Integrative Phytochemical, Morphological and Molecular Analyses Reveal Intraspecific Diversification in Wild Iranian Populations of Heracleum persicum Desf. ex Fischer

Heracleum persicum Desf. ex Fischer is an aromatic and medicinal plant with substantial natural variation, yet its population-level differentiation remains poorly resolved. We applied an integrative framework combining leaf chemical profiling (GC–MS), fruit morphometrics, multilocus molecular markers (ITS, psbA–trnH, rpl32–trnL), and ecological gradients to investigate intraspecific differentiation among 13 wild populations. We identified 90 chemical compounds belonging to 15 chemical classes, with substantial variation in fatty acids and aliphatic hydrocarbons. Multivariate analyses revealed three distinct chemical groups, including populations enriched in unsaturated fatty acids, a group associated with saturated fatty acids and alkanes, and the highly differentiated Zeri population characterized by elevated anethole. Fruit morphological traits and molecular relationships showed correspondence with chemical differentiation, particularly in the Margoon–Komehr and Alashtar–Kamandan–Naran groups. Canonical correspondence analysis indicated associations between chemical composition and altitude, temperature, and precipitation. Overall, the correspondence among phytochemical, morphological, molecular, and ecological datasets demonstrates substantial geographically structured intraspecific differentiation in H. persicum. These findings highlight the value of integrating independent character systems for recognizing and characterizing population lineages and provide a biosystematic framework for understanding natural variation within H. persicum.