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Summary Two endemic fishes of the upper I(lamath basin (Figure S-1), the short- nose sucker (Chasmistes brevirostris) ancT the Lost River sucker (Deltistes Fixates), were listecT as enciangerecT uncler the fecleral EnciangerecT Species Act (ESA) in 1988 by the U.S. Fish ancT WilcTlife Service (USFWS). USFWS cited overfishing, water management, habitat alteration, nonnative species, poor water quality, ancT several other factors as likely contributors to the clecline of the fishes, which once were very abundant. In 1997, the Southern Oregon Northern California Coast revolutionarily significant unit" of coho salmon (Oncorhynchus kisutch), which is native to the I(lamath basin ancT several adjacent drainages, was listecT by the National Marine Fisheries Service (NMFS) as threatened uncler the ESA. NMFS cited water manage- ment, water quality, loss of habitat, overfishing, ancT several other potential causes of clecline for the coho salmon. In 2001, in response to biological assessments prepared by the U.S. Bureau of Reclamation (USBR), the two listing agencies issued biological opinions that requirecT USER to take numerous actions, inclucTing mainte- nance of higher water levels in Upper I(lamath Lake ancT two reservoirs on the Lost River ancT higher flow of the I(lamath River below Iron Gate Dam. Release of the two biological opinions coinciclecT with a severe drought. Because of the new biological opinions ancT the drought, USER was prohib- itecT from releasing large amounts of water to farmers servecT by its I(lamath Project, which cTiverts waters from Upper I(lamath Lake ancT the upper Lost River for use in irrigation through USBR's I(lamath Project. The unex- pectecT restrictions on water supply, which severely impaired or eliminatecT 1

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2 FISHES IN THE KLAMATH RIVER BASIN ~ OREGON FIGURE S-1 Map of the Klamath River basin showing surface waters and land- marks. Source: Modified from USFWS. ~ As, Dwinnell Lake Dank ~~ ,,, ~ ~~l ,,WJ Lake ~ ~ ~ ~ it-' ~ , ~ _ ~ a.<,...... .... ',! \,: lo e - : Crater ~ ~~ N A' <\ Ri ~'`\ ~ ~` \ Sprague MedEo :< :3K1a1~ath ; ~ ~~ ,~ ~ ,, 7-~ ~/~ Lake Clear Lake f '3 fin'.,. no"{ ~ .'~'~'~1 SO `N ^~ ~ l. CALIFORNIA ,. . agricultural production on the 220,000 acres irrigated by the Klamath Project, causecT agricultural water users ancT others to question the basis for water restrictions, while other parties, fearing adverse effects of the Klamath Project on the enciangerecT ancT threatened fishes, supported the restrictions. In late 2001, the Department of the Interior ancT the Department of Commerce askecT the National Academies to form a committee (the Com- mittee on EnciangerecT ancT Threatened Fishes in the Klamath River Basin)

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SUMMARY 3 to evaluate the strength of scientific support for the biological assessments ancI biological opinions on the three listecI species, ancI to identify require- ments for recovery of the species. The committee was charged to complete an interim report in early 2002, focusing on effects of the Klamath Project, ancI to complete a final report in 2003 that wouicI take a broacI view of the scientific aspects of the continued survival of the listecI species (Box Sop. This is the committee's final report. In its interim report of February 2002, the committee founcI substantial scientific support for all recommendations macle by the two listing agencies for the benefit of the enciangerecI ancI threatened species, except for recom- menciations requiring more stringent controls over water levels in Upper Klamath Lake ancI flows at Iron Gate Dam. The committee also noted, however, that USBR hacI not proviclecI any substantial scientific support for its own proposal of revised operating procedures, which might have lecI to lower mean water levels or lower minimum flows. In 2002, USBR issued a new biological assessment that clealt with the two enciangerecI sucker species ancI the threatened coho salmon. In re- sponse, USFWS prepared another biological opinion on the suckers, ancI NMFS prepared another biological opinion on the coho salmon. These documents reflect a closer interaction between the agencies than in previous years. USBR moved toward more restrictive operational practices than it hacI previously proposed ancI toward clevelopment of reserve water sup- plies; USFWS ancI NMFS were more cautious in requiring actions whose basis wouicI be contraclictecI by site-specific studies, ancI they acknowlecigecI the neecI to consult with parties in aciclition to USBR. The biological assess- ment anti the two biological opinions for 2002 cover a 10-yr interval (2002- 2012), cluring which time the listing agencies may require aciclitional con- sultation ancI may revise their biological opinions. PRINCIPAL FINDINGS OF THE COMMITTEE Lost River ant! Shortnose Suckers Upper Klamath Lake Although suckers of all age classes are present in Upper Klamath Lake, population densities of suckers are low, ancI there are no signs that the populations are returning to their previously high abundance. Suckers spawn in tributaries to Upper Klamath Lake, but they are blockecI from much potentially suitable spawning habitat by Chiloquin Dam on the Sprague River (Figure S-11. Numerous smaller blockages ancI diversions also are present but are poorly clocumentecI. Expansion of spawn- ing on the Sprague River couicI increase the abundance of fry clescencling to

