Archaeological research in the New World tropics has many different foci. Investigating the nature of subsistence practices in this diverse region, especially the transition to agriculture, figures prominently among these. However, recovering direct evidence of subsistence (for example, the remains of plants used by people), is a formidable challenge facing archaeologists who work in the neotropics. Preservation of macroremains (seeds, tubers, wood, corn cob fragments and the like) is limited to charred materials in all but the most arid settings. Even when charring occurs, macroremains may be highly fragmented due to expansion and contraction of soils, making their detection and recovery difficult during excavation. The problems of identifying such fragmented materials are rendered more complex by the high species diversity of the tropical flora. This necessitates a large botanical comparative collection and the occasional application of specialized identification techniques, such as scanning electron microscopy (Pearsall 1989).

Problems of preservation, recovery, and identification of botanical remains are not unique to paleoethnobotanists working in the neotropics, but the environments of the moist lowlands seem to “conspire” to create the worse possible conditions for recovering subsistence data. As Mangelsdorf remarked in his review of Agricultural Origins and Dispersals, in which Carl Sauer (1952) proposed the riverine zone of the moist tropical forest as a likely hearth of agricultural origins: