Urbanisation and genetic homogenisation in mediaeval Low Countries: a ten-century ancient genomic study of the city Sint-Truiden
Processes shaping the formation of the present-day population structure in highly urbanised Northern Europe are still relatively poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration and disease pandemics during and after the Middle Ages had on these processes. To address these questions, we sequenced to coverage >0.1x the genomes of 338 individuals spanning ten centuries (8-18th century) in the city of Sint-Truiden in Flanders, northern part of Belgium. We found that the Early/High Mediaeval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less kinship ties than observed today between individuals whose grandparents were born in the same province of present-day Flanders. Over time, the city population became more homogenous and similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the High Mediaeval period, and the continuous process of local admixture of Germanic and Gaulish ancestries, which formed the genetic cline observable today in the Low Countries. We find differences in genes associated with vitamin D levels, including higher Germanic ancestry in individuals carrying red hair causing alleles on one hand, and higher Gaulish ancestry in individuals carrying at least one G allele of the rs7944926 variant associated with higher vitamin D levels in blood. Although evidence of  Yersinia pestis infection was found in 7 of the 58 Late Mediaeval burials, we were unable to detect a major population-scale impact of plague pandemics on genetic diversity or on the elevated differentiation of immunity genes.