Evolutionary history and taxonomy of the genus Zea

Premise Taxonomic differentiation of teosinte species ( Zea spp.), the closest relatives of maize ( Z. mays ) is crucial for understanding their distribution, ecology, and evolutionary history. Resolving the taxonomic uncertainties is of scientific interest and has practical implications for biodiversity management, preservation, and utilization. Methods We examined the evolutionary history of Zea based on species representation, improved multilocus phylogenies and estimation of relative times of diversification. Relationships among 379 samples, representing all species of Zea , were inferred from genotyping‐by‐sequencing (GBS) data, morphological, and climatic descriptors. Results Phylogenies from GBS data were congruent, and species and races were identified; multivariate analysis with morphological data and those combining genomic and climatic variables supported the taxonomy and relationships among species. Phylogenetic results showed that Huehuetenango is a sister group to the Mexican annual teosintes, while Zea nicaraguensis is not differentiated from Zea luxurians . The newly discovered populations are distinct from each other and from other Zea species and represent three new entities. Our results reinforce the hypothesis of historical gene introgression events, such as between Zea luxurians and Zea mays subsp. parviglumis . Modern maize originated from Z. mays subsp. parviglumis through a single evolutionary event in northern Guerrero. In the central highlands, maize admixed with what is known as the Chalco race of teosinte, which facilitated its domestication and subsequent adaptation. Conclusions Evidence from multiple independent sources augments previous knowledge of the relationships, origin, and migration of Zea species, supporting a new classification to resolve the taxonomy of this genus.