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1 INTRODUCTION

The Klamath River Basin is isolated from other fresh waters by its direct drainage into the Pacific Ocean ( Figure 1). Its isolation and diverse freshwater habitats, including perennial tributary and main-stem flows, extensive marshlands, and large shallow lakes, have favored the genetic isolation of freshwater and anadromous fishes in the basin. Thus, the Klamath River Basin contains endemic freshwater fishes as well as genetically distinctive stocks of anadromous fishes that are shared with nearby basins on the Oregon and California coasts.

Endemic freshwater fishes of the Klamath River Basin include the shortnose sucker (Chasmistes brevirostris) and the Lost River sucker (Deltistes luxatus). These two species, which are long-lived, reach relatively large sizes, and have high fecundity (Moyle 2002), occupy primarily lakes as adults but also use tributary streams and springs for spawning. The two sucker species were abundant in Upper Klamath Lake and elsewhere in the drainage prior to 1900; they were used extensively by Native Americans as well as settlers, and were the basis for commercial fisheries (USFWS 2001). During the twentieth century, particularly after the 1960s, the populations declined substantially. Reduction in abundance of the suckers has been generally attributed to changes in water quality, excessive harvesting, introduction of exotic fishes, alteration of flows, entrainment of fish into water-management structures, and physical degradation of spawning areas (USFWS 2001). Both the shortnose sucker and the Lost River sucker were classified as endangered under the federal Endangered Species Act (ESA) in 1988 (USFWS 1988).



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Page 6 1 INTRODUCTION The Klamath River Basin is isolated from other fresh waters by its direct drainage into the Pacific Ocean ( Figure 1). Its isolation and diverse freshwater habitats, including perennial tributary and main-stem flows, extensive marshlands, and large shallow lakes, have favored the genetic isolation of freshwater and anadromous fishes in the basin. Thus, the Klamath River Basin contains endemic freshwater fishes as well as genetically distinctive stocks of anadromous fishes that are shared with nearby basins on the Oregon and California coasts. Endemic freshwater fishes of the Klamath River Basin include the shortnose sucker (Chasmistes brevirostris) and the Lost River sucker (Deltistes luxatus). These two species, which are long-lived, reach relatively large sizes, and have high fecundity (Moyle 2002), occupy primarily lakes as adults but also use tributary streams and springs for spawning. The two sucker species were abundant in Upper Klamath Lake and elsewhere in the drainage prior to 1900; they were used extensively by Native Americans as well as settlers, and were the basis for commercial fisheries (USFWS 2001). During the twentieth century, particularly after the 1960s, the populations declined substantially. Reduction in abundance of the suckers has been generally attributed to changes in water quality, excessive harvesting, introduction of exotic fishes, alteration of flows, entrainment of fish into water-management structures, and physical degradation of spawning areas (USFWS 2001). Both the shortnose sucker and the Lost River sucker were classified as endangered under the federal Endangered Species Act (ESA) in 1988 (USFWS 1988).

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Page 7 ~ enlarge ~ FIGURE 1 Map of the Upper Klamath River Basin showing surface waters and landmarks mentioned in this report. Source: modified from USFWS. The main stem and tributaries of the Klamath River support endemic populations of a genetically distinctive population of coho salmon (Oncorhynchus kisutch). This group of coho is part of the Southern Oregon/Northern California Coasts (SONCC) evolutionarily significant unit

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Page 8 (ESU), which also occupies several other drainages near the Klamath River Basin. These fish mature in marine waters off the California and Oregon coasts, move up the Klamath main stem and into tributaries for spawning, descend back to the main stem for the smolt phase, and then exit to the Pacific. The present distribution of the species within the Klamath Basin extends to the Iron Gate Dam, although it probably extended farther upstream prior to the construction of main-stem dams (NMFS 2001). Stocks of native coho salmon have declined greatly in the Klamath River Basin over the past several decades. Potential causes of the decline include overexploitation (now largely curtailed), habitat degradation, manipulation of flows in the main stem, excessive warming of waters, degradation or blockage of tributaries, and introduction of large numbers of competitive hatchery-reared coho salmon only partially derived from the native stock (NMFS 2001). The SONCC coho ESU was classified as federally threatened under the ESA in 1997. In response to the listing of the two sucker species and the SONCC coho, the Bureau of Reclamation (USBR), which operates the Klamath River water distribution project (Klamath Project), prepared biological assessments of the effects of Klamath Project operations on the suckers and on the coho (USBR 2001a, b). Because the listing processes for these fish referenced water level in Upper Klamath Lake and other lakes in the Upper Klamath Basin and amounts of flow in the main stem of the Klamath River below Iron Gate Dam as potential points of concern for the welfare of the species, the USBR assessments were intended to make a case for specific flows and water levels in portions of the basin strongly affected by operations of the Klamath Project. In response to the USBR assessment of the endangered suckers, the U.S. Fish and Wildlife Service (USFWS) issued a biological opinion (USFWS 2001). A separate biological opinion was issued on the coho population by the National Marine Fisheries Service (NMFS 2001), which has the prime responsibility for ESA actions on these fish because they are anadromous. The two biological opinions differed sharply from the two corresponding USBR assessments by calling for maintenance of higher lake levels and higher main-stem flows. Year 2001 brought a severe drought to the Klamath River Basin. The U.S. Department of the Interior (DOI) determined that the actions to protect the endangered and threatened species called for in the biological opinions of the USFWS and NMFS must take priority over other uses of water. The amounts of water specified as reasonable and prudent alternatives (RPAs) in the biological opinions should be maintained to the degree possible before provision of water for consumptive use as specified by contracts between