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4 FISHES IN THE KLAMATH RIVER BASIN Box S-1. Statement of Task The committee will review the government's biological opinions regarding the ef- fects of Klamath Project operations on species in the Klamath River Basin listed Under the Endangered SPQCje8 Act' including coho salmon and shoftnose and Cost River suckers. The committee will assess whether the bloioglcal opinions are consistent with the available sciontiflc information. It will consoler hyClrclogic anti other environmental parametem (including water quality anti habitat awai|abi|ity) affecting those species at critical times In their life cycles, the probate conse- quences to them of not realizing those environmental parameters and the inter- relationship of these e0Viroomental conditions necessary to recover and sustain The listed species. PlTo complete its charge, the committee will 1. Review ebb evaluate the science underlying the Blologlcal Assessments (USBR 2001 a,b) and Biological Opinions (US6WS 20017 NMFS 2 ). A. Review and evaluate environmental parameters critical to the survival and recover of listed species. 3. Identify scientific information relevant to evaluating the Effects of project operallons that has become available since USFWS and NMFS prepared the bio- loglcal opl'lons 4. Identify gaps in the ki owledge and sclei tific information that are i ceded to develop comprehensive strategies for recovering listed species at d provide at estimate of the time and funding it would require. A brief Interim report will be or~vitled by Ja' ugly 31, p002. The interim report will focus on the February 2001 biological assessments of the Bureau of Reclama- tlon and the April 9001 biological opl' ioi s of the U.S. Eish and Wildlife Service and National Marli e Fisheries Service regarding the effects of operation s of the Bu- reau of Reclamation 's K|amath Pioject on listed species. The committee wll; pr~- wlde a preliminary assessment of the scientific it formation used by the Bureau of [Reclamation, the Fish and Wildlife Service, and the National Maii'~e Fisheries Service, as cited In those dock ents' and will consider to what degree the abaly- sis of effects in the biological opl' ions of the Fish and Wildlife Service and Natio' al Marli e Fisheries Service is consistent with that sciet tific it formation. The commlt- tee will islet tify any reievai t scientific information it is aware of that has become available since the Fish and Wlidjife Seiwlce and Ratio' al Marine Fisheries Ser- wlce prepared the biological opinloi~s. FlThQ committed will also co' sided any other relevai t scientific information of which it is aware. The final report will thoroughly address the scientific aspects related to the cot tinued survival of coho salmoi and shoit' ose and Lost River suckers it the Klamath River Basin. The committee will identity gaps in the k' owledge and sclen- tific information that are neetletl awl or~v'Lle appi~o~lmate estimates of the time and funding needed to fill those gaps, if such estimates see possible. The commlt- tee we also provide an assessment of sclet tific considerations relevant to strate- gies to' piomotl' ~ the recover of listed species in the Klamath Basin.

