Advancing Research on Ancient Agriculture Through Ancient Environmental DNA

Agriculture transformed human societies and ecosystems by reshaping biodiversity, landscapes, and interactions among humans, crops, and the environment. Reconstructing the origin, spread and long-term evolution of agricultural systems is therefore important for understanding past societies and the resilience of future food systems. Conventional archaeological and palaeoecological approaches provide incomplete views of ancient agriculture, while modern genomics largely infers past processes from contemporary populations. Ancient environmental DNA (eDNA), recovered from sediments and archaeological deposits, may help overcome these limitations by recovering genetic information from crops, their wild relatives, associated organisms, and surrounding ecosystems. This structured narrative review draws on targeted literature searches and synthesises empirical studies. Research was selected for its direct relevance to ancient eDNA applications in agricultural research, alongside the broader methodological and conceptual literature. We review widely demonstrated applications to early farming, subsistence, and landscape transformation, and distinguish these from emerging gene-level, genome-wide, and population-level approaches that remain methodologically constrained. We propose a hierarchical framework spanning genes, genomes, populations, communities, agroecosystems, and landscapes, and outline major challenges in sampling, laboratory methods, bioinformatics, ecological modelling, and biological interpretation. Integrating ancient eDNA with archaeobotanical, archaeological, ecological, and genomic evidence could significantly advance research on crop domestication, agricultural evolution, and human–environment interactions under future trends of climate change.