The genetic structure of 14 populations of bull trout Salvelinus confluentus from the upper Flathead River basin was examined by means of (1) restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) amplified by polymerase chain reaction and (2) three microsatellite loci. Analysis of mtDNA suggests colonization by at least two lineages of bull trout after the last glaciation. Both genetic markers showed little variation within bull trout populations but substantial differences among them. A large proportion of the observed population differentiation was attributable to genetic differences among populations within drainages, which suggests that even geographically adjacent populations are highly isolated reproductively. The temporal allele frequency differences detected in some samples suggest that genetic drift owing to recent demographic decline could have increased the genetic divergence among bull trout populations. We found no evidence for a metapopulation structure characterized by frequent extinction-recolonization events in these populations. These results suggest that bull trout populations have a low probability of recolonization through dispersal from adjacent populations after local populations go extinct. Therefore, the long-term persistence of bull trout requires ensuring that the local populations are maintained.
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