Ancient DNA studies revealed that, in Europe from 6500 to 4000 bce, descendants of western Anatolian farmers mixed with local hunter-gatherers resulting in 70–100% ancestry turnover1, then steppe ancestry spread with the Corded Ware complex 3000–2500 bce2. Here we document an exception in the wetland, riverine and coastal areas of the Netherlands, Belgium and western Germany, using genome-wide data from 112 people 8500–1700 bce. A distinctive population with high (approximately 50%) hunter-gatherer ancestry persisted 3,000 years later than in most European regions, reflecting incorporation of female individuals of Early European Farmer ancestry into local communities. In the western Netherlands, the arrival of the Corded Ware complex was also exceptional: lowland individuals from settlements adopting Corded Ware pottery had hardly any steppe ancestry, despite a Y-chromosome characteristic of people associated with the early Corded Ware complex. These distinctive patterns may reflect the specific ecology that they inhabited, which was not amenable to full adoption of the early Neolithic type of farming introduced with Linearbandkeramik3, and resulted in distinct communities where transfer of ideas was accompanied by little gene flow. This changed with the formation of Lower Rhine–Meuse Bell Beaker users by fusion of local people (13–18%) and Corded Ware associated migrants of both sexes. Their subsequent expansion then had a disruptive impact across a much wider part of northwestern Europe, especially in Great Britain where they were the main source of a 90–100% replacement of local Neolithic ancestry.