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SUMMARY Upper I(lamath Lake anti wouicI beneficially extend the interval over which they arrive at the lake. The water quality of the tributaries to Upper I(lamath Lake is poor for some native fishes but is probably adequate for the listecI suckers. The tributaries clo, however, show loss of riparian vegetation anti wetiancI (largely clue to agricultural practices), which couicI aciversely influence the survival of fry. The physical condition of channels in general anti spawning areas in particular is clegraclecI, but the nature anti extent of clegraciation is poorly clocumentecI for the tributaries. EnciangerecI suckers also spawn near springs that emerge at the margin of Upper I(lamath Lake. Some apparently suitable spawning sites are no longer usecI, probably because entire groups of fish that used the sites were eliminatecI cluring the era of fishing, which enclecI in 1987. Lakeside spawn- ing behaviors are associated with a specific range of depth. During ciry years, the amount of appropriate spawning substrate with appropriate wa- ter clepth is reclucecI by cirawclown of the lake. Data on year-class strength show no indication of a relationship between year-class strength anti water level, which might be expected if cirawclown were strongly suppressing pro- cluction of fry. Fry are strongly clispersecI from their points of origin by currents ancI ultimately are founcI in shallow water in or near emergent vegetation at the margins of the lake. Loss of such vegetation, especially near the tributary mouths, couicI be clisacivantageous to the fry. The area around the lake associated with preferred depths ancI presence of emergent vegetation varies with water level; cirawclown, especially in ciry years, recluces this area. StanciarclizecI sampling of fry anti studies of year-class strength for large fish clo not, however, indicate associations between water level ancI abundance of larvae. luveniles seek somewhat creeper water than larvae. There is substantial juvenile mortality, but current information is insufficient to show whether it is extraordinary in comparison with mortality in other lakes that have more favorable living conditions. Subaclult anti aclult fish seek creeper water than younger fish anti con- gregate in specific areas of Upper I(lamath Lake. In contrast to the tributar- ies, poor water quality in the lake itself appears to be their greatest vuiner- ability. Direct evidence of harm to large fish by poor water quality inclucles physical indications of stress anti mass mortality of large fish ("fish kills") at times of exceptionally poor water quality. Mass mortality of large fish occurs cluring the second half of the grow- ing season, but not in all years. Upper I(lamath Lake is hypertrophic (ex- tremely procluctive) because its rich supplies of phosphorus leacI to extreme abundance of phytoplankton clominatecI by Aphanizomenon flos-aq?vae, a nitrogen-fixing bluegreen (cyanobacterial) alga. High abundances of

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6 FISHES IN THE KLAMATH RIVER BASIN Aphanizomenon incluce high pH through high rates of photosynthesis. Al- though strong algal blooms of this type occur each year, conditions for mass mortality are associated with a specific sequence of weather events involving calm weather succeeclecI by wincly weather. Low concentrations of clissolvecI oxygen probably are the immediate cause of cleath of enciangerecI suckers cluring episodes of mass mortality, but other water-quality factors may contribute to stress. Mass mortality of large fish in Upper I(lamath Lake has occurred for many clecacles, but anthropogenic factors, especially those leacling to strong dominance of Aphanizomenon, probably have increased its severity ancI frequency. Poor water quality may also challenge the sucker populations in other ways. High pH, for example, couicI be harmful to young fish even if they are not subject to the mass mortality of larger fish. Because hypertrophic conditions indicate very high supplies of phos- phorus, much attention has been given to the possibility of reducing the phosphorus loacI passing from the watershed to Upper I(lamath Lake. The prospects for suppressing algal blooms by this means in Upper I(lamath Lake seem poor, however, because about 60% of the external phosphorus loacI is clerivecI from natural sources. In aciclition, the anthropogenic com- ponent of loacI is accounted for by clispersecI sources, which are clifficult to control, ancI the internal loacI (phosphorus releasecI from lake secliments) is about clouble the external loacI. The key change over the last 50 yr in Upper I(lamath Lake probably was the rise of Aphanizomenon, which replacecI diatoms as the dominant type of algae. Diatoms probably were limitecI by nitrogen clepletion ancI thus were unable to use fully the rich phosphorus supplies of the lake, whereas Aphanizomenon is able to fix nitrogen ancI thus can fully exploit the high availability of phosphorus, which causes it to reach very high abundances. Various anthropogenic factors couicI have contributed to the rise of Aphanizomenon; one example is increased transparency of the lake caused by disconnection of its associated wetiancis, which were sources of ciark humic compounds. Reestablishment of these sources wouicI seem acI- visable but may be impractical because the organic deposits in the wetiancis oxiclizecI extensively after the wetiancis were cirainecI. There is no evidence of a causal connection between water level ancI water quality or fish mortality over the broacI operating range in the l990s, the period for which the most complete ciata are available for Upper I(lamath Lake. Neither mass mortality of fish nor extremes of poor water quality shows any cletectable relationship to water level. Thus, despite theoretical speculations, there is no basis in evidence for optimism that manipulation of water levels has the potential to moderate mass mortality of suckers in Upper I(lamath Lake. Planning must anticipate that poor water quality will con- tinue to affect the sucker populations of Upper I(lamath Lake.

