Deciphering the genetic structure of the Quebec founder population using genealogies

The Quebec founder population represents one of the world's best documented population bottlenecks, providing a unique opportunity to study the effects of population founding events on genetic diversity. Here we present the first genome-wide characterization of Quebec's demographic history using both genomic and genealogical data. We analyzed 1,415 individuals of French Canadian ancestry with genome-wide SNP data and deep genealogical information spanning up to 15 generations. Our results reveal a complex demographic history involving multiple founding events and variable population growth rates across different regions of Quebec. We identified strong population structure between different Quebec regions, with the highest differentiation observed between the Saguenay-Lac-Saint-Jean region and other areas. Through genealogical analysis, we traced the ancestry of modern Quebec French Canadians to a relatively small number of founding lineages, with approximately 80% of the gene pool deriving from founders who arrived before 1700. We also detected signatures of recent population expansion and regional founder effects that have shaped the contemporary genetic landscape. These findings provide new insights into the genetic consequences of population founding events and have important implications for medical genetics research in founder populations.