Overrepresentation analysis for K = 4.

Inferring the genetic structure at the subpopulation level is crucial for understanding the demographic histories that shape genetic diversity. Among the most widely used approaches are methods based on admixture and structure modeling—named after the respective software tools—which have become standard due to their intuitive, interpretable outputs. In this study, we address a key methodological question: how does the traditional admixture-based decomposition of genetic components in multilocus population data relate to clustering approaches that leverage machine learning, specifically Self-Organizing Maps (SOMs)? We implemented this approach through our custom SOM-based tool, SOMmelier, which enables the portrayal of genetic structure by identifying modules of co-mutated SNPs and arranging them in a topology-aware genetic landscape. Topology-awareness refers to the organization of genetic modules in a two-dimensional map, where their spatial proximity reflects mutual similarity. We applied Admixture and SOMmelier to investigate the population genetics of European grapevine. Based on prior literature, we considered up to six genetic components, which formed a genetic landscape that closely mirrors the geographic expanse of the classical Mediterranean world—from Western Asia through the Caucasus to Western Europe. The resulting topology reflects the dynamic spatial and temporal nature of grapevine domestication and diffusion. We demonstrate that SOMmelier can recover the genetic components identified by Admixture solely through statistical clustering. By integrating the topological structure of SNP co-variation, it offers perspectives on population structure, evolutionary history, and trait associations in grapevine—and has applicability to other species and systems in population genetics.