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SUMMARY 7 Suckers in Upper Klamath Lake also are affected by entrainment from the Link River near the outflow of the lake. Screens installecI at the main irrigation-water withcirawal point probably will be beneficial, but loss of small fish still can be expected. The Link River Dam intakes still are not screened. Nonnative fishes, which are diverse ancI abundant in Upper Klamath Lake, may be suppressing the populations of enciangerecI suckers there, but no practical mechanisms for reducing their abundance are known. Other Locations in the Klamath Basin Below Upper Klamath Lake, waters of the upper basin collect through the Lost River system, which is regulatecI by the Klamath Project (Figure S- 11. The heac~waters inclucle tributaries to Clear Lake anti Gerber Reservoir. These tributaries support recurrently successful spawning of enciangerecI suckers, as shown by the apparently stable populations of suckers in the two reservoirs. UnprececlentecI cirawclown of both reservoirs in the drought year of 1992 coinciclecI with deteriorating body condition anti increased incidence of parasitism in the suckers. Thus, the conditions of 1992 have been used by USFWS in setting threshoicis of water level for these lakes. On the Lost River below Gerber Reservoir anti Clear Lake (Figure S-1), all waters are strongly affected by the Klamath Project anti are unsuitable for suckers, although they still offer some opportunities for restoration, especially through increases in water clepth for Tule Lake Sumps anti Lower Klamath Lake. Reservoirs of the main stem Klamath have created new habitat capa- ble of hoicling enciangerecI suckers, but recruitment of young fish has not been observed. Reservoirs have low potential to support self-sustaining populations. Coho Salmon The peak migration of aclult coho salmon in the Klamath basin occurs between late October anti micI-November; the fish spawn primarily in tribu- taries. Fry reach peak abundance in March anti April, ancI can disperse as far as the tributary mouths, but most appear to stay close to the areas where they originate. Coho clevelop through the juvenile stage in the tributaries over about 1 yr. They may occupy the main stem at times but are nearly absent from it by late summer, when the water is warmest. Winter habitat in the tributaries is critical for the juvenile coho but has not been well stucliecI. luveniles smoltify anti migrate downstream in spring, with a peak in April. Short transit times facilitatecI by high flow couicI be favorable to the

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8 FISHES IN THE KLAMATH RIVER BASIN migrating smolts, although this has not been clemonstratecI for the Klamath River. Smolts spencI approximately 1 ma in the estuary ancI then enter the ocean, where they spencI about 1.5 yr before returning to the Klamath River. Ocean conditions such as productivity affect the strength of year classes. The most important cause of impairment of coho salmon probably is excessively high summer temperatures in tributary waters. Coho salmon, unlike Chinook salmon, remain in freshwater for an entire year, cluring which they mainly occupy tributaries, where summer water temperatures can be ciangerously high. Causes of extreme temperatures inclucle diversion of coicI flows for use in agriculture, flow clepletion that leacis to warming of coo! water, ancI destruction of riparian vegetation that leacis to loss of shacling. Temperatures also are excessively high in the main stem, but at present high temperatures there probably are more relevant to other species that are more likely than coho to use the main stem for rearing. Decrease in main-stem temperatures by augmentation of main-stem flows is problem- atic because augmentation water must be clerivecI from the surface layer of Iron Gate Reservoir, which is very warm in summer. Projections of benefit to be expected from possible thermal manipulations may not have taken into account the exceptional importance of nocturnal thermal minimums in determining the energetic balance of coho exposed to high temperatures; nocturnal minimums can be as important as ciaily maximums in cletermin- ing the survival of juvenile coho salmon. Barriers to passage causecI by clams ancI diversion structures are impor- tant to coho salmon. The main-stem clams on the Klamath River block spawning movements, as clo Dwinnell Dam on the upper Shasta River ancI the Trinity River Diversion project on the Trinity River. Numerous small clams used by incliviclual irrigators or clitch companies also block movement of coho in tributaries. Dams also have contributed to habitat clegraciation. Coho habitat has been seriously clegraclecI in the tributaries. Lack of cover ancI impairment of substrate through deposition of sediments are common. Woocly clebris, which is critical as cover for young fish, has largely been lost as a result of human activity. Excessive clepletion of flow may separate fish from adequate habitat in the last half of summer. Competition between hatchery coho ancI the smaller wilcI coho cluring migration to the estuary may be severe. Probably even more important are competition ancI preciation from large numbers of Chinook salmon ancI steelheacI that are releasecI from hatcheries to the main stem when smol- tification of the coho is in progress. The Klamath River Fish Kill of 2002 During the second half of September 2002, numerous fish cliecI in the lowermost 40 mi of the Klamath River main stem, 150 mi below Iron Gate