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Page 9 irrigators and the USBR through its Klamath Project. Consequently, most of the water that would have been delivered to irrigators through the Klamath Project was not delivered. Substantial agricultural losses occurred, along with damage to the economic base of the Klamath River Basin (actual losses are still being estimated, but the work of Adams and Cho (1998) shows that direct losses to farmers alone would probably exceed $20 million). Given the strong economic consequences for implementation of the biological opinions through their effect on the Klamath Project, the DOI determined that the scientific basis for the two opinions should be reviewed. The National Research Council (NRC) was asked to form a committee to review the two opinions. Sponsors of the review are USBR and the USFWS of the DOI and the NMFS of the U.S. Department of Commerce. A portion of the work of the NRC committee and the committee's interim conclusions are summarized in this report. The two biological opinions and the two biological assessments contain valuable literature reviews. The committee cites these documents in lieu of the primary literature for much of the background subject matter of this report, but cites individual studies that are of particular importance to the committee's conclusions wherever appropriate. TASKS OF THE NRC COMMITTEE The work of the NRC Committee on Endangered and Threatened Fishes in the Klamath River Basin is divided into two phases (see statement of task, Appendix). The first phase, reported here, involves a preliminary assessment of the scientific validity of the two biological opinions and their RPAs, particularly as they relate to the near-term operation of the Klamath Project. In a second phase, the committee will conduct a broad-based study of the evidence related to the welfare of the endangered and threatened species. Whereas the interim report focuses specifically on the biological opinions, the final report may extend beyond the biological opinions to deal more extensively with water pollution or other such subjects that are not directly under control of the Klamath Project. This effort will culminate in a second report that will give the committee's consensus view of the long-term requirements of the species. Although the interim report specifically deals with the two biological opinions, the committee also gives its conclusions about the two biological assessments upon which the biological opinions are based. If the biological opinions

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Page 10 were rejected fully or in part, the presumed alternative for operation of the Klamath Project would be as prescribed in the USBR assessments. Thus, the committee must not only evaluate the validity of the biological opinions, but also extend the same sort of evaluation to the assessments. The tasks of the committee encompass only the scientific and technical issues that are relevant to the endangered sucker and threatened coho species. The committee is not charged with investigating or reporting on economic dislocation or with forecasting the economic consequences of continued implementation of flows specified in the biological opinions. Given the background materials provided to the committee, however, all committee members are aware of the importance of any change in historical management of flows to water users in the Klamath Basin. Also, the committee is aware of the long-standing interest of Native American tribes of the Klamath River Basin in the maintenance and expansion of fish stocks, including Tribal Trust species not covered in this report, and of the interests of numerous other parties in water resources, wetlands, and the welfare of fishes and other aquatic life. Although the committee will not analyze economic or socioeconomic questions, it recognizes the interest of individuals and communities in the Klamath Basin in the conclusions of the committee. Not only from an economic and social point of view but also from a perspective of ecological and biological resources, the work of the NRC committee focuses on its statement of task and on the inherent requirements of the ESA, which prohibits federal actions that jeopardize continued existence of listed species through interference with their survival or recovery (50 CFR 402.02). The Klamath River Basin is home to hundreds of species of fish and wildlife and to distinctive native ecosystems, including wildlife refuges of national significance. Many of these natural resources have been greatly restricted or altered through human action. In fact, changes in the flow regime in the Klamath River may affect other fishes that have not yet been proposed for listing as threatened species but have not yet been listed (e.g., ESUs of steelhead and chinook salmon). The committee is charged, however, with studying the requirements of the shortnose and the Lost River suckers and the coho salmon and not those of other species in the Klamath River Basin.