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Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery (2004)

Chapter:6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers

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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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Suggested Citation:"6. Causes of Decline and Strategies for Recovery of Klamath Basin Suckers." National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: The National Academies Press. doi: 10.17226/10838.
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6 Causes of Decline and Strategies for Recovery of I(lamath Basin Suckers When the Lost River anti shortnose suckers were listecI uncler the En- ciangerecI Species Act (ESA), the U.S. Fish anti WilcIlife Service (USFWS) anti others iclentifiecI numerous factors that couicI explain their clecline anti their failure to recover after elimination of the sucker fishery (Chapter 5, Scoppettone anti VinyarcI 19911. Since the listing, many of these factors have been stucliecI. As a result, unclerstancling of the biology of Klamath suckers anti of requirements for their recovery has improved. Information on suckers is founcI in over 500 articles, reports, memoranda, anti critiques, although most are unpublishecI anti so have not benefited from scientific peer review. The number of persons working on the suckers has grown from a few ichthyologists to several clozen scientists, resource managers, policy clevelopers, consultants, anti informed citizens. New information clerivecI from the increased pace of documentation anti research supports increasingly firm judgments on the current status of the species, probable causes of their clecline, priorities for further study, anti actions that shouicI anti can be taken to move the species toward the ultimate goal of recovery, as clescribecI in this chapter. CRITERIA FOR JUDGING STATUS AND RECOVERY OF SUCKER POPULATIONS Criteria for the assessment of status anti recovery provide a useful point of departure for the causal analysis of clecline of the enciangerecI suckers anti for evaluating proposals for their restoration. Criteria presented here 214

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 215 are intenclecI as a too! of convenience for present purposes; other criteria might be useful for other purposes. Because each life-history stage of a population is linkecI to all other stages, unusual suppression of any life-history stage may be reflectecI ulti- mately in the suppression of the population as a whole. Thus, trencis in the abundance of any stage can be chosen arbitrarily as an inclex of the status of a population. For the enciangerecI suckers, the most convenient life stage to use as an inclex of status is the aclult. As explainecI in Chapter 5, other stages are clifficult to observe or sample, especially in large lakes, although attempts to clo so are essential to the diagnosis of mechanisms that affect specific life-history stages. If aclults are used as an inclex of the status of the populations, three criteria, taken together, wouicI indicate recovery: diversity in the age clistri- bution of aclults, annual entry of at least some inclivicluals into the aclult stage in most years from the younger life stages couplecI with entry of large numbers of such recruits in some especially favorable years, ancI a popula- tion size that reflects carrying capacity for an environment that is generally well suited, although not necessarily optimal, for the suckers. The presence of multiple age classes of aclults wouicI indicate past recruitment to the aclult stage ancI persistence of conditions suitable for the maintenance of aclults. The combination of new recruitment in most years ancI very high recruitment in some years wouicI indicate the general welfare of younger stages ancI successful spawning. The maintenance of populations at a clen- sity that approaches expected carrying capacity wouicI indicate that growth ancI reproduction occur at sufficient rates to offset mortality through the life cycle as a whole. As inclicatecI in Chapter 5, the status of geographically clefinecI sub- populations of the two enciangerecI suckers varies cirastically. Table 6-1 summarizes the status of various geographic subpopulations on the basis of the aclults. As shown in Table 6-1, Clear Lake ancI Gerber Reservoir sup- port apparently stable subpopulations ancI therefore provide a basis for comparison with other subpopulations. The Upper I(lamath Lake subpopu- lations, in contrast, clo not meet the criteria for recovery, nor clo they indicate recovery in progress. These subpopulations took an important positive turn after elimination of fishing in 1987, through the entry of new fish into the subaclult ancI aclult populations each year ancI through the production of one very strong year class (1991) ancI several moclerately strong year classes cluring the clecacle of the l990s (Chapter 51. Indications of no recovery without further environmental change, however, inclucle the failure of aclults to show an upward turn in overall abundances ancI the lack of a cliversifiecI age structure among oicler age classes, presumably because of repeated mass mortality of large fish.