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SUMMARY 9 Dam (Figure S-11. Most of the cleacI fish were aclult Chinook salmon that hacI just entered the lower I(lamath River. At least 33,000 Chinook, of a total estimated spawning run of about 130,000, cliecI. The immediate cause of cleath was massive infection by two types of pathogens that are wiclely clistributecI ancI generally become harmful to fish uncler stress, particularly if crowding occurs. The fish kill, although important for Chinook salmon, clicI not involve many coho salmon (about 1% of the total cleacI fish) be- cause coho enter the river later than Chinook, ancI thus were mostly absent when conditions leacling to mass mortality occurred. The California Department of Fish ancI Game (CDFG), through an analysis of environmental conditions over 5 yr of low flow within the last 15 yr, showed that neither the flows nor the temperatures that occurred in the second half of September 2002 were unprececlentecI. A stucly by the U.S. Geological Survey (USGS) supports this conclusion. Thus, no obvious ex- planation of the fish kill basecI on unique flow or temperature conditions is possible. CDFG has proposed that the shape of the channel in the lowermost reaches of the I(lamath main stem changed in 1997-1998 uncler the influ- ence of high flows, which causecI fish entering the river to be unable to proceed upstream uncler low-flow conditions. An alternate hypothesis is that an unusual combination of temperature, flow, ancI migration concli- tions occurred in 2002, possibly in association with weather that prevented the river from showing nocturnal cooling to an extent that wouicI usually be expected. The two hypotheses or others that may be proposed are clifficult to test because the conditions coinciding with the fish kill were unexpected ancI therefore largely unmonitored. If a lasting change in channel configura- tion was responsible, recurrence of the episode can be expected with similar low flows in the future. If other factors were responsible, recurrence may be much less likely. It is unclear what the effect of specific amounts of acicli- tional flow drawn from controllable upstream sources (waters from reser- voirs on the Trinity River or Iron Gate Reservoir) wouicI have been. Flows from the Trinity River couicI be most effective in lowering temperature. Legal, Regulatory, ant! Administrative Context of Recovery Actions Adaptive management is accepted in principle by the listing agencies but has not been implementecI in the I(lamath basin for the benefit of the listecI species, except as part of the Trinity River Restoration Project. Infor- mation collectecI through monitoring ancI research has been valuable, but the absence of an integrated, evolving management plan connected to moni- toring, research, review, anti periodic readjustment of management actions will hamper progress in the future. Although agencies must meet the re-

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10 FISHES IN THE KLAMATH RIVER BASIN quirements of the ESA, many actions that couicI benefit the listecI species can also be justified from the viewpoint of ecosystem management favor- able to numerous other species, some of which are perilously close to listing, ancI to ecosystem functions that have great practical value. Specifically with reference to ESA Section 4(f), USFWS ancI NMFS recovery planning for the three listecI species has stallecI ancI neecis to be revived. leoparcly consultations, which have focused on operation of the I(lamath Project, must be broaclenecI geographically because critical envi- ronmental resources of the listecI species are found not only in but also beyond the I(lamath Project. Furthermore, USFWS ancI NMFS appear to have overiookecI take (mortality ancI impairment) of the listecI species that is inciclental to agricultural practice, private water management, ancI other activities beyond the control of USBR, ancI thus have not taken full acivan- tage of their authorities uncler ESA Section 9. The listing agencies have been criticized for using pseudoscientific rea- soning (" junk science") in justifying their requirements for the protection of species in the upper I(lamath basin. The committee disagrees with this criticism. The ESA allows the agencies to use a wicle array of information sources in protecting listecI species. The agencies can be expected, when information is scarce, to extend their recommendations beyond rigorously tested hypotheses ancI into professional judgment as a means of minimizing risk to the species. In allowing professional judgment to override site-spe- cific evidence in some cases cluring 2001, however, the agencies accepted a high risk of error in proposing actions that the available evidence inclicatecI to be of cloubtful utility. The committee, as explainecI in its interim report, found some proposed actions as given in the 2001 biological opinions to lack substantial scientific support. In their biological opinions of 2002, the listing agencies appear to have resolvecI this issue either by obtaining con- cessions from USBR through mechanisms that are generally consistent with USBR's goal of clelivering irrigation water (for example, through establish- ment of a water bank) or by redesigning their requirements to bring them into greater conformity with the existing evidence. RECOMMENDATIONS Recovery of enciangerecI suckers ancI threatened coho salmon in the I(la- math basin cannot be achieved by actions that are exclusively or primarily focused on operation of USBR's I(lamath Project. While continuing consulta- tion between the listing agencies ancI USBR is important, distribution of the listecI species well beyond the boundaries of the I(lamath Project ancI the impairment of these species through lancI- ancI water-management practices that are not uncler control of USBR require that the agencies use their author- ity uncler the ESA much more broacIly than they have in the past.

