Distinguishing Yellowstone Cutthroat Trout, Rainbow Trout, and Hybrids by Use of Field-Based Phenotypic Characteristics

Native and nonnative salmonids within the same genus sometimes hybridize, and the hybrids are often difficult to visually distinguish from parental species. We compared phenotypic delineations (based on several visual characteristics) and genotypic screening (using seven nuclear DNA loci) for 323 fish collected from an Idaho stream where Yellowstone Cutthroat Trout O. clarkii bouvieri were introgressed with Rainbow Trout O. mykiss to evaluate our ability to visually distinguish Yellowstone Cutthroat Trout from Rainbow Trout and hybrids. Assuming that the genotypes were 100% accurate, correct phenotypic classification was highest for Yellowstone Cutthroat Trout (the genotype confirmed the phenotype 94% of the time), followed by hybrids (79%) and Rainbow Trout (71%). All errors were between pure and hybrid fish. All of the measured phenotypic characteristics were useful for differentiating Yellowstone Cutthroat Trout from hybrids, but the most informative characteristics were the lack of a white leading tip on the anal and dorsal fins, the presence of fewer than five spots on the top of the head, and the presence of a bright red-orange throat slash. Fish size did not influence correct phenotypic identification, although fry were excluded from our study. A logistic regression model predicted that biologists were more than 50% likely to visually detect Rainbow Trout traits in a hybrid when its level of hybridization was greater than 22% (95% confidence interval = 4-30%). For an additional 189 fish in three other Idaho streams, phenotypic differentiation of Yellowstone Cutthroat Trout from Rainbow Trout and hybrids was 91% accurate. These results can be used to screen for introgression in Yellowstone Cutthroat Trout populations or to selectively remove Rainbow Trout and hybrids from Yellowstone Cutthroat Trout populations. However, in most cases, genetic confirmation of purity or introgression would still be valuable for identifying low levels of hybridization in individuals or in the population at large.