Endangered and Threatened Fishes in the Klamath River Basin Table 7-2. Nonnative Fishes of the Lower Klamath and Trinity Rivers Name American shad, Alosa sapidissima Life History Status A Comments Goldfish, Carassius auratus Fathead minnow, Pimephales prom elas Golden shiner, Notemigonus chrysoleucas Brown bullhead, Ameiurus nebulosus Wakasagi, Hypomesus nipponensis Kokanee, Oncorhynchus nerka Brown trout, Salmo trutta Brook trout, Salvelinus fontinalis Brook stick l aback, Culea incons tans Green sunfish, Lepomis cyanellus Bluegill, L. macrochirus Pumpkinseed, L. gibbosus Largemouth bass, Micropterus salmoides Spotted bass, M. punctulatus Smallmouth bass, M. dolomieui Yellow perch, Percaflavescens N N N N N N N. A N N N N N N N N N Uncommon Uncommon Uncommon Uncommon Locally abundant Locally abundant Locally abundant Common in some streams Common Locally abundant, spreading Common Common Uncommon Common Locally common Locally common Locally common Small annual run in lowermost reach r ~ Or river Ponds and reservoirs Invading from upper basin where extremely abundant Important bait fish in California Ponds and reservoirs, especially Shasta River; some in mainstem In Shastina Reservoir but a few downstream records Reservoirs Sea-run adults rare Only in headwater streams and lakes Recent introduction into Scott River Warm streams, ditches, and ponds Ponds and reservoirs Abundant in upper basin Ponds and reservoirs Only in Trinity River reservoirs Only in Trinity River reservoirs Abundant in upper basin, including Iron Gate Reservoir Abbreviations: A, anadromous; N. non-migratory. COHO SALMON The coho salmon (Figure 7- ~ ~ once was an abundant and widely distributed species in the Klamath River and its tributaries, although its historical numbers are poorly known because of the dominance of Chinook salmon. Snyder (1931) reported that coho were abundant in the Klamath River but also indicated that reports of the salmon catch probably lumped coho and Chinook. Historically, coho saImon occurred throughout the Klamath River and its tributaries, at least to a point as high up in the system as the California-Oregon border. It is possible that they once migrated well into the upper Klamath basin (above Klamath FalIs), as did Chinook and steelhead, but there are no records of this, perhaps because most people are unable to distinguish them (Snyder 1 93 1 1. Today coho salmon occupy remnants of their original range wherever suitable habitat exists and wherever access is not prevented by dams and diversions (Brown et al. ~ 994, Moyle 2002~. Because the coho salmon is clearly in a long-term severe decline throughout its range in California, all populations in the state have been listed as threatened under both state and federal endangered species acts (CDFG 20021. 216

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 217 Fishes of Tule Lake (ancI of the associated Lost River) show no signs whatsoever of recovery according to the criteria shown in Table 6-1. Lack of recruitment of young fish into the subaclult ancI aclult stages indicates lack of reproduction or negligible survival of young fish. Two aciclitional locations, Lower I(lamath Lake ancI Lake of the Woods, are listecI even though they lack enciangerecI suckers. These are locations where sucker populations conceivably couicI be establishecI in the future. The main-stem reservoirs also are listecI but belong to a somewhat different category be- cause, as explainecI in Chapter 5 ancI further in this chapter, the potential for creation of suitable conditions for the entire life cycle is probably lower for these waters than for Upper I(lamath Lake or the other waters where the suckers originally thrived. REQUIREMENTS FOR PROTECTION AND RECOVERY The ESA requires both protection ancI recovery of listecI species (Chap- ter 91. Protection is accomplishecI by prohibitions of take ancI preserva- tion of habitat. Protection alone is insufficient, however, in that the popu- lations as a whole have shown a drastic clecline over the last several clecacles, ancI there is no evidence that the populations are recovering. At the subpopulation level, as inclicatecI in Chapter 5, the balance between protection ancI remecliation clepencis on location. Because the subpopula- tions of Clear Lake ancI Gerber Reservoir are the only ones in the upper I(lamath basin that meet the criteria for recovery as outlinecI above, their protection is of utmost importance for the long-term survival of the two enciangerecI sucker species in the upper I(lamath basin as a whole. These subpopulations appear to clepencI entirely on tributary spawning. There- fore, maintenance of tributary conditions suitable for spawning is an essential element of their protection. It is important that neither of the reservoirs be drawn clown to extremes that wouicI produce summer or winter mortality. Given the historical experience of the l990s, the re- quirements of the 2002 biological opinion appear to be aclequately pro- tective in this respect, but it is critical for these subpopulations that no errors in judgment leacI to extremes in cirawclown beyond that observed in the l990s. The subpopulations of Upper I(lamath Lake also have high priority but have different status. As explainecI in Chapter 5, they showed some encour- aging responses to the curtailment of the snag fishery, but the numerical abundance of aclults ancI the continuing attrition of oicI fish appears to be hoicling the population clown ancI may even be driving it closer to extirpa- tion. The pathway to recovery for this population is not clear. A great clear of the analysis of cause ancI effect in the remaining part of this chapter is clevotecI to the Upper I(lamath Lake subpopulations because of their his-

