Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks

Evolutionary and conservation biologists often use molecular markers to eva luate whether populations have experienced demographic bottlenecks that res ulted in a loss of genetic variation. We evaluated the utility of microsate llites for detection of recent, severe bottlenecks and compared the amounts of genetic diversity lost in bottlenecks of different sizes. In experiment al mesocosms, we established replicate populations by releasing 1,2 4 or 8 pairs of the western mosquitofish, Gambusia affinis (Poeciliidae). Using ei ght polymorphic microsatellite loci, we quantified seven indices of genetic diversity or change that have been used to assess the effects of demograph ic bottlenecks on populations. We compared indices for the experimentally b ottlenecked populations to those for the source population and examined dif ferences between populations established with different numbers of founders . Direct count heterozygosity and the proportion of polymorphic loci were n ot very sensitive to genetic changes that resulted from the experimental bo ttlenecks. Heterozygosity excess and expected heterozygosity were useful to varying degrees in the detection of bottlenecks. Allelic diversity and tem poral variance in allele frequencies were most sensitive to genetic changes that resulted from the bottlenecks, and the temporal variance method was s lightly more correlated with bottleneck size than was allelic diversity. Ba sed on comparisons to a previous study with allozymes, heterozygosity, temp oral variance in allele frequencies and allelic diversity, but not proporti on of polymorphic loci, appear to be more sensitive to demographic bottlene cks when quantified using microsatellites. We found that analysis of eight highly polymorphic loci was sufficient to detect a recent demographic bottl eneck and to obtain an estimate of the magnitude of bottleneck severity.