Richard N. Williams

A General Protocol for Restoration of Regulated Rivers

Large catchment basins may be viewed as ecosystems in which natural and cultural attributes interact. Contemporary river ecology emphasizes the four-dimensional nature of the river continuum and the propensity for riverine biodiversity and bioproduction to be largely controlled by habitat maintenance processes, such as cut and fill alluviation mediated by catchment water yield. Stream regulation reduces annual flow amplitude, increases baseflow variation and changes temperature, mass transport and other important biophysical patterns and attributes. As a result, ecological connectivity between upstream and downstream reaches and between channels, ground waters and floodplains may be severed. Native biodiversity and bioproduction usually are reduced or changed and non-native biota proliferate. Regulated rivers regain normative attributes as distance from the dam increases and in relation to the mode of dam operation. Therefore, dam operations can be used to restructure altered temperature and flow regimes which, coupled with pollution abatement and management of non-native biota, enables natural processes to restore damaged habitats along the river’s course. The expectation is recovery of depressed populations of native species. The protocol requires: restoring peak flows needed to reconnect and periodically reconfigure channel and floodplain habitats; stabilizing baseflows to revitalize food-webs in shallow water habitats; reconstituting seasonal temperature patterns (e.g. by construction of depth selective withdrawal systems on storage dams); maximizing dam passage to allow recovery of fish metapopulation structure; instituting a management belief system that relies upon natural habitat restoration and maintenance, as opposed to artificial propagation, installation of artificial instream structures (river engineering) and predator control; and, practising adaptive ecosystem management. Our restoration protocol should be viewed as an hypothesis derived from the principles of river ecology. Although restoration to aboriginal state is not expected, nor necessarily desired, recovering some large portion of the lost capacity to sustain native biodiversity and bioproduction is possible by management for processes that maintain normative habitat conditions. The cost may be less than expected because the river can do most of the work.

Return to the River: Scientific Issues in the Restoration of Salmonid Fishes in the Columbia River

Abstract The Columbia River once was one of the most productive river basins for anadromous salmonids on the West Coast of North America; however, its current runs total less than 10% of historic levels. The Independent Scientific Group (ISG) of the Northwest Power Planning Council reviewed regional salmon management actions described in the Columbia River Basin Fish and Wildlife Program and concluded that the current program is unlikely to recover declining salmon and steelhead stocks. Adoption of a salmon life history ecosystem concept as a guiding foundation is needed to recover depressed stocks. Increasing natural ecosystem processes and functions should rebuild salmon populations to more abundant, productive, and stable levels. Elements of a salmon recovery program that increase these normative conditions include restoration of habitat for all life history stages (including migrations), reduction of mortality sources (including harvesters), planning of hydropower mitigation measures in the context of...

Genetic Detection of Putative Hybridization between Native and Introduced Rainbow Trout Populations of the Upper Snake River

Abstract Native trout populations throughout western North America have declined because of habitat alteration, introgression with introduced trout, or competitive exclusion by nonnative species. Consequently, identification and preservation of native trout are now the goals of many management programs. We examined allozyme and mitochondrial DNA (mtDNA) variation in seven naturally occurring populations and one hatchery population of rainbow trout Oncorhynchus mykiss from southern Idaho and northern Nevada to determine their genetic origins. Allozyme and mtDNA results were concordant in identifying three populations as genetically pure interior rainbow trout and one population as a hybrid swarm. Results for the remaining four populations were discordant. However, these latter four populations were best classified as hybrid swarms due to the nature of either the allozyme or mtDNA data, which included genetic characteristics of both coastal and interior rainbow trout. Our study demonstrates the utility of m...

Native fish conservation areas: A vision for large-scale conservation of native fish communities

Abstract The status of freshwater fishes continues to decline despite substantial conservation efforts to reverse this trend and recover threatened and endangered aquatic species. Lack of success is partially due to working at smaller spatial scales and focusing on habitats and species that are already degraded. Protecting entire watersheds and aquatic communities, which we term “native fish conservation areas” (NFCAs), would complement existing conservation efforts by protecting intact aquatic communities while allowing compatible uses. Four critical elements need to be met within a NFCA: (1) maintain processes that create habitat complexity, diversity, and connectivity; (2) nurture all of the life history stages of the fishes being protected; (3) include a long-term enough watershed to provide long-term persistence of native fish populations; and (4) provide management that is sustainable over time. We describe how a network of protected watersheds could be created that would anchor aquatic conservation...

Localized Genetic Effects of a Long-Term Hatchery Stocking Program on Resident Rainbow Trout in the Metolius River, Oregon

Abstract Hatchery rainbow trout Oncorhynchus mykiss have been stocked in the Metolius River in central Oregon since 1938, and legal-sized (≥160 g) yearling trout were stocked annually from 1947 until 1995. In 1996, management objectives shifted to emphasize wild trout, and hatchery stocking ceased. We examined allozyme and mitochondrial DNA (mtDNA) variation among three naturally occurring populations of rainbow trout in the Metolius River to investigate possible hybridization with hatchery-produced rainbow trout. We also examined two commonly used hatchery strains of rainbow trout, one of which has supplied nearly all of the catchable hatchery trout in the Metolius. Both allozyme and mtDNA data showed the two hatchery samples to have genetic characteristics typical of hatchery populations derived from coastal rainbow trout O. mykiss irideus. Rainbow trout sampled from the lower Metolius River, approximately 30 km downstream of the headwaters, had allozyme and mtDNA characteristics typical of interior rai...

