In less than 100 years, anadromous fish were extirpated from the Malheur River Subbasin that included chinook salmon Oncorhynchus tshawytscha, steelhead trout Oncorhynchus mykiss, pacific lamprey Lampetra tridentata, and possibly coho salmon Oncorhynchus kisutch.  The construction of hydropower and irrigation facilities in the Columbia River Basin has decreased the range of anadromous fish.  The construction of Brownlee Dam in 1958 extirpated the remaining populations of anadromous fish in the upper Snake River Drainage.  The diet of the Paiute people included fish (including a great deal of salmon) birds, mule deer Odocoileus hemionus, rocky mountain elk Cervus elaphus, small mammals i.e. yellow-bellied marmot Marmota flaviventris, plants i.e. Camas Camassia quamash, and roots i.e. bitter root Lewisia rediviva.  Due to the elimination of anadromous fish, resident fish species have been the focus of recovery efforts in the Malheur River Subbasin.

Native resident fish have suffered significant habitat loss and degradation due to land-use factors such as timber harvest, livestock production and irrigation withdrawals. Management and conservation of bull trout populations and native redband trout populations have become high priorities for many state and federal agencies due to dramatic population declines throughout their historic native ranges.  Bull trout are currently listed as threatened under the Endangered Species Act, and redband trout are recognized as a “species of special concern” or a “sensitive species” by the State of Oregon, U.S. Fish and Wildlife Service, the U.S. Forest Service, the Bureau of Land Management, the American Fisheries Society, and all other states throughout their historic range.  Despite their sensitive status, quantitative data on the current distribution, population status and trends, habitat, life history needs, limiting factors, and threats to persistence of native salmonids in the Malheur River Subbasin is limited.

For the Malheur River Subbasin, little is known about the population status and trend of redband trout.  However, native redband trout, rainbow trout, and bull trout population throughout their native habitat are declining due to a variety of complex, contributing factors. Those include, but are not limited to habitat degradation, over-fishing, and the extensive stocking of non-native, hatchery-produced, rainbow trout which have hybridized with or replaced native redband trout, and brook trout Salvelinus fontalis hybridize with bull trout populations throughout their historic native range.  Work by Currens et al. (1990) and Shiozawa and Evans (1995) suggest sampling headwaters areas throughout the redband trout historic distribution are likely to locate remnant populations.  Hatchery rainbow trout with coastal genetics are stocked in the Malheur River.  Genetic sampling showed some genetic influence in redband trout genetics in systems that where stocked with coastal rainbow trout.
  
As of today most of the fish population data collection has occurred in the headwater streams of the upper Malheur and North Fork Malheur Rivers by US Forest Service, Oregon Department of Fish and Wildlife, and Burns Paiute Tribal personnel.  The populations of salmonids in the upper Malheur River Subbasin are extremely sensitive to annual environmental conditions.   Data collection has occurred over a 40 year time period with no systematic or comprehensive effort to determine population trend.  Due to an overall harsh, arid environment and sporadic sampling effort, land and fish managers cannot conclusively determine current fish population response to land management activities.  

Many hatchery programs in eastern Oregon have used and are currently using hatchery produced rainbow trout from the McCloud River in California. Management response to these declines has likewise been complex and has involved numerous private, tribal, state and federal agencies working together for the purpose of outlining recovery and conservation strategies. The results of these collaborations have been the production of detailed management planning documents that have stressed as goals and objectives the importance of:
                                                                                                                                  
- Identifying and conserving remaining pure, native, salmonid populations and the genetic diversity present within them, and
- Increasing or maintaining the number of native salmonid populations within their native range through habitat improvements

However, current management plans are severely hampered in reaching these objectives by the lack of the required genetic and population information needed for effective conservation and restoration efforts.  This project serves to provide detailed genetic information with regards to levels of hybridization and introgression, genetic diversity, and genetic population structure of redband trout populations throughout the Malheur Subbasin.  Electrophoresis and histochemistry analysis from two streams in the Malheur River Subbasin concluded that the redband populations in these streams had a high probability of being genetically distinct from each other.  In addition, distinct populations of redband trout are assumed to occur in several tributaries that do not have perennial flows in their lower reaches.  With very little life history and genetic information available, the state of Oregon manages all tributary populations as distinct breeding populations.  The Oregon Department of Fish and Wildlife have identified the presence of redband trout in 76 streams in the Subbasin.  

