Dissecting Continental and Intra-European Genetic Structure Using Chromosome 22 SNPs from the 1000 Genomes Project

Abstract

Understanding the population structure of global human groups remains fundamental to population genetics and medical genomics. In this study, I analyzed genomic variation from Chromosome 22 using publicly available data from the 1000 Genomes Project, focusing on four populations: Yoruba (YRI), Iberian (IBS), Tuscan (TSI), and Utah residents of Northern/Western European ancestry (CEU). Using ~50,000 high-quality biallelic SNPs, I applied principal component analysis (PCA), ADMIXTURE, pairwise F_ST, multidimensional scaling (MDS), and phylogenetic clustering to characterize inter-population relationships. PCA revealed a strong continental split between African and European individuals, with minimal separation among the European subgroups. ADMIXTURE analysis (K = 4) confirmed this pattern, showing consistent European ancestry clusters and distinct divergence from African ancestry. Pairwise F_ST values highlighted low differentiation among the European groups (F_ST ≈ 0.0016–0.0030) and a much higher divergence from the YRI population (F_ST > 0.137). The site frequency spectrum was dominated by rare variants, in line with recent population expansions. This study demonstrates that even a single chromosome’s SNP subset can robustly capture major axes of genetic structure, offering a scalable model for population genomics education and exploratory research.