Organization of genetic variation at the molecular level: Lessons from Drosophila

The allelic variation in DNA revealed by molecular methods has become a panacea for resolving questions about the evolutionary history and structure of natural populations. The problem we are interested in considering here involves the use of sequence variation for making inferences about the past history of a population: the extent of population subdivision, the level of gene flow, the historical patterns of population movement, the origins or genealogy of particular races or subpopulations, or the phylogenetic relationships among groups. In order to answer historically contingent questions such as these with molecular variation, it is necessary to interpret the patterning of that variation in terms of population-level forces rather than in terms of specific forces acting at or near the locus. What assumptions about the way in which DNA is evolving allow such an interpretation? And what is known about their validity?