Perspective: Highly variable loci and their interpretation in evolution and conservation

Although highly variable loci, such as microsatellite loci, are revolutionizing both evolutionary and conservation biology, data from these loci need to be carefully evaluated. First, because these loci often have very high within-population heterozygosity, the magnitude of differentiation measures may be quite small. For example, maximum G(ST) values for populations with no common alleles at highly variable loci may be small and are at maximum less than the average within-population homozygosity. As a result, measures that are variation independent are recommended for highly variable loci. Second, bottlenecks or a reduction in population size can generate large genetic distances in a short time for these loci. In this case, the genetic distance may be corrected for low variation in a population and tests to detect bottlenecks are advised. Third, statistically significant differences may not reflect biologically meaningful differences both because the patterns of adaptive loci may not be correlated with highly variable loci and statistical power with these markers is so high. As an example of this latter effect, the statistical power to detect a one-generation bottleneck of different sizes for different numbers of highly variable loci is discussed. All of these concerns need to be incorporated in the utilization and interpretation of patterns of highly variable loci for both evolutionary and conservation biology.