Domesticated from a wild teosinte grass in southern Mexico more than 6,500 years ago, and perhaps much earlier, maize (Zea mays ssp. mays) is one of the world’s most important crops. Over a span of more than six millennia, the domesticate has undergone considerable and rapid evolution under human selection, as it responded to a wide range of different growing conditions and selective pressures.
Genetic analysis of well-preserved maize samples recovered from archaeological contexts of different ages and from different regions of the Americas hold the promise of providing a detailed understanding of the complex evolutionary history of maize, and the timing and sequence of development of different selective traits.
Here we present the genome sequence of a 5300-year-old cob recovered from an archaeological site located ~450 km from the domestication center, in the Tehuacan Valley of Mexico. We compared our data to a reference dataset comprising 23 modern landraces and 17 wild teosinte genomes. By using D-statistics, a model-based clustering algorithm, and a multidimensional scaling analysis, we show that the specimen derives from the same source population that gave rise to modern maize, and that it represents an evolutionary branch during the early stages of domestication. Moreover, we show that 5,300 years ago, the maize genome was already more similar to modern maize than to its wild counterpart. Finally, we find that this ancient maize carries several domestication genes in the ancestral state, and only few in the domesticated state, supporting the idea of a punctuated domestication process.