Ancient maize from the American Southwest

Rute R da Fonseca 1, Bruce Smith2, Nathan Wales1, Enrico Cappellini1, Matteo Fumagalli3, Pontus Skoglund4, Anders Albrechtsen1, Jeff Ross-Ibarra5, Tom Gilbert1
1Copenhagen University, Copenhagen, Denmark, 2Smithsonian Institution, Washington D.C., USA, 3UC Berkeley, Berkeley, USA, 4Uppsala University, Uppsala, Sweden, 5UC Davis, Davis, USA

Maize was domesticated from a teosinte grass in Southern Mexico more than 6,000 years ago and experienced significant human and environment driven selection through time. We sequenced nuclear DNA extracted from 30 ancient archaeological maize samples in search for evidence of such strong directional selection. We used methods that rely on genotype probabilities instead of called genotypes on ancient and modern maize Hapmap2 individuals to i) determine population structure, ii) measure population differentiation and inbreeding coefficients, and iii) perform neutrality tests. We were able to detect signatures of selection in several genes associated with different stages of the domestication process. Furthermore, TreeMix analyses and D-statistics provided strong evidence for a route of diffusion of maize into North America, a previously undocumented journey.