Genetic and environmental drivers of intraspecific variation in foliar metabolites in a tropical tree community

Plant interactions with abiotic and biotic environments are mediated by diverse metabolites, which are crucial for stress response and defense. These metabolites can not only support diversity by shaping species niche differences but also display heritable and plastic intraspecific variation, which few studies have quantified in terms of their relative contributions. To address this shortcoming, we used untargeted metabolomics to annotate and quantify foliar metabolites and restriction-site associated DNA (RAD) sequencing to assess genetic distances among 300 individuals of 10 locally abundant species from a diverse tropical community in Southwest China. We quantified the relative contributions of relatedness and the abiotic and biotic environment to intraspecific metabolite variation, considering different biosynthetic pathways. Intraspecific variation contributed most to community-level metabolite diversity, followed by species-level variation. Biotic factors had the largest effect on total and secondary metabolites, while abiotic factors strongly influenced primary metabolites, particularly carbohydrates. The relative importance of these factors varied widely across different biosynthetic pathways and different species. Our findings highlight that intraspecific variation is an essential component of community-level metabolite diversity. Furthermore, species rely on distinct classes of metabolites to adapt to environmental pressures, with genetic, abiotic, and biotic factors playing pathway-specific roles in driving intraspecific variation.