Overview:

Native resident salmonids are in decline in many portions of their historical range due in part to a variety of anthropogenic factors such as irrigation diversions, agriculture impacts, and hydropower dams (both federal and private). As a result, bull trout are listed as threatened under the Endangered Species Act (ESA), and redband trout and Yellowstone cutthroat trout have been petitioned to be listed. This is a multi-phased project by the Idaho Department of Fish and Game with the goal of protecting and restoring populations of native salmonids (those listed above, and mountain whitefish) in the Upper Snake River Basin (USRB) above Hell's Canyon Dam in Idaho to self-sustaining, harvestable levels. The overall objectives (or phases) are to: 1) Assess stock status, population trends, and fish habitat; 2) Identify life history and habitat needs, and limiting factors; and 3) Develop, implement, and monitor the effectiveness of recovery and protection plans for populations at risk. The first phase of inventorying fish and their habitat was completed in FY05; status assessments have been finalized for bull trout and Yellowstone cutthroat trout and are underway for redband trout and mountain whitefish. We have randomly sampled stream locations to assess the current status of native salmonids throughout the USRB, and assess what factors influence that status. Relating fish abundance and distribution to stream and adjacent habitat conditions leads directly to limiting factor analysis (Phase II), which is ongoing. Limiting factor analysis has included identifying life history needs, causes for population declines, threats to persistence, and opportunities for restoration. Once limiting factors are identified, the third phase uses this information to develop recovery and protection plans for populations at risk. Expected outcomes are activities and resource management plans that result in the recovery, protection, and long-term persistence of native salmonids in the USRB.

Background:

Since the construction of Swan Falls dam in 1901, the USRB has been heavily impacted by hydroelectric development. Currently there are approximately 92 hydroprojects and countless irrigation diversions making use of Snake River water in the Idaho portion of the basin. These activities, as well as habitat alteration due to logging and grazing practices, and the introduction of exotic fish species, have had impacts on native salmonids. Anadromous salmon and steelhead that used to inhabit the Snake River and its tributaries below Shoshone Falls have been extirpated by dam construction and hydroelectric operations.

Bull trout, redband trout, and Yellowstone cutthroat trout populations have experienced significant reductions in distribution and abundance in much of their historical range and have been petitioned to be or are listed under the ESA. Mountain whitefish are the only other native salmonid in the USRB, and their current status is not well known. Despite the sensitive status of these salmonids, quantitative data on the current distribution, trends, habitat, life history needs, limiting factors, and threats to persistence of native salmonids in the USRB were minimal for most populations before the initiation of this project.

The extent of declines in distribution was unclear because most prior assessments of native salmonid status were largely qualitative, and based on professional judgment. Our approach has been to randomly select sampling sites across streams, entire river drainages, and a species' range in Idaho (and adjacent states) to determine present distribution and abundance of salmonids in the Middle and Upper Snake River provinces. We have also gathered as much information as possible from several other sources (federal; states including Wyoming, Utah, Nevada, and Oregon; university, etc.) relative to presence/absence and abundance estimates. Based on these results, current status, effective population size, genetic purity, and interconnectedness of populations of native salmonids are being determined.  Recovery strategies will be developed and implemented where necessary.

Recovery strategies cannot be developed for declining or at-risk populations without knowledge of what factors are contributing to the decline. Most commonly, declines in distribution and abundance of native salmonids throughout western North America have been attributed to exotic species introductions, habitat alteration, and over harvest . Our study design incorporates all of these factors. However, to date, little research has been done on a broad scale to identify factors influencing the persistence of native salmonids in some areas concurrent with declines in others.

In addition to the influence habitat and other conditions have on native salmonids, their inability to persist in the presence of exotic salmonids is one of the most predominantly cited explanations for the decline of native salmonids in North America. Non-native salmonids have been introduced throughout the USRB above Hell's Canyon Dam, and pose threats to native salmonids in terms of ecological (competition and predation) and genetic (hybridization) interactions in many locations. Strategies developed to recover many at-risk populations of bull trout, cutthroat trout, and redband trout in the USRB may benefit from the removal of sympatric non-native salmonids. The work of others and our own has demonstrated the difficulty in removing non-natives with electrofishing alone. We believe the use of chemical treatments with rotenone and antimycin, are likely to be much more cost effective and successful at completely eradicating non-native salmonids under most circumstances. We have identified brook trout populations where eradication would yield the highest benefit to native salmonids, and in an early initiation of Phase III of this project (and in this SOW), we propose to begin implementing such projects on an experimental basis as part of an on-the-ground restoration of Yellowstone cutthroat trout in the USRB.

Hybridization with non-native rainbow trout can reduce or eliminate cutthroat trout populations through introgressive hybridization. In our work on Yellowstone cutthroat trout in the USRB, we surveyed over 900 stream locations to determine the distribution and abundance of salmonids. We found that, at the level of individual study sites, only 19% of the sites that contained Yellowstone cutthroat trout also contained rainbow trout or hybrids. However, at the sub-population level, at least 49% contained rainbow trout or hybrids. Such a discrepancy suggests that even within presumed sub-populations, hybridization is not always uniform, or it has not yet spread throughout some sub-populations. In Phase II of the project (and in this SOW), we propose to test whether introgressive hybridization can be reduced in streams where it presently exists.

The work elements for this Statement of Work (SOW) fall into 5 main Biological Objectives:

1: Finish analysis and writing of a mountain whitefish status assessment.
2: Assess whether removing non-native rainbow trout and hybrids improves the genetic purity of Yellowstone cutthroat trout to >90% in populations that are heavily hybridized.  
3: Assess whether the overall level of hybridization occurring in the Upper Blackfoot River drainage is <10%, to assess whether broad-scale hybridization reduction efforts are necessary.
4: Determine the spatial distribution of brook trout in 5 streams in eastern Idaho to determine their suitability for chemical treatment to remove brook trout before reestablishing a Yellowstone cutthroat trout population.
5: Continue to evaluate growth of redband trout when water temperatures are at stressful levels to look for differences in growth between fish from desert vs. montane streams.