Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales^1,2,3,4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution^5,6,7. 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.

全新世欧亚大陆的重大迁移事件在广泛的区域尺度上具有遗传特征 ^1,2,3,4 。然而，由于缺乏以高时空分辨率 ^5,6,7 采样的古代基因组数据，对接触区种群动态的了解受到了阻碍。在这里，为了解决这个问题，我们分析了丹麦中石器时代、新石器时代和青铜时代早期 7,300 年的 100 具骨骼的鸟枪序列基因组，并将这些基因组与饮食（ ¹³ C 和 ¹⁵ N 含量）、流动性（ ⁸⁷ Sr/ ⁸⁶ Sr 比率）和植被覆盖（花粉）的代理相结合。我们观察到，丹麦中石器时代 Maglemose、Kongemose 和 Ertebølle 文化的个体形成了一个与其他西欧狩猎采集者相关的独特遗传集群。尽管物质文化发生了变化，但他们表现出遗传同质性，从现在之前的 10,500 年到 5,900 年左右，当具有安纳托利亚血统的新石器时代农民到来时。尽管新石器时代的过渡相对于中欧推迟了一千多年，但它非常突然，并导致人口更替，而当地狩猎采集者的遗传贡献有限。与漏斗烧杯文化相关的新石器时代人口只持续了大约 1,000 年，然后具有东部草原血统的移民就到达了。这第二次也是同样迅速的人口更替产生了单坟文化，其祖先特征更类似于今天的丹麦人。在我们的多代理数据集中，这些主要人口统计事件表现为基因型、表型、饮食和土地利用的平行变化。