Patterns of Demography and Selection During and Since Maize Domestication

The domestication of maize from the wild grass teosinte began in central Mexico approximately 9,000 years ago. Previous genetic studies focusing on coding sequences have demonstrated a loss of diversity due to a domestication bottleneck, but have been unable to estimate the parameters of the bottleneck. Here, we use whole-genome sequence information from 13 teosinte and 23 maize inbred lines, collected across the range of both taxa, to better understand the demography of the domestication process. We observe differences in the site frequency spectrum between coding and non-coding regions, implying an interaction between selection and demography in determining patterns of diversity. By comparing genetic diversity surrounding synonymous and nonsynonymous substitutions we find evidence that classical hard-sweeps were rare in both maize and teosinte. A stronger reduction in diversity near genic regions is seen for teosinte than for maize, suggesting that purifying selection may have been weaker in maize, likely due to a smaller effective population size. Together, these findings allow us to elucidate details of the domestication process and its lasting effects on genetic diversity in the maize genome. These results have implications for understanding the functional consequences of diversity and may guide future strategies for improvement of one of the world’s most important crops.