Domestication as a process: modeling demography and selection in maize using ancient DNA

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Over 10,000 years ago humans began to domesticate wild plants, leading to profound changes in human lifestyles and communities referred to as the Neolithic Revolution. Crop domestication is in fact often modeled as a revolutionary event that separated the crop from wild plant: field studies have suggested that under the right conditions domestication could have occurred in a matter of decades, and evolutionary genetic models of crop domestication have followed this suit, treating domestication as an instantaneous event followed by expansion of the domesticated population. Archaeological remains, in contrast, suggest that domestication-related phenotypes took millennia to evolve. Elucidating this discrepancy between archaeological records and population genetic analyses will provide a better understanding of crop domestication and early human civilization.Maize is an ideal model to study crop domestication and adaptation, as its domestication history is well known and there is an enormous base of genomic and phenotypic data available. Archaeological data are also plentiful, including recently available genomic data from dozens of ancient samples. This project proposes to use maize as a model to investigate the timing and mode of selection during domestication. We propose two advances to the study of domestication. First, we will make use of new methodological approaches in quantitative genetics to study phenotypic evolution in ancient samples. While most phenotypes of such historical samples remain unknown, because only small parts of the plants persist, integrating genomic data from ancient samples with mapping data available from studies of extant populations with phenotypes allows us to study changes in the genetic component of phenotypes of interest. This allows us to investigate phenotypes under selection in ancient samples and the timing of phenotypic change. Second, we will take advantage of time series models to study the demographic history of maize during domestication. Until now, time series modeling has been employed for experimental evolution with microorganisms that have short generation times. However, including ancient samples into evolutionary modeling of domestication provides the opportunity to reconstruct the history of crops using time series modeling. Combined, these approaches will help to clarify the discrepancy between archaeology and population genetics on the question of duration of domestication.The proposed project leverages the extensive phenotypic and genotypic resources from modern maize inbreds, traditional maize landraces from the center of domestication, ancient maize samples from across the early extension range of the crop and the wild ancestor of maize to study selection on polygenic traits and maize demography over time. The study introduces the emerging field of paleopopulation genetics into crop research and the results will improve our understanding of crop domestication and selection of complex traits.