Variation and divergence of death valley pupfish populations at retrotransposon-defined loci

A population survey of the Death Valley pupfishes (Cyprinodontidae: Cyprinodon sp.) for insertional variation associated with "Swimmer 1" (SW1), a retrotransposon family, was conducted with Southern blot hybridization. Numerous polymorphic insertion sites were detected, providing compelling evidence that SW1 has been retrotranspositionally active in the recent history of the Death Valley pupfishes. This extensive variation revealed marked genetic divergence among some populations that were indistinguishably monomorphic by other molecular techniques. Large disparities were also detected among populations in the levels of genetic diversity exhibited at SW1-defined loci. These differences may have resulted from either variability among populations in SW1 retrotranspositional activity (i.e., mutation rates) or variable rates of genetic drift mediated by differences in effective population size. The patterns of genetic variation suggest that most polymorphic sites derive from a common ancestor and that recent population divergence has occurred primarily through loss of variability via drift.