Ecological and genetic determinants of essential oil diversity in Mediterranean Thymus

The Mediterranean Basin is a hotspot of plant diversity, with many species producing aromatic essential oils that mediate ecological interactions and stress responses. Within Lamiaceae, the genus Thymus shows remarkable chemical variability, yet high intraspecific essential oil variation often limits its taxonomic resolution. We investigated essential oil composition, genetic structure, and environmental influences across 39 populations of Thymus sect. Mastichina in the Iberian Peninsula, using GC-MS alongside soil and climatic data to assess drivers of chemical variation and refine taxonomic characterization. We identified 14 major compounds, dominated by oxygenated monoterpenes. Most populations exhibited 1,8-cineole-rich chemotypes, yet seven populations showed relatively higher linalool levels, and multiple chemotypes often co-occurred within the same populations, revealing high intrapopulation chemical diversity. Minor compounds, including camphor, borneol, and camphene, varied among genetic clusters and were significantly correlated with temperature and precipitation gradients. Differences in essential oil relative abundances were also detected between ploidy levels and genetic groups, although the major compounds remained relatively consistent, suggesting both conserved and locally adaptive chemical traits. These findings suggest that essential oil diversity in Thymus sect. Mastichina arises from a complex interplay of environmental conditions, genetic background, and ploidy. Integrating chemical, genetic, and ecological data provides a comprehensive framework for understanding the evolutionary and ecological drivers of essential oil variation in Mediterranean aromatic plants, with implications for taxonomy, conservation, and the study of adaptive chemical traits. • Essential oil profiles reveal high intra- and interpopulation chemical diversity. • Major chemotypes are conserved, while minor compounds show adaptive variability. • Chemotypic differences are associated with genetic clusters and ploidy levels. • Environmental gradients contribute to shaping chemotypic variation. • Integrative analyses reveal drivers of essential oil variation.