218 FISHES IN THE KLAMATH RIVER BASIN torical numerical importance anti the lack of clarity about the means of achieving their recovery. The Tule Lake subpopulations consist of a very small number of appar- ently healthy aclults, but they fail to meet all three of the criteria outlinecI above for recovery: there is no evidence of recruitment into the aclult stage, there is no diversification of age structure for aclults, anti abundances per unit area are low. Because the suckers are long-livecI, the aclults of the Tule Lake population are of high value, anti also couicI be supplementecI with salvagecI inclivicluals from other locations. The first step toward recovery of the Tule Lake subpopulations wouicI be to establish spawning capability, which wouicI require intensive work with tributary waters. Acquisition of water rights anti steps toward the creation of (potentially artificial) physical habitat suitable for spawning anti for larvae wouicI be necessary initial steps toward recovery of these subpopulations. The Tule Lake subpopulations, although small, neecI not be written off as unrecoverable. Listed fifth in Table 6-1 is Lake of the Woods. As explainecI in Chapter 5, this was the location of a population probably consisting of shortnose suckers, but the population was eliminatecI. The present fish populations of Lake of the Woocis shouicI be eliminate cI, anti aclult shortno se suckers anti other native fishes shouicI then be reintroclucecI. If the suckers meet the recovery criteria outlinecI above after a number of years, fish biologists couicI consider the reintroduction of game fish (fish other than suckers probably will have colonizecI the lake by that time in any event). Lower I(lamath Lake lacks suckers anti is probably unsuitable for them (Chapters 3 anti 5), but alteration of these conditions couicI be feasible. Steps shouicI be taken toward acquisition of water rights suitable for main- tenance of higher water levels in Lower I(lamath Lake if feasibility studies support this approach. Aclult suckers from salvage (as clescribecI later in this chapter) shouicI then be transferred to Lower I(lamath Lake. Water quality anti habitat conditions may be unsuitable, but suitability can be cleterminecI most effectively by monitoring of trial reintroductions. To the extent that maintenance of higher water levels wouicI interfere with agricultural use of lancI, its establishment wouicI require negotiations anti compensation for . . . . . . acquisition ot private rig nts. The last subpopulations mentioned in Table 6-1 are the ones in main- stem reservoirs. These reservoirs have value primarily for long-term storage of large suckers. They clo not have high priority for recovery, because they are not part of the original habitat complex of the suckers anti probably are inherently unsuitable for completion of life cycles by the suckers. Mainte- nance of aclults in these locations cloes, however, provide some insurance against loss of other subpopulations. Construction of fish laciclers for suckers at the clams might facilitate return of fish from main-stem reservoirs to Upper I(lamath Lake. A fish

