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Final Report 1-7 September 2000 As a result of these and other ecological changes, many of the native fishes of the Colorado River system are in jeopardy and protected under the 1973 Endangered Species Act, as amended, or by one or more of the basin states (Carlson and Muth 1989, 1993). All of the "big-river" fishes endemic to the Colorado River basin are in jeopardy (Minckley 1973; Tyus et al. 1982a; Behnke and Benson 1983; Williams et al. 1985; Minckley et al. 1991a; Tyus 1991a), including the federally endangered humpback chub (USFWS 1967), bonytail (USFWS 1980), Colorado pikeminnow (USFWS 1974), and razorback sucker (USFWS 1991 b). Remaining populations of humpback chub occur in the Grand Canyon in the lower Colorado River basin and in five canyon regions in the upper basin (Valdez and Ryel 1995, 1997). The bonytail, originally widespread and abundant, is now considered functionally extinct in the wild (USFWS 1990b). Wild Colorado pikeminnow are extirpated from the lower basin (Tyus 1991a), and the razorback sucker exists naturally as only a few disjunct populations or as scattered individuals (Minckley et al. 1991a). 1.2.1 The Green River System Completion of Flaming Gorge Dam on the Green River in 1962 had profound effects on downstream conditions. Before construction of the dam, the Green Ri ver was an unregulated, turbid, temperate stream that exhibited seasonal variations in flow and temperature on the basis of natural flow cycles. The natural flow pattern (Section 3.4.1) featured a high spring peak flow and low base flows with periodic spates caused by localized rainfall. Water temperatures in the river ranged from near freezing in winter to greater than 200C in summer (Vanicek et al. 1970). A diverse assemblage of warm-water species dominated the aquatic macroinvertebrate fauna (Holden and Crist 1981), and vegetation along the river occupied two distinct zones (Fischer et al. 1983). Plants in the flood zone nearest the river were predominantly annual or scour-tolerant perennials such as wild licorice Glycyrrhiza lepidota, dogbane Apocynum spp., and sedges Carex spp. Dominant plants above the flood zone included box elder Acer negundo, squawbush Rhus trilobata, Fremont cottonwood Populus fremontii, and coyote willow Salix exigua (Holmgren 1962). The fish community of the main-stem river consisted of 12 native species (Table 4.1), represented primarily by warm-water cyprinids (minnows) and catostomids (suckers), as well as at least six species of introduced nonnative fishes (Table 4.2; Vanicek et al. 1970). The presence and historic operation of Flaming Gorge Dam greatly altered seasonal and daily flow (Section 3.4) and temperature patterns (Section 3.5) in the Green River. The magnitude and duration of spring peak flows were reduced, the magnitude of base flows was increased, daily fluctuations in flow were increased, and hypolimnetic releases of water from the reservoir affected water temperatures and increased water clarity. These changes rendered sections of the Green River directly downstream of the dam largely unsuitable for many native fishes (Chapter 4); shifted the local aquatic macroinvertebrate community to species tolerant of clear, cold water (Vinson 1998); and allowed the establishment of a tailwatertrout fishery (Modde et aI. 1991). When the large annual floods were eliminated, riparian vegetation from adjacent riparian and upland areas colonized much of the old flood zone and in-channel sand or gravel bars; it formed dense stands along shorelines in