Data from: Complex patterns of local adaptation in Teosinte

Populations of widely distributed species encounter and must adapt to
local environmental conditions. However, comprehensive characterization of
the genetic basis of adaptation is demanding, requiring genome wide
genotype data, multiple sampled populations, and an understanding of
population structure and potential selection pressures. Here, we used SNP
genotyping and data on numerous environmental variables to describe the
genetic basis of local adaptation in 21 populations of teosinte, the wild
ancestor of maize. We found complex hierarchical genetic structure created
by altitude, dispersal events and admixture among subspecies that
complicated identification of locally beneficial alleles. Patterns of
linkage disequilibrium revealed four large inversion polymorphisms showing
clinal patterns of frequency. Population differentiation and environmental
correlations suggest that both inversions and intergenic polymorphisms are
involved in local adaptation.