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 219 lacicler at Link River Dam, which is scheclulecI for completion in lanuary 2006, shouicI receive high priority; movements of fish through the lacicler shouicI be monitored. SUPPRESSION OF ENDANGERED SUCKERS IN UPPER KLAMATH LAKE: CAUSAL ANALYSIS AND REMEDIES For several reasons, causal analysis of the suppression of enciangerecI suckers deserves more attention for the Upper Klamath Lake subpopula- tions than for other subpopulations. First, despite severe suppression of enciangerecI suckers in Upper Klamath Lake, these subpopulations still con- tain many fish. Second, the subpopulations in Upper Klamath Lake were large as recently as 50 yr ago, so it seems reasonable, lacking evidence to the contrary, that they couicI be restored by a reversal of one or more critical human-inclucecI impairments that have occurred over the last 50 yr. Third, water management involving Upper Klamath Lake is the responsibility of the fecleral government through the U.S. Bureau of Reclamation (USBR), which has access to substantial resources anti also has legal responsibility for reversing or moderating any adverse effects of its management of Upper Klamath Lake if causal linkages between management anti harm to the suckers can be establishecI. Fourth, even though the subpopulations of enciangerecI suckers are suppressed in Upper Klamath Lake, all life stages are present anti some recruitment appears to be occurring from one life stage to another every year; recovery seems feasible if some key factors can be iclentifiecI anti changed. Actual or potential cause-ancI-effect relationships that explain the sta- tus of a population are hierarchical. For present purposes, immediate causes can be explainecI in terms of suppression of one or more stages of the life cycle. For example, suppression of the entire population couicI be explainecI entirely or in part by exceptionally high mortality of larvae. Suppression of more than one component of a population couicI prevent it from recover- ing. There can be more than one immediate cause of suppression of a population. Proximate causes are environmental factors. An example is poor water quality that leacis to mass mortality of aclult fish. A single proximate cause may be linkecI to more than one immediate cause. For example, poor water quality may suppress not only aclults but also other life-history stages. Ultimate causes, in the present context, are clirect or indirect results of human actions. For example, operation of unscreened canals is an ultimate cause of mortality of fish in various life stages. Human actions that have lecI to changes in the water quality of Upper Klamath Lake are ultimate causes of mass mortality of large fish.

220 FISHES IN THE KLAMATH RIVER BASIN Recovery of the populations of enciangerecI suckers can be approached most efficiently through analysis of the three levels of causation that ex- plain failure of the fish to recover. Because the possible combinations of cause ancI effect are numerous, remeclial actions, which are expensive, must focus on chains of cause ancI effect that are most likely to produce recovery. Winnowing the importance of cause-ancI-effect relationships requires infor- mation, some of which must be quantitative to be useful. The task of the researcher or the monitoring team is to produce information, typically over a period of years, that can be used to support estimates of the suppression of the population by chains of causation involving specific life-history stages (immecliate causes), specific environmental factors (proximate causes), ancI specific human actions (ultimate causes). I(nowlecige of causation can pro- cluce estimates of the beneficial effect of remecliating the effects of human actions. Intensive research on the enciangerecI suckers has been uncler way for a relatively short time, especially in view of the complicating effects of natu- ral variation caused by climate ancI other factors that are not uncler human control. Only a few causal relationships are known well enough to support remeclial action with confidence, but some of these are among the most important because they explain notable mortality of one or more stages of the population. Eventually, some of the more subtle but still important types of impairment ancI their causes must be clarifiecI, as inclicatecI in the following overview ancI analysis of cause ancI effect. The analysis of causal connectivity is summarized in Figure 6-1. The figure shows the life stages of the enciangerecI suckers as presented in Chap- ter 5 ancI identifies potential proximate causes of suppression of each life stage. Because the life stages are interconnected clevelopmentally, the un- clerlying premises of the diagram are that suppression of any life stage contributes at least potentially to suppression of the overall population ancI that a potential remedy for the suppression of the population lies in the identification ancI reversal of the suppression of incliviclual life stages. It is not a foregone conclusion, however, that reversal of a particular type of suppression on a specific life stage will move a population notably toward recovery. Figure 6-1 shows connections between immediate, proximate, ancI ulti- mate causes as solicI or ciashecI lines. SolicI lines indicate causal connections that are well establishecI scientifically; typically these connections involve phenomena that are easily observed or clocumentecI (such as mass mortality of aclults or cleath clue to entrainment). Dashed lines indicate causal connec- tions that are uncler stucly ancI for which there is insufficient evidence to show them as unimportant, moclerately important, or important. The figure shows convergence of multiple lines on incliviclual immecli- ate causes in some cases. Thus, the diagram indicates the likelihoocI that