Research, Monitoring, and Evaluation of Fish and Wildlife Restoration Projects in the Columbia River Basin: Lessons Learned and Suggestions for Large-Scale Monitoring Programs

Abstract The year 2006 marked two milestones in the Columbia River Basin and the Pacific Northwest regions efforts to rebuild its once great salmon and steelhead runs—the 25th anniversary of the creation of the Northwest Power and Conservation Council and the 10th anniversary of an amendment to the Northwest Power Act that formalized scientific peer review of the councils Fish and Wildlife Program and its varied individual projects. The authors of this article served as peer reviewers in the last decade. Restoration efforts in the Columbia River constitute a massive long-term attempt at fisheries and ecosystem restoration. In this article we examine some of the lessons we learned in reviewing the research, monitoring, and evaluation efforts of projects and their effects on advancing knowledge (i.e., adaptive management) in the Columbia River Basin Fish and Wildlife Program, one of the most ambitious and expensive long-term ecological restoration programs in the United States.

Historical Influences of Volcanism and Glaciation in Shaping Mitochondrial DNA Variation and Distribution in Yellowstone Cutthroat Trout across Its Native Range

Abstract While Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri are probably the best known and one of the most extensively researched of all the subspecies of cutthroat trout, relatively little is known about their genetic structure and evolutionary history. In this study, we assessed the genetic variability and population structure among 50 populations of Yellowstone cutthroat trout over a large portion of their range in Idaho, Montana, Utah, Wyoming, and Nevada using restriction fragment length polymorphism and sequencing analysis of the mitochondrial ND1 and ND2 gene regions. Among the more than 1,000 samples analyzed, a total of 17 haplotypes were observed. These data indicate significant geographic structuring of the genetic variation between drainages and varying levels of reproductive isolation among populations within drainages. Much of this genetic structuring is clearly the product of long-term historical processes (basaltic volcanism and glaciations) that have isolated populations for...

13 – Return to the River: Strategies for Salmon Restoration in the Columbia River Basin

Returning the river to a more natural state runs counter to the management philosophy that has guided salmon restoration in the Columbia River Basin (CRB) for much of the 20th century. For this reason, restoration or improvement of the ecological conditions will require an examination of the values that underlie Columbia River management. However, the conceptual foundation provides a scientific basis for that debate. In the recent past, failure of the scientific community to resolve key restoration issues was often used to justify maintaining the status quo and avoid the necessary public debate over the social and economic costs of salmon recovery. However, expecting scientists to agree on each of the key questions is an unrealistic assumption. The healthy exercise of scientific debate should not be used as an excuse to hold progress hostage to the unattainable goal of a perfect scientific consensus. If the region is genuine in its desire to restore Pacific salmon in the Columbia Basin, continuing the status quo is not an option. The first step in developing a scientifically-sound restoration program for salmon is to clearly articulate the conditions needed for salmon relative to the regions salmon recovery goals. The next step is to determine what changes in the federal hydropower system and other uses of the river are needed to achieve these conditions. The next step is the difficult job of debating the cost and benefits of salmon restoration. Significant changes will require painful decisions, perhaps even congressionally mandated alteration of federal hydrosystem project operations. Other lesser changes might limit; however, not eliminate, the regions ability to use the Columbia River as a navigation corridor and to supply some irrigation needs.

3 – Developing a New Conceptual Foundation for Salmon Conservation

This chapter synthesizes relatively recent knowledge pertinent to the conservation of salmonid populations. Ecosystems supporting salmonid species are dynamic rather than static systems, experiencing changes in state or structure that are driven by biological and physical processes operating at a variety of spatial scales. These natural processes create spatially and temporally diverse habitats with a high degree of connectivity among habitat patches. Habitat variation in space and time creates a template for development of diverse life histories and complexes of locally adapted populations that may be genetically and demographically linked by movement of individuals among populations. Life history and population diversity, both being distinguishing features of salmonid species, are essential for sustaining productivity of the salmonid species within a geographic region. Salmonid conservation should be directed at protection and restoration of both the physical processes that create diverse habitats and the biological processes that allow individuals, populations, and population complexes to persist in those habitats. A dynamic view of the ecosystems also suggests that restoration should not be directed at attempting to maintain the ecosystems in a particular state defined by a specific set of performance attributes or standards.

1 – Introduction and Background of the Columbia River Salmon Problem

The problem of decline in salmon has not gone unattended. The 20th century saw several salmon recovery programs, most of which were associated with mitigation for fishery impacts from development of the rivers hydroelectric potential. This chapter presents an introduction to salmon and steelhead management in the Columbia Basin, and suggests a new conceptual foundation for salmon management in the 21st century. The regions failure to halt the decline in salmon populations is the result of numerous social, economic, and scientific issues, most of which are generally recognized and discussed extensively. The lack of an explicit and scientifically based conceptual foundation and the consequences of this lack on salmon management and recovery actions, is not recognized. A conceptual foundation or world view is fundamental to the interpretation of the facts garnered from observation or scientific investigation and, in turn, the management of human interactions with the environment. The commodities- driven conceptual foundation that guided much of 20th-century fishery management was based first on the belief in nearly inexhaustible resources, and later on the faith in technology to replace natural functions lost as a result of human actions. The decline of salmon in the Columbia Basin over the course of the 20th century, despite massive infusions of money and technology, proves the failure of the old paradigm and the need for a new conceptual foundation for salmon management. A conceptual foundation for 21st-century salmon management stresses the role of the environment—with all its variability and complexity–in shaping species performance and persistence.