Origin, fate, and architecture of ecologically relevant genetic variation

Recent advances in molecular genetics combined with field manipulations are yielding new insight into the origin, evolutionary fate, and genetic architecture of phenotypic variation in natural plant populations, with two surprising implications for the evolution of plant genomes. First, genetic loci exhibiting antagonistic pleiotropy across natural environments appear rare relative to loci that are adaptive in one or more environments and neutral elsewhere. These ‘conditionally neutral’ alleles should sweep to fixation when they arise, yet genome comparisons find little evidence for such selective sweeps. Second, genes under biotic selection tend to be of larger effect than genes under abiotic selection. Recent theory suggests this may be a consequence of high gene flow among populations under selection for local adaptation.

► Field experiments add novel insight into the genomic basis of local adaptation. ► Antagonistic pleiotropy is rare, contrary to theoretical expectations. ► Effect sizes are larger for genes under biotic relative to abiotic selection. ► Future studies of non-model organisms and positional cloning of QTL are needed.