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SUMMARY 11 Recommendation 1. The scope of ESA actions by NMFS anti USFWS shouicI be expanclecI in several ways, as follows (Chapters 6, 8, 91. NMFS anti USFWS shouicI inventory all governmental, tribal, anti private actions that are causing unauthorized take of enciangerecI suckers anti threatened coho salmon in the I(lamath basin anti seek either to autho- rize this take with appropriate mitigative measures or to eliminate it. NMFS anti USFWS shouicI consult not only with USER, but also with other fecleral agencies (e.g., U.S. Forest Service) uncler Section 7(a)~11; the fecleral agencies collectively shouicI show a will to fulfill the interagency agreements that were macle in 1994. NMFS anti USFWS shouicI use their full authority to control the actions of fecleral agencies that impair habitat on feclerally managed lancis, not only within but also beyond the I(lamath Project. Within 2 yr, NMFS shouicI prepare ancI promulgate a recovery plan for coho salmon, anti USFWS shouicI clo the same for shortnose anti Lost River suckers. The new recovery plans shouicI facilitate consultations uncler ESA Sections 7(a)~1), 7(a)~2), anti lO(a)(l) across the entire geographic ranges of the listecI species. NMFS anti USFWS shouicI more aggressively pursue opportunities for non-regulatory stimulation of recovery actions through the creation of demonstration projects, technical guidance, anti extension activities that are intenclecI to encourage anti maximize the effectiveness of non-govern- mental recovery efforts. Recommendation 2. Planning anti organization of research anti moni- toring for listecI species shouicI be implementecI as follows (Chapters 6, 8, 101. Research anti monitoring programs for enciangerecI suckers shouicI be guiclecI by a master plan for collection of information in clirect support of the recovery plan; the same shouicI be true of coho salmon. A recovery team for suckers anti a second recovery team for coho salmon shouicI administer research anti monitoring on the listecI species. The recovery team shouicI use an aciaptive management framework that serves as a clirect link between research anti remecliation by testing the effectiveness anti feasibility of specific remecliation strategies. Research anti monitoring shouicI be reviewed comprehensively by an external pane! of experts every 3 yr. Scientists participating in research shouicI be requirecI to publish key findings in peer-reviewecI journals or in synthesis volumes subjected to external review; administrators shouicI allow researchers sufficient time to clo this important aspect of their work. Separately or jointly for the upper anti lower basins, a broacIly basecI, diverse committee of cooperators shouicI be establishecI for the purpose of pursuing ecosystem-basecI environmental improvements throughout the

