Metabolomic discrimination of the Primula auricula genetic complex

Understanding how evolutionary history and ecological pressures shape plant chemical diversity is central to ecology and evolution, yet it remains unclear whether metabolomic data can reliably detect fine-scale, intraspecific divergence, particularly in morphologically cryptic taxa. While metabolomics has revealed broad patterns of chemical evolution across lineages, its power to resolve genetically structured variation within species is still underexplored. Here, we investigated the alpine Primula auricula complex, a morphologically uniform but genetically subdivided taxon distributed across the Alps. Using ultra-high-performance liquid chromatography coupled with mass spectrometry, we profiled the metabolomes of individuals sampled from 37 populations spanning three main genetic clades and an outlier group, previously identified through ddRADseq phylogeography. We found that metabolomic diversity carries a strong phylogenetic signal: each clade exhibited distinct chemical profiles, with exclusive or enriched metabolite superclasses such as carotenoids in one clade and phenylpropanoids in another. Outlier populations displayed reduced metabolomic richness, consistent with potential genetic drift or bottlenecks. While phylogenetic structure was the dominant driver of chemical variation, climatic variables, particularly temperature and precipitation, modulated certain stress-related metabolite groups, such as octadecanoids. Our results demonstrate that metabolomic profiling can capture both historical divergence and ecological adaptation in cryptic alpine taxa. By linking chemical, genetic, and environmental variation, this study highlights metabolomics as a cost-effective and high-resolution approach to uncover cryptic diversity, refine taxonomy, and inform conservation strategies in biodiversity hotspots increasingly threatened by climate change. • The metabolomic variation of P. auricula complex is related to its phylogegeography • Climatic and genetic related variation of the metabolome could be disentangled. • Complex history of the Alps shape alpine genetic and metabolomic diversification. • Metabolomics can serve to delineate crypric diversity and infer evolutionary history.