Local PCA shows how the effect of population structure differs along the genome

Population structure leads to systematic patterns in measures of mean relatedness between individuals in large genomic datasets, which are often discovered and visualized using dimension reduction techniques such as principal component analysis (PCA). Mean relatedness is an average of the relationships across locus-specific genealogical trees, which can be strongly affected on intermediate genomic scales by linked selection and other factors. We show how to use local principal components analysis to describe this meso-scale heterogeneity in patterns of relatedness, and apply the method to genomic data from three species, finding in each that the effect of population structure can vary substa