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2 FISHES IN THE KLAMATH RIVER BASIN basin for the benefit of all fish species as a means of preventing future listings while also preserving economically beneficial uses of water that are compatible with high environmental quality. Where possible, existing fecI- eral ancI state legislation shouicI be used as a framework for organization of this effort. Recommendation 3. Research ancI monitoring on the enciangerecI suckers shouicI be continued. Topics for research shouicI be acljustecI annually to reflect recent findings ancI to aciciress questions for which lack of knowlecige is a handicap to the clevelopment or implementation of the recovery plan. Gaps in knowlecige that require research in the near future are as follows (Chapters 5, 61. Efforts shouicI be expanclecI to estimate annually the abundance or relative abundance of all life stages of the two enciangerecI sucker species in Upper I(lamath Lake. At intervals of 3 yr, biotic as well as physical ancI chemical surveys shouicI be concluctecI throughout the geographic range of the enciangerecI suckers. Suckers shouicI be samplecI for indications of age distribution, qualitative measures of abundance, ancI condition factors. Sampling shouicI inclucle fish other than suckers on grouncis that the presence of other fish is an indicator of the spreacI of nonnative species, of changing environmental conditions, or of changes in abundance of other endemic species that may be approaching the status at which listing is neeclecI. Habitat conditions ancI water-quality information potentially relevant to the welfare of the suckers shouicI be recorclecI in a manner that allows comparison across years. The resulting survey information, along with the more cletailecI information available from annual monitoring of populations in Upper I(lamath Lake, shouicI be synthesized as an overview of status. DetailecI comparisons of the Upper I(lamath Lake populations (which are suppressed ancI the Clear Lake ancI Gerber Reservoir popula- tions (which are apparently stable), in combination with studies of the environmental factors that may affect welfare of the fish, shouicI be con- cluctecI as a means of diagnosing specific life-history bottlenecks that are affecting the Upper I(lamath Lake populations. Multifactorial studies uncler conditions as realistic as pract~can~e shouicI be macle of tolerance ancI stress for the listecI suckers relevant to poor water-quality conditions in Upper I(lamath Lake ancI elsewhere. Factors affecting spawning success ancI larval survival in the Williamson River system shouicI be stucliecI more intensively in support of recovery efforts that are focused on improvements in physical habitat pro- tection for spawners ancI larvae in rivers. An analysis shouicI be concluctecI of the hyciraulic transport of larvae in Upper I(lamath Lake. 1 1

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SUMMARY 13 Relevant to the water quality of Upper I(lamath Lake, more inten- sive studies should be macle of water-column stability ancI mixing, espe- cially in relation to physiological status of Aphanizomenon ancI the occur- rence of mass mortality; of mechanisms for internal loading of phosphorus; of winter oxygen concentrations; ancI of the effects of limnohumic acicis on Aphanizomenon. A demographic model of the populations in Upper I(lamath Lake should be prepared ancI used in integrating information on factors that affect incliviclual life-history stages. Studies should be clone on the clegree ancI importance of predation on young fish by nonnative species. Aciclitional studies should be clone on the genetic identities of sub- populations. Recommendation 4. Recovery actions of highest priority basecI on current knowledge of enciangerecI suckers are as follows (Chapter 61. Removal of Chiloquin Dam to increase the extent of spawning habi- tat in the upper Sprague River ancI expand the duration over which larvae enter Upper I(lamath Lake. Removal or facilitation of passage at all small blockages, clams, diversions, ancI tributaries where suckers are or could be present. Screening of water intakes at Link River Dam. Modification of screening ancI intake procedures at the A Canal as recommenclecI by USFWS (20021. Protection of known spawning areas within Upper I(lamath Lake from disturbance (inclucling hydrologic manipulation, in the case of springs), . . . . except: -or restoration activities. For river spawning suckers of Upper I(lamath Lake, protection ancI restoration of riparian conditions, channel geomorphology, ancI sediment transport; elimination of disturbance at locations where suckers clo spawn or could spawn. These actions will require changes in grazing ancI agricultural practices, lancI management, riparian corridors, ancI public education. Seecling of abanclonecI spawning areas in Upper I(lamath Lake with new spawners ancI physical improvement of selected spawning areas. Restoration of wetland vegetation in the Williamson River estuary ancI northern portions of Upper I(lamath Lake. Use of oxygenation on a trial basis to provide refugia for large suckers in Upper I(lamath Lake. Rigorous protection of tributary spawning areas on Clear Lake ancI Gerber Reservoir, where populations are apparently stable. Reintroduction of enciangerecI suckers to Lake of the Woocis after elimination of its nonnative fish populations.

