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The first steps toward maize ( subspecies ) domestication occurred in the Balsas region of Mexico by ∼9,000 calendar years B.P. (cal B.P.), but it remains unclear when maize was productive enough to be a staple grain in the Americas. Molecular and microbotanical data provide a partial picture of the timing and nature of morphological change, with genetic data indicating that alleles for some domestication traits were not yet fixed by 5,300 cal B.P. in the highlands of Mexico. Here, we report 88 radiocarbon dates on the botanical remains from El Gigante rockshelter (Honduras) to establish a Bayesian chronology over the past ∼11,000 y spanning the transition to maize-based food production. Botanical remains are remarkably well preserved and include over 10,000 maize macrofossils. We directly dated 37 maize cobs to establish the appearance and local change of maize at the site. Cobs are common in deposits dating between 4,340 and 4,020 cal B.P., and again between 2,350 and 980 cal B.P. The earliest cobs appear robustly domesticated, having 10-14 rows, suggesting strong selection for increased yield. The later cobs are comparable to these earliest ones, but show clear emergence of diverse traits, including increased cob width, rachis segment length, and cupule width. Our results indicate that domesticated landraces of maize productive enough to be a staple grain existed in Central America by 4,300 cal B.P.

Productive applications of geophysics to anthropological questions in American archaeology necessarily involve specific research questions or agendas.While only some anthropological questions can be addressed by shallow geophysics, these techniquesprovide an opportunity to address someimportant questionsthat are fundamental to archaeology. One such agenda is the investigation of 'persistent places' , which is rooted in anthropological inquiry and which can be investigated, at least in part, by shallow geophysical techniques.For the next stage in the use of remote sensing that goesbeyondmere prospection, research agendasmust be clearlylinkedwithbroader theoreticalconcepts of what we term inquiry-based archaeogeophysics.Specifically with regard to the application ofgeophysics to the study of persistent places, we propose four categories of research that relate to the meaning, context and changing function of such places. These categories include: construction variation, continuity and discontinuity in the use of space, studying natural and/or culturallandscape modifications over time and space, and constancies in the use of space and architecture at the regional level. In order to illustrate these points, we provide examples from sites in Mexico and the USA that represent different time periods (2500 BC to AD 1000), adaptations (hunter^gatherers to intensive agriculturists), and levels of socio-political complexity (egalitarian to stratified societies).The use of geophysics at these persistent places contributes to our understanding of changes in the use of space and architecture through time.

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.

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