The development of agricultural societies made possible by plant and animal domestication was one of the most transformative events in human and ecological history. Independent beginnings of agriculture occurred between 12,000 and 10,000 years ago in a number of world regions, including the American tropics, southwest Asia, and China. Plant domestication was at its core an evolutionary process involving both natural and human selection for traits favorable for harvesting and consumption. Ever-improving analytic methods for retrieving empirical data from archaeological sites, together with advances in genetic, genomic, and experimental research on living crops and their wild ancestors are providing new understandings of, and mechanisms for domestication and early agriculture (see discussion under Research Focus). Scholars have long debated why hunters and gatherers became farmers, a question that will also see increasing understanding.

Prominent scholars once believed that the Neotropical forest vegetation and landscape were little altered by pre-Columbian cultures. It is now known that significant, sometimes profound, human environmental modification of many types (fire, vegetation clearing; depression of preferred prey through over-exploitation; construction of earthworks and roads) has a deep history in the American tropics. However, some regions remain understudied. Still not understood, for example, is when and how a human presence may have modified landscapes across the vast terra firme (interfluvial) forest zone of the Amazon Basin. Multi-proxy analyses of lake sediments and terrestrial soils (e.g., pollen, phytoliths, charcoal) are at once improving our resolution of both natural- and human-cased environmental change in Amazonia and elsewhere, and expanding the types of locations such evidence can be found in.

Plant microfossils such as phytoliths, starch grains, and pollen can be used to effectively study prehistoric plant exploitation and agriculture. In the Neotropics, many important crops such as maize, squashes, manioc, and yams can be identified. Archaeological materials offering robust contexts for microfossil study now include stone tools, ceramics, sediments, and human teeth. Future research should expand the number of identifiable taxa and refine current identifications, discover more about the types of plant preparation and consumption the microfossils can reveal (e.g., chicha-making?), and add to understanding of their roles in documenting prehistoric plant usage in the Neotropics and elsewhere.