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4 FISHES IN THE KLAMATH RIVER BASIN Reestablishment of spawning anti recruitment capability for encian- gerecI suckers in Tule Lake anti Lower I(lamath Lake, even if the attempts require alterations in water management, proviclecI that preliminary studies indicate feasibility; increased control of sedimentation in Tule Lake. Review of all proposed changes in I(lamath Project operations for potential adverse effects on suckers; maintenance of water level limits for the near future as proposed by USER in 2002 but with modifications as required by USFWS in its most recent biological opinion (20021. Recommendation 5. Needs for new information on coho salmon are as follows (Chapters 7, 81. Annual monitoring of aclults ancI juveniles shouicI be concluctecI at the mouths of major tributaries anti the main stem as a means of establish- ing a record of year-class strength for coho. Every 3 yr, synoptic studies of the presence anti status of coho shouicI be macle of coho in the I(lamath basin. Physical ancI chemical conditions shouicI be clocumentecI in a manner that allows interannual comparisons. Not only coho but other fish species present in coho habitats shouicI be samplecI simultaneously on grouncis that changes in the relative abundance of species are relevant to the welfare of coho ancI may serve as an early warning of cleclines in the abundance of other species. Results of synoptic studies, along with the annual monitoring at tributary mouths, shouicI be synthesized as an overview of population status at 3-yr intervals. DetailecI comparisons shouicI be macle of the success of coho in specific small tributaries that are chosen so as to represent gradients in potential stressors. The objective of the stucly shouicI be to identify thresh- oicis for specific stressors or combinations of stressors anti thus to establish more specifically the tolerance threshoicis for coho salmon in the I(lamath basin. The effect on wilcI coho of fish releasecI in quantity from hatcheries shouicI be cleterminecI by manipulation of hatchery operations according to aciaptive-management principles. As an initial step, release of hatchery fish from Iron Gate Hatchery (all species) shouicI be eliminatecI for 3 yr, ancI indicators of coho response shouicI be clevisecI. Complementary manipula- tions at the Trinity River Hatchery wouicI be clesirable as well. SelectecI small tributaries that have been impaired shouicI be experi- mentally restored, ancI the success of various restoration strategies shouicI be cleterminecI. Success of specific livestock-management practices in improving channel conditions anti promoting clevelopment of riparian vegetation shouicI be evaluatecI systematically. Relationships between flow ancI temperature at the junctions of tributaries with the main stem ancI the estuary shouicI be quantified; pos-

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SUMMARY 15 sible benefits of coordinating flow management in the Trinity anti I(lamath main stem shouicI be stucliecI. Recommendation 6. Remecliation measures that can be justified from cur- rent knowlecige inclucle the following (Chapter 81. Reestablishment of coo! summer flows in the Shasta anti Scott rivers in particular but also in small tributaries that reach the I(lamath main stem or the Trinity main stem where water has been anthropogenically warmed. Reestablishment of coo! flows shouicI be pursued through purchase, tracI- ing, or leasing of grounc~water flows (inclucling springs) for clirect clelivery to streams; by extensive restoration of woocly riparian vegetation capable of providing shacle; anti by increase of summer low flows. Removal or provision for effective passage at all small clams anti diversions throughout the distribution of the coho salmon, to be completecI within 3 yr. In aciclition, serious evaluation shouicI be macle of the benefits to coho salmon from elimination of Dwinnell Dam anti Iron Gate Dam on grouncis that these structures block substantial amounts of coho habitat anti, in the case of Dwinnell Dam, clegracle downstream habitat as well. Prescription of lancI-use practices for timber management, roacI con- struction, anti grazing that are sufficiently stringent to prevent physical clegraciation of tributary habitat for coho, especially in the Scott, Salmon, anti Trinity river basins as well as small tributaries affected by erosion. Facilitation through cooperative efforts or, if necessary, use of ESA authority to recluce impairment of spawning gravels anti other critical habi- tat features by livestock, fine sediments clerivecI from agricultural practice, timber management, or other human activities. Changes in hatchery operations to the extent necessary, inclucling possible closure of hatcheries, for the benefit of coho salmon as cleterminecI through research by way of aciaptive management of the hatcheries. COSTS The costs of remecliation actions are clifficult to estimate without more cletail on their mocle of implementation by the agencies. Based on general knowlecige of costs of research anti monitoring at other locations, an ap- proximate figure for the recommendations on enciangerecI suckers over a 5- yr period is $15-20 million, inclucling research, monitoring, anti remeclial actions of minor scope. ExcluclecI are administrative costs anti the costs of remeclial actions of major scope (e.g., removal of Chiloquin Dam), which wouicI neecI to be evaluatecI incliviclually for cost. For coho salmon, re- search, monitoring, anti remeclial projects of small scope over 5 yr is esti- matecI at $10-15 million. Thus, the total for all three species over 5 yr is $25-35 million, exclucling major projects such as removal of clams. These

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1 6 FISHES IN THE KLAMATH RIVER BASIN costs are high relative to past expenditures on research anti remecliation in the basin, but the costs of further deterioration of sucker ancI coho popula- tions, along with crisis management ancI disruptions of human activities, may be far more costly. A hopeful vision is that increased knowlecige, improved management, anti cohesive community action will promote re- covery of the fishes. This outcome, which wouicI be of great benefit to the I(lamath basin, couicI provide a mocle! for the nation.