Abstract
Anthraquinones and flavonoids form an environmentally responsive, co-regulated chemical system that wild plants use to withstand multi-stress environments and structure ecological interactions. This review shows that these metabolites draw on shared precursors (especially malonyl-CoA and type III polyketide synthases) but are wired into partially distinct biosynthetic routes and regulatory networks, allowing plants to flexibly rebalance carbon flux between them under changing abiotic and biotic pressures. Across wild taxa, field and experimental data reveal that light and UV, temperature extremes, drought and flooding, edaphic heterogeneity, herbivory, pathogens, mutualists, and competitors drive predictable shifts in the anthraquinone:flavonoid ratio, generating fine-scale “phytochemical mosaics” and locally adapted chemotypes along latitudinal, altitudinal, and soil gradients. The review highlights functional complementarity rather than simple trade-offs: flavonoids predominantly buffer abiotic stress and mediate signaling, whereas anthraquinones provide high-intensity antimicrobial, antiherbivore, and allelopathic defenses, often acting through phototoxicity and soil-active residues. At the same time, pronounced intraspecific variation, strong phenotypic plasticity, and context-dependent metabolic trade-offs underscore the importance of regulatory hubs (MBW complexes, hormone cross-talk, and emerging epigenetic mechanisms) and of carbon-partitioning constraints in shaping AQ–flavonoid portfolios in nature. The review identifies major gaps—including the underrepresentation of anthraquinones in ecological genomics, a lack of multi-factor field experiments, limited integration of metabolomics with fitness and community data, and a large “dark metabolome” of uncharacterized AQ–flavonoid derivatives—and proposes an eco-metabolomic research agenda to link genes, pathways, environmental drivers, and fitness in order to predict how these dual defense systems will reorganize under rapid global change.