Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders

The extent and impact of Early Medieval population movements on the establishment of trade and cultural networks across the North Sea have been the subject of debate for centuries. Analyzing ancient genomes from the Flemish coast, we find two distinct ancestry groups merging in a Late Merovingian community: the major group with a dense network of distant relationships among individuals and genetic affinity to populations around the North Sea coast and the minor group representing likely continental Gaulish ancestry of unrelated individuals from various inland sources. We also find evidence of local continuity suggesting that similarly to Britain, the Early Medieval population movements had a long-term impact and were integral to the formation of the Flemish population. The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother?daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.