Genetic diversity is a resource, yet very little genetic information is available to local fish and land managers.  The native rainbow trout of the interior basins of the Oregon desert that are commonly referred to as redband trout, evolved unique adaptations to survive in harsh, fluctuating, arid environments.  Gall et al. (1981) conducted an electrophoretic analysis on redband trout from Wolf Creek (upper Malheur) and Bear Creek (upper North Fork Malheur River) and concluded that these fish represent a distinguishable group of trout and have a high probability of being native to their respective drainages.  In addition, electrophoresis studies in the early 1990’s suggest a presence of a divergent population of rainbow trout from the native population, most likely the result from the introduction of non-native rainbow trout in the Malheur River system.  Most of the sampled drainages in the 1990’s are small mainstem tributaries that flow into the Malheur River downstream of Juntura, Oregon.  In addition, microsatellite analysis of redband trout from the North Fork Malheur River drainage suggests little genetic differentiation among the rainbow populations when compared to microsatellite-based studies of most other inland salmonids.  Advanced analytical methods have been developed that has increase accuracy and confidence in determining population structure, quantification of gene flow, and inference of demographic history.  This project proposes to precisely identify the genetic integrity of redband trout and assist managers directly by:

- Assessing current and future genetic risks,
- Preserving existing genetic variability,
- Delineating and prioritizing local populations for conservation and management purposes,
- Estimating effective population size,
- Understanding genetic population structure,
- Identifying suitable populations for translocations and reintroductions,
- Identifying suitable populations for broodstock development, and
- Addressing genetic concerns in possible future ESA petitions.

Based on these results, current status, effective population size, genetic purity and interconnectedness of populations of native salmonids can be determined, and recovery strategies can be developed and implemented where necessary, regardless of what the exact historical distribution might have been.

This proposal is an ongoing cooperative project with the Burns Paiute Tribe, Oregon Department of Fish and Wildlife, US Bureau of Reclamation, Bureau of Land Management, US Forest Service, and US Fish and Wildlife Service.  The current ongoing project has focused on bull trout in the past and shall shift to more of a redband focus in the next cycle.  The data collected from this proposal shall provide local fish and land management agencies the genetic makeup, distribution, densities of native salmonids populations throughout the Malheur River Subbasin.  This project will assist fish and land managers in: 1) developing a more detailed restoration and protection strategies to ensure the long-term persistence of self-sustaining, complex interacting populations of redband trout distributed across the species’s range and 2) develop a systematic monitoring and evaluation guidelines or plan to effectively track native salmonids populations.  Through the development of the cooperative plan for redband trout, the Burns Paiute Tribe shall adopt the monitoring of those sites that are associated with the Malheur River Wildlife Mitigation Project (2000-02-700), Logan Valley Mitigation Property (2000-09-000), and other associated Tribal acquisitions.

Much of the past effort has focused on documenting the life history of bull trout.  The Tribe has collected much data on the seasonal migration, critical spawning areas, genetic integrity and genetic effects from non-native brook trout.  The goal is still to gain a better understanding of native resident fish in the Malheur River Subbasin so land and fish managers can make defensible management decisions but focus shall be on redband trout were existing data is limited.  Objectives are:

Biological Objective #1 – Determine the population status and distribution of native salmonids, redband trout in particular, and develop a draft monitoring and evaluation plan for population trend in the Malheur River Subbasin utilizing approximately 180 reference sites.   We propose to accomplish this objective by implementing the Environmental Monitoring and Assessment Program (EMAP) probabilistic sampling design to characterize the status and distribution of native salmonids at the Subbasin scale.  Preliminary discussions with Oregon Department of Fish and Wildlife (ODFW) and Environmental Protection Agency (EPA) in Corvallis, Oregon suggest 180 reference sites are suitable to determine the population status of salmonids in the Malheur River Subbasin.  Through coordination with state and federal land and fish management agencies, develop a monitoring and evaluation plan that will effectively track population trend of salmonids.

Biological Objective #2 - Develop a draft monitoring and evaluation plan for bull trout population trend in the Malheur River Subbasin utilizing redd count surveys on approximately 36 miles of stream.  In 1992, ODFW initiated spawning surveys for bull trout within the North Fork and Upper Malheur river system.  Since 1999, Tribal staff has played an important role in assisting ODFW in conducting these surveys.  This project will identify methods, schedule, and responsibility of future monitoring tasks.  

Biological Objective #3 – Determine the population integrity and rates of introgression/hybridization for 56 redband trout populations.  One of our goals is to improve conservation and recovery efforts for redband trout by determining whether fish within a basin are part of one metapopulation or represent multiple discreet populations.  The project proposes to genetic analyze and characterize the fine-scale population structure of redband trout within the Malheur River Subbasin.  In addition, the genetic analysis will seek to determine the influence of non-native hatchery stocks of rainbow trout have on native redband trout.  The null hypotheses are: 1) There is no genetic differentiation among redband trout collected from different tributaries in the Malheur River Subbasin; 2) There is no genetic influence of past and current stocking of hatchery produce rainbow trout collected from the tributaries in the Malheur River Subbasin, and 3) There is no genetic evidence of a bottleneck occurrence in redband trout collected from different tributaries in the Malheur River Subbasin.