Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2003-2004 Annual Report.

Abstract

Despite the substantial declines in distribution and abundance that the Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri has experienced over the past century, quantitative evaluations of existing population sizes over broad portions of its historical range have not been made. In this study, we estimate trout abundance throughout the Upper Snake River basin in Idaho (and portions of adjacent states), based on stratified sample extrapolations of electrofishing surveys conducted at 961 study sites, the vast majority of which (84%) were selected randomly. Yellowstone cutthroat trout were the most widely distributed species of trout (caught at 457 study sites), followed by brook trout Salvelinus fontinalis (242 sites), rainbow trout O. mykiss and rainbow x cutthroat hybrids (136 sites), and brown trout Salmo trutta (70 sites). Of the sites that contained cutthroat trout, more than half did not contain any other species of trout. Where nonnative trout were sympatric with cutthroat trout, brook trout were most commonly present. In the 11 Geographic Management Units (GMUs) where sample size permitted abundance estimates, there were about 2.2 million trout {ge}100 mm, and of these, about one-half were cutthroat trout. Similarly, we estimated that about 2.0 million trout <100 mm were present, of which about 1.2 million were cutthroat trout. The latter estimate is biased low because our inability to estimate abundance of trout <100 mm in larger-order rivers negated our ability to account for them at all. Cutthroat trout were divided into approximately 70 subpopulations but estimates could be made for only 55 subpopulations; of these, 44 subpopulations contained more than 1,000 cutthroat trout and 28 contained more than 2,500 cutthroat trout. Using a logistic regression model to predict the number of spawning cutthroat trout at a given study site, we estimate that an average of about 30% of the cutthroat trout {ge}100 mm are spawners. We compared visually-based phenotypic assessments of hybridization with subsequent genetic analyses from 55 of the study sites and found that: (1) genetic analysis corroborated our visual determination that hybridization was absent at 37 of 55 sites; (2) at the seven sites where we visually failed to discern genetically-detected hybridization, the percent of rainbow trout alleles in the population was low (<1 %) at all but two locations; and (3) where we detected hybridization both visually and genetically (11 sites), levels of introgression were positively correlated between methods (r{sub 2} = 0.65). Based on this strong agreement, we phenotypically classified cutthroat trout as ''pure'' and ''{ge}90% pure'' at 81% and 90%, respectively, of the study sites within these GMUs. Our results suggest that, despite the presence of nonnative threats (genetic and competitive) in much of their current range in Idaho, Yellowstone cutthroat trout populations remain widely distributed and appear healthy in several river drainages in the Upper Snake River basin. Nevertheless, ongoing efforts to secure core cutthroat trout populations, protect areas from further nonnative invasions, and restore disturbed habitat are recommended for further protection of Yellowstone cutthroat trout in Idaho.