Throughout its native range, the Yellowstone cutthroat trout (YCT), Oncorhynchus clarkii bouvieri, is declining dramatically in both abundance and distribution as a result of introgression with introduced rainbow trout (RBT), O. mykiss. We sampled over 1,200 trout from the South Fork of the Snake River (SFSR) watershed, in southeastern Idaho and western Wyoming, and measured the extent of introgression of RBT genes into native gene pools of YCT using seven species-specific, co-dominant nuclear genetic markers. We also used mitochondrial DNA (mtDNA) haplotype differences between the two parental trout species to determine the directionality of the hybridization. We found low levels of RBT introgression (only 7% of sampled individuals had one or more RBT alleles) into YCT gene pools, with the majority of hybrids (78%) occurring in mainstem localities of the SFSR and in lower elevation reaches of certain tributaries. Hybridization was bidirectional with respect to mtDNA haplotype, but the majority of hybrids (75%) had YCT maternal haplotypes, indicative of the greater proportion (90%) of YCT-genotypes in the SFSR watershed. The primary factor influencing the geographic distribution of RBT introgressed individuals was fluvial distance from localities of stocking origin. To a lesser extent, elevation, also influenced the distribution of hybrid genotypes, with several entire tributaries and all upper elevation reaches within tributaries harboring only YCT-genotypes. Important management implications of the study suggest targeting particular tributaries and upper reaches within tributaries for YCT protection and exclusion of RBT hybrid colonization.

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Hybridization between native and introduced species is considered a serious threat for many native fish populations. In western North America, native cutthroat trout Oncorhynchus clarkii subspecies are declining dramatically across their ranges; competition and hybridization with nonnative rainbow trout O. mykiss are recognized as key factors in their decline. Presently, identification of cutthroat trout × rainbow trout hybrids is commonly made using molecular genetic markers because morphological differences are thought to be inaccurate. We sampled trout from the South Fork of the Snake River and 10 tributary streams to test for morphological differences that could predict genetic identity of individual Yellowstone cutthroat trout O. clarkii bouvieri, rainbow trout, and their hybrids. We found distinctive body shape differences among the three groups: Yellowstone cutthroat trout and hybrids had larger heads than rainbow trout. Yellowstone cutthroat trout had shallower bodies and caudal peduncles than rainbow trout, whereas hybrids exhibited intermediate body depth and caudal peduncle depth. Using logistic regression with a suite of morphological measurements, we found an overall rate of 92% for correctly classifying trout as Yellowstone cutthroat trout, hybrids, or rainbow trout. Over 99% of Yellowstone cutthroat trout and 80% of rainbow trout were correctly categorized; however, the correct classification rate for hybridized individuals was considerably lower. This study demonstrates that consistent morphological differences exist between Yellowstone cutthroat trout and rainbow trout in the wild, and the degree of introgression accounts for a significant portion of morphological variation in Yellowstone cutthroat trout × rainbow trout hybrids, thus causing difficulty in the use of morphology alone to classify trout.

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