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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 7000 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.
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