Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century

The Ashkenazi Jewish (AJ) population, which has its recent origins largely in Eastern and Central Europe, carries dozens of Mendelian pathogenic variants likely due to medieval founder events. However, little is known about these events or the early origins of the population. We report the first DNA data from historical-era AJ, from 33 individuals whose remains were rescued during salvage excavations of the medieval Jewish cemetery of Erfurt, Germany, dated to the 14th century. The Erfurt individuals are genetically similar to modern AJ and have substantial Southern European ancestry. However, the Erfurt individuals also show variability in Eastern European-related ancestry not present in modern AJ. The genetic variability was correlated with oxygen isotope ratios in tooth enamel, implying differential exposure to water sources during childhood and thus diverse geographic origins. About a third of the Erfurt individuals carried the K1a1b1a Ashkenazi-specific mitochondrial DNA haplogroup, and we detect in the Erfurt individuals 11 pathogenic variants known to affect AJ today, including alleles in the genes BRCA1, GBA, F11, CLRN1, and G6PC. Together with high genome-wide levels of runs of homozygosity, these observations suggest that the Erfurt community descended from a population that had already experienced the major reduction in size that also affected modern AJ. Modeling identical-by-descent haplotypes shows that the Erfurt founder event was more severe than expected based on reconstructions from modern AJ, implying substructure in medieval AJ whereby different groups have experienced different founder event intensities. Our results suggest that the AJ founder event and the acquisition of the main sources of AJ ancestry pre-dated the 14th century, while highlighting late medieval genetic heterogeneity no longer present in modern AJ.