Taxonomically complex groups (TCGs) are difficult to assign to species. Analyses of genetic structure have the potential to determine distinct species and improve taxonomic delimitation. Euphrasia provides a good non-model plant system for investigating species differences in TCGs. Genotyping-by-sequecing of diverse UK eyebright samples revealed both species and geographic differences: 1) northern E. micrantha is genetically distinctive, indicating a different colonization history. 2) geography plays an important role. We hypothesized that this is related to geographic differentiation caused by selfing / local hybridisation; 3) closely related species showed low species-level differentiation with a few outlier regions, these regions might underlie species differences.
