Fine-scale structure of a whole regional population through genetics and genealogies

The Saguenay–Lac-Saint-Jean (SLSJ) region of Quebec, Canada, a population shaped by a prominent founder effect, has long been considered genetically homogeneous. This study comprehensively investigates the fine-scale population structure within SLSJ by integrating genotype data from the CARTaGENE cohort with extensive genealogical records from the BALSAC population register. A novel, time-efficient algorithm was developed to compute billions of kinship coefficients from genealogies, overcoming previous computational limitations and enabling the analysis of an entire generation. We demonstrate a striking concordance between realised (genetic) and expected (genealogical) kinship (r = 0.78). From both kinship measures, we reveal fine-scale population structure at the municipal level within SLSJ, challenging the notion of regional homogeneity. Our analysis highlights an east–west genetic gradient and uncovers migratory streams and differential founders’ genetic contributions that shaped the genetic landscape of this population. This research provides insights into the interplay of genetics, demography, and historical events, underscoring the importance of fine-scale population structure in genetic studies and reaffirming the power of large-scale genealogical data.