DNA markers allow us to study quantitative trait loci (QTL) - the genes that control adaptation and quantitative variation. Experiments can map the genes responsible for quantitative variation and address the evolutionary and ecological significance of this variation. Recent studies suggest that major genes segregate within and among natural populations. It is now feasible to study the genes that cause morphological variation, life history trade-offs, heterosis and speciation. These methods can determine the role of epistasis and genotype-by-environment interaction in maintaining genetic variation. QTL mapping is an important tool used to address evolutionary and ecological questions of long-standing interest.