Schematic representation of a network-based construction of a population structure tree (PST) from genomic data. (A) For each SNP, an inter-individual genetic-similarity network (adjacency matrix) is constructed using a frequency-weighted allele-sharing genetic-similarity measure (Equation 1). To produce a genome-wide genetic-similarity matrix, the mean over all loci is taken. (B) Weak edges are pruned from the matrix, by setting low matrix entries to 0 until a community structure emerges, as detected using network community-detection algorithms. Each community (numbered submatrices) is then analyzed independently in a similar manner. Notice that finer-scale clusters are characterized by darker matrices, indicating structures characterized by higher genetic similarities. (C) The analysis is summarized as a PST diagram, summarizing the hierarchical levels of population structure and their relationships.