221 . o U) ~ ~ o =s o ~ o U) ~ .- ~ .$ U) x no so o be to / ~ I ~ I l l l o ~ . - o o be be an, ~ o o ~ 1 -' 1 U) o he :~= C) C) o U) U) o he o ·~ ~ U) ~ by ~ I / —_ -__ o o U) o U) bC 0 9 _ .— O · - (~) · ~ U) O o o /' l 11/ I ~ I I · - 1 9 C) U) U) ~ . - -.> ~ u) ~ u) c) o x o o c) o u) o ~ - \ o o * 6*> ~ ~o o u) ·k ~ o ~ ) · - . - ~ bC ~ o Q, ~ o o ~ u) ¢ l / — ~ ~ o G bO X O . 0-= _ ~ ~ — _ C) o U) o . - U) . - U) ~ ', o o 6*> ~ ~0 \ ~ ,= o o * 6*> ~0 X 9 ,= o o 6*> ~0 ¢ C~ C~ ('d c~ ~ c~ o bO 50 Q Q ~ O ~ _ ·_4 C~ 50 C~ C~ r~ ·_4 - 50 o bO C~ ~ bO ~ ·~ o C~ o C~ Q~ O Q o o o o ~, C~ C~ 50 Q Q 11 C~ ~ - C~ C~ ·_4 C~ o .~, o . ~ - _ (~d · _4 C~ . C~ ~ ~ ~ ~ · 04 _ ~ ~ C~ C~ O 50 0 O O C~ · - bO .= ~ ·~ O C~ O · - _ O 50

222 FISHES IN THE KLAMATH RIVER BASIN some immediate causes of clecline are explainecI by multiple factors ancI that the factors might interact in their effects on a specific life-history stage. In aciclition, the diagram indicates that some environmental factors (proxi- mate causes) have multiple connections with immediate causes; that is, they can affect more than one life stage. This is also expected from the literature on fish populations. The last column in the diagram lists remeclial mea- sures; the clegree of certainty in their effectiveness is cliscussecI below. Even though the life-history stages are interclepenclent ancI so must be consiclerecI together in the final prescriptions for recovery, it is useful to consider them incliviclually first because each stage is affected by a distinctive suite of environmental factors. The discussion therefore follows the life-history sequence. Production ant! Viability of Eggs The production of eggs is usually cliscussecI in terms of spawning fish, which are much more easily observed than eggs. The eggs themselves are the concern, however, ancI successful spawning is only one element of their final value to the population. Low viability of eggs, for example, couicI undermine the effectiveness of successful spawning. No researchers have attempted to make a case that the viability of eggs differs in Upper I(lamath Lake or its tributaries from what wouicI be expected in an unimpaired environment. Thus, the present discussion focuses on spawning, but it shouicI be noted that lack of discussion of the fate of eggs after spawning is clue partly to lack of information. Dams Small clams are found in the tributaries of Upper I(lamath Lake. Where it can be shown that the clams clo not allow passage of fish attempting to spawn, they shouicI be removed or, if a clam must be retained, it shouicI be fitted with a functional bypass. The only moclerately large clam on a tributary to Upper I(lamath Lake is Chiloquin Dam, which blocks the Sprague River near its confluence with the Williamson River (Figure 1-31. Construction of Chiloquin Dam in the early 1900s (1918-1924 the exact ciate is unclear) may have eliminatecI more than 95°/O of the historical spawning habitat in the Sprague River (53 FecI. Reg. 61744 F19881, p. 51. This possibility is basecI on total river miles above the clam ancI cloes not take into account unusable portions of the river or the ascent of the clam by at least a few spawning fish via the fish lacicler each year. There are more fish below than above the clam, however, ancI few fish enter the fish lacicler (e.g., Janney et al. 2002), although the actual number is unknown. Improved access to the upper Sprague River

