  Populations of widely distributed species often encounter and adapt to
specific environmental conditions. However, comprehensive characterization of
the genetic basis of adaptation is demanding, requiring genome-wide genotype
data, multiple sampled populations, and a good understanding of population
structure. We have used environmental and high-density genotype data to
describe the genetic basis of local adaptation in 21 populations of teosinte,
the wild ancestor of maize. We found that altitude, dispersal events and
admixture among subspecies formed a complex hierarchical genetic structure
within teosinte. Patterns of linkage disequilibrium revealed four mega-base
scale inversions that segregated among populations and had altitudinal clines.
Based on patterns of differentiation and correlation with environmental
variation, inversions and nongenic regions play an important role in local
adaptation of teosinte. Further, we note that strongly differentiated
individual populations can bias the identification of adaptive loci. The role
of inversions in local adaptation has been predicted by theory and requires
attention as genome-wide data become available for additional plant species.
These results also suggest a potentially important role for noncoding
variation, especially in large plant genomes in which the gene space represents
a fraction of the entire genome.
