia, these dynamics resulted in two episodes of large-scale genetic turnover in Denmark and southern Sweden within a period of roughly 1,000 years 34 (Fig. 3).…”

“…Samples cover many of the key Mesolithic and Neolithic cultures in western Eurasia, such as the Maglemose, Ertebølle, Funnel Beaker (TRB) and Corded Ware/ Single Grave cultures in Scandinavia; the Cardial in the Mediterranean; the Körös and Linear Pottery (LBK) in southeastern and central Europe; and many archaeological cultures in Ukraine, western Russia and the trans-Ural region (for example, Veretye, Lyalovo, Volosovo and Kitoi). Our sampling was particularly dense in Denmark, from where an accompanying paper presents a detailed and continuous sequence of 100 genomes spanning the Early Mesolithic to the Bronze Age 34 . Dense sampling was also obtained from Ukraine, western Russia and the trans-Ural region, spanning the Early Mesolithic through to the Neolithic, up to around 5,000 bp.…”

Productivity of the eelgrass biotope and the resilience of fisher-hunter-gatherers in prehistoric Denmark

“…Danish Mesolithic human collagen δ 13 C versus median calibrated 14 C age, after DRE correction (3.3.3). Data from (Allentoft et al 2024; Allentoft et al 2022; Fischer et al 2007a; Price et al 2007). …”

“…Danish Mesolithic human collagen δ 13 C and δ 15 N. Data from (Allentoft et al 2024; Allentoft et al 2022; Fischer et al 2007a; Price et al 2007). Colours reflect k-means clustering (k=3) of isotope values.…”