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 223 wouicI increase the extent of spawning habitat ancI expand the range of times ancI the conditions uncler which larvae enter Upper I(lamath Lake. Proposals for improving access of suckers to spawning grouncis on the upper Sprague River involve two possibilities: removal of the clam ancI improved fish passage at the clam. Scoppettone ancI VinyarcI (1991) recom- menclecI removal of the clam, as have others since then (e.g., I(lamath Water Users Association 20011. Stern (1990) estimated the cost of removing the clam at about $500,000 ancI of fish passage improvements at $560,000. CH2M HILL (1996) presented cletailecI plans for improvement of passage ancI estimated the cost at $1.445 million but gave no estimate for removal of the clam. The plan of CH2M HILL inclucles construction of a new vertical-slot lacicler on the left bank (looking upstream) that wouicI replace the present lacicler, which is ineffective. The new lacicler wouicI be basecI on fish passage structures through which cui-ui (Chasmistes cujus) move up the Truckee River ancI into Pyramid Lake. CH2M HILL (1996, p. 2) clismissecI removal of Chiloquin Dam be- cause of "too many environmental concerns . . . as well as a lack of local support." The environmental concerns were not enumerated; presumably they are relatecI to release of sediment ancI the clifficulty of predicting how fish wouicI responcI to the new hyciraulic conditions (e.g., Stern 19901. Issues relatecI to sediments arise with virtually any clam-removal project, but often they can be resolvecI (Heinz Center 20021. The response of the fish is unknown, but removal of the clam is likely to result in a natural migratory response, at least by young spawners that have not aireacly clevel- opecI the habit of spawning downstream of the clam. Lack of local support for removal of Chiloquin Dam is explainecI in part by water clelivery via the clam to the Mocloc Point Irrigation District (MPID). MPID involves about 60 farms ancI irrigates 3,000-5,300 acres annually, or less than 3°/O of the irrigable acreage in the basin. The MPID apparently has "acloptecI a Resolution indicating its willingness to partici- pate in a project to restore fish passage" (I(lamath Water Users Association, unciatecI memo, about 2001) ancI is willing to consider moving its point of diversion away from Chiloquin Dam (E. Bartell, The Resource Conser- vancy, Inc., Fort I(lamath, Oregon, unpublishecI report, 20021. Coopera- tion with MPID is important to the removal of Chiloquin Dam. Removal of Chiloquin Dam has high priority ancI shouicI be pursued aggressively. In the interim, spawning fish couicI be captured at the base of the fish lacicler anti releasecI immecliately above it; some of the releasecI fish shouicI be fitted with transmitters. Such a program wouicI immecliately give more fish access to the Sprague River ancI wouicI show what upstream areas are favored by the fish. Continued monitoring below the clam also wouicI provide information on numbers of aclults returning downstream anti num- bers of larval fish reaching the lake. A summer sampling program couicI

224 FISHES IN THE KLAMATH RIVER BASIN determine whether juveniles are in the river anti wouicI demonstrate the status of other native fishes in the river. Water Level in Upper Klamath Lake Spawning occurs at shoreline sites around Upper I(lamath Lake from late February to May; maximum spawning activity occurs in March anti April. More than 60% of spawning occurs in water more than 2 ft creep at locations with inflowing stream water (e.g., Reiser et al. 2001; see also Chapter 51. Inundation to a depth of at least 2 ft may be necessary for successful use of spawning substrate. At Sucker anti Ouxy springs, two of the most frequently used sites (Hayes et al. 2002~' lake elevations below 4~142.5 ft place 55°/0 anti 67%' respectively, of the spawning area in water shallower than 2 ft. Reiser et al. (2001' p. 7-2~' in a separate analysis, concluclecI that lake elevations below 4~142.0 ft "severely diminish avail- able spawning habitat"; they recommencI that Upper I(lamath Lake be kept at full pool elevation (4~143.3 ft) from micI-March to as late as micI-May to provide adequate water depth for spawning. Uncler recent operating re- gimes, water levels have remained above 4~143 ft for extenclecI intervals in wet years but have fallen well below 4~143 ft in ciry years (Figure 6-2~. Figure 6-2 shows the effect of water-level regulation in Upper I(lamath Lake on spawning area according to the criteria proposed by Reiser et al. (2001~. Uncler natural conditions, spring water levels wouicI have been at or near full pool (4~143.3 ft). Uncler conditions prevailing in 1990-2001' full pool elevation was achieved cluring the spawning interval in 6 of 10 yr; in 4,143.5 4,143.0 Upper Klamath Lake Water Level, March - May au au ` 4,142.5 au 1 5- au 4,142.0 4,141.0 4,140.5 , , , , , , , , , , , MAM MAM MAM MAM MAM MAM MAM MAM MAM MAM MAM MAM 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 Undiminished Somewhat Diminished Diminished Severely Diminished au 5- . - I con FIGURE 6-2 Water levels for 5-day intervals in Upper I(lamath Lake over months of most vigorous spawning by suckers (March, April, and May MAM), shown in context with spawning habitat designations given by Reiser et al. (2001~.

