Amber M. VanDerwarker

Molecular research suggests that avocados ( Persea americana Mill.) were domesticated multiple times in the Americas. Seed exchange, hybridization, and cloning have played an essential role across their wild distribution from Mexico to South America to create the modern varieties of today. Archaeological sites with well-preserved and directly radiocarbon-dated botanical assemblages are rare, however, so we know very little about the complexities of the domestication process. Here, we define an early locus of avocado domestication using well-dated desiccated and carbonized avocado remains from El Gigante rockshelter in western Honduras spanning the last 11,000 y. Measurements of avocado seeds and rinds show evidence for long-term management resulting in selection for larger, more robust fruits through time that culminated by 2,250 to 2,080 calendar B.P. (cal. B.P.). However, human-directed selection for larger fruits with thicker rinds is evident as early as 7,565 to 7,265 cal. B.P. Seed morphology is similar to P. americana var. guatemalensis and is congruent with genetic data for the development of this variety in both the highlands of Guatemala and Honduras. Increases in seed size and rind thickness through time are consistent with genetic evidence for the enrichment of putative candidate genes for fruit development and ripening in this variety.

Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica. Significance Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently fixed and improved varieties developed away from the influence of wild gene flow. We demonstrate that hybrids of some of these improved varieties were likely reintroduced back to Central America. We hypothesize that this backflow of South American genetic material may have contributed to the development of a more productive staple, which was related to the growth and aggregation of human populations, and the formation of more complex social and political structures regionally.