Identification of population substructure among Jews using STR markers and dependence on reference populations included

Using 32 autosomal STR markers and the program STRUCTURE, we differentiated between Ashkenazi (AJ, N = 135) and non-Ashkenazi (NAJ, N = 226) Jewish populations in the form of Northern and Southern geographic genetic components (AJ north 73%, south 23%, NAJ north 33%, south 60%). The ability to detect substructure within these closely related populations using a small STR panel was contingent on including additional samples representing major continental populations in the analyses.Although clustering programs such as STRUCTURE are designed to assign proportions of ancestry to individuals without reference population information, when Jewish samples were analyzed in the absence of proxy parental populations, substructure within Jews was not detected. Generally, for samples with a given grandparental country of birth, STRUCTURE assignment values to Northern, Southern, African and Asian clusters agreed with mitochondrial DNA and Y-chromosomal data from previous studies as well as historical records of migration and intermarriage.The genetics of Jewish populations, particularly that of Ashkenazi Jews, has been studied extensively to answer questions of human evolutionary, historical, and medical significance [1-11]. Human evolutionary or anthropological studies have typically focused on mitochondrial DNA (mtDNA) or Y-chromosomal data, because the absence of recombination in these regions of the genome allows researchers to infer past human behaviors and evolutionary events such as migrations, founder events, population bottlenecks or expansions, relative male and female contributions to an admixed population, marriage practices, and mode of transmission of languages [12-15]. However, medical research necessitates the use of autosomal data. The depth of data collection and the necessary characterization of subpopulations to control for population stratification during case-control association studies provide a unique resource to augment mtDNA and Y-chromosomal studies an