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scientific Tovaluation of Rio, ogical Opinions nn Pndenprcd and Thmntchcd T?iahclz in the Klamath RivcrA, cant intoriln Report (2002) Mnr_ �nsxei. n; Ip, c1Nh�PCM�nynrflN�N +97aU�h.mVthanl. mCyfiph� 7J)f12. W)I'lAc NalWa1 Ac YlOVY 1-*50W" .011 elghrn IMW-cd 1. Introduction Th Klamath River Basin is isolated from other fresh waters by its direct drainage to the Pac' c (Figure 1). This isolation and a diversity of freshwater habitats including perennial utary and main -stem flows, extensive marshlands, and large shallow lakes, have favo genetic isolation of freshwater and anadromous fishes in the basin. Thus, the K1amaRiver Basin contains endemic freshwater fishes as well as genetically distinctive Stocks of wmdromous fishes that are shared with nearby basins on the Oregon and Califlorpia coasts. En4nnic freshwater fishes of the Klamath River Basin include the shortnose sucker (Chasmistel brevirostris) and the Lost River sucker (Deldstes luxatus)_ These two species, which are long-lived, reach relatively large sizes, and have high fecundity (Moyle 1976), occupy primarily lakes as adults but use tributary streams as well as 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 20th century, and particularly after the 1960s, the populations substantially declined in abundance. 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). Botts the shortnose sucker and the Lost River sucker were classified as federally endangered under the Endangered Species Act (ESA) in 1988 (USFWS 1988). 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 (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 -stern 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 (NUTS 2001)_ The SONCC who BSU 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 (USSR), 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 its Upper Klamath Lake and other lakes in the Upper Klamath Basin and amounts of flow in the main stem of the Klamath River 966 -d BEO /810'd 9EZ -1 895E998EOE snnosu 1danm 100 -Woad BE:[[ ZOOZ- 80 -93d