Unanticipated departures from breeding designs can be detected using microsatellite DNA parentage analyses

Using microsatellite analysis, a partial pedigree was constructed from an experiment designed to evaluate differences between hatchery Chinook salmon (Oncorhynchus tshawytscha) and their wild donor stocks. First generation (F1) progeny were created by crossing both hatchery and wild females with hatchery and wild males to create hybrid and control lines. The pedigree analysis revealed an accidental switch of a half-sib control and hybrid F1 family, which most likely occurred during incubation and led to the misclassification of individuals in those families. The experimental error propagated into the F2 lines. The pedigree also revealed a number of unintended full-sib matings in the F2 crosses. This resulted from the small numbers (5 females, 14 males) of wild fish available for the experiment and differential family survival of the F1 fish. Because researchers used group-specific physical marks to track typed crosses and not family groups, and because physical marks cannot detect inadvertent movement of fish until they are large enough to mark, experimental error occurred that would have influenced the results had a DNA-based analysis not been employed to verify the integrity of the experiment.