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

A population survey of the Death Valley pupfishes (Cyprinodontidae: Cyprino don sp.) for insertional variation associated with "Swimmer 1" (SW1), a ret rotransposon family, was conducted with Southern blot hybridization. Numero us polymorphic insertion sites were detected, providing compelling evidence that SW1 has been retrotranspositionally active in the recent history of t he 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 p opulations in the levels of genetic diversity exhibited at SW1-defined loci . These differences may have resulted from either variability among populat ions in SW1 retrotranspositional activity (i.e., mutation rates) or variabl e rates of genetic drift mediated by differences in effective population si ze. The patterns of genetic variation suggest that most polymorphic sites d erive from a common ancestor and that recent population divergence has occu rred primarily through loss of variability via drift.