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 225 the other 4 yr the water level was slightly lower to much lower, with cor- responcling consequences for the inundation of spawning sites. It seems clear that cirawclown of Upper I(lamath Lake decreases the area of lakesicle spawning habitat for the enciangerecI suckers. Thus, a reasonable hypothesis is that lake levels below 4,143 ft. anti especially those below 4,142 ft. suppress the production of larvae by reducing production of viable eggs, thus potentially affecting the population. In the absence of scientific informa- tion on the recruitment of larvae or other stages in years showing various amounts of water-level cirawclown, professional judgment wouicI be the only recourse for assigning significance of variations in spawning habitat to the relationship between production of larvae anti water level in the lake. As a result of intensive stucly of the suckers, however, there is some clirect evidence by which the hypothesis can be tested in a preliminary way. Larval suckers have been samplecI systematically since 1995 (Simon anti Markle 20011. If cirawclown suppresses spawning success substantially, one wouicI expect lower relative abundance of larvae in years of extreme cirawclown. The relationship between water level anti abundance of larvae or juveniles wouicI not necessarily be linear; it might involve threshoicis rather than graclual changes in production of viable larvae. Figure 6-3 shows the relationship between water level of Upper I(la- math Lake in April (in the micicIle of the critical period anti relative abun- ciances of larvae as shown by the stanciarclizecI sampling program. Minor differences in relative abundances of larvae shouicI not be consiclerecI sig- nificant because the sampling variance for any given year is substantial (95°/0 confidence limits extend 50-100% around the mean in most cases). 30 25 an ~ 15 20 10 5 - O- · 1999 · 1997 1998 - · 2000 · 1996 · 1995 4142.0 4142.2 4142.4 4142.6 4142.8 4143.0 4143.2 April Water Level, Feet FIGURE 6-3 April water level and larval abundance (mean catch per unit effort LCPUE1) in Upper I(lamath Lake. 95% confidence limits for annual means typically are 50-100% of the mean. Source: Simon and Markle 2001.

226 FISHES IN THE KLAMATH RIVER BASIN Thus, 1998 ancI 2000 might be consiclerecI distinctive in their scarcity of larvae, whereas 1995-1997 ancI 1999 belong to a second category of years involving much higher larval abundances that are virtually inclistinguish- able from each other because of sampling variance. The year of lowest water levels cluring April was 1999, cluring which spawning habitat varied from somewhat climinishecI to severely climinishecI according to the criteria of Reiser et al. (2001; Figure 6-21. In all other years of the 6-yr record, the restriction of area was substantially less than in 1999. Thus, the hypothesis that diminution aciversely affects production of larvae from eggs is contraclictecI by this test. The test is not particularly strong, because extremes of diminution ancI repeated years of diminution are not available in the record. Further observation might demonstrate some relationship that is not now evident. For the present there is no indication of a strong relationship between spawning success, as inferred from abundance of larvae, ancI water level in Upper I(lamath Lake. One other empirical test is possible. It is more remote in a life-history sense because it involves the relative abundance of aclult fish. Its advantage is that it involves ciata that extend into different water years from those available for testing through larval abundance. As explainecI in Chapter 5, mass mortality of fish provides insight into the age structure of the encian- gerecI sucker populations. Specifically, the relative abundance of age classes of subaclult ancI aclult fish can be jucigecI on the basis of their relative frequency of appearance among fish that are collectecI after the fish kill. As inclicatecI in Chapter 5, any use of this information must be consiclerecI provisional because the relationship between the actual age structure of the population ancI the age structure reflectecI in the fish kill is unknown. Given the assumption that large fish are killecI in relation to their abundance in the population, relative abundance of specific year classes of fish shouicI reflect the clevelopmental history of each year class. If repression of larval production through restriction of spawning areas is critical in years of low water level in the lake, years affected by low level shouicI stancI out as producing a reclucecI population of large fish, given that large fish are ultimately a byproduct of successful spawning. The relationship between lake level ancI relative abundance (percentage frequency) of fish is shown in Figure 6-4. As inclicatecI in the figure, the 2 yr of extraorclinarily low water levels (1992 ancI 1994), which wouicI be expected to show most strongly the negative signal involving larval production, clo not indicate any repres- sion of the year classes relatecI to water level. Further research may show a relationship between inundation of the spawning area ancI larval recruitment. Present ciata suggest, however, that any such relationship wouicI be either weak or indirect. Thus, the connec- tion cloes not appear to be especially important for the population. This conclusion seems counterintuitive, but there are several potential explana-

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 40 35 30 25 20 15 10 5 O 1987 A, 4141.6 4141.8 4142.0 4142.2 4142.4 Mean April Water Level, Feet 227 · 1991 :~: A. . · Shortnose Suckers ~ Lost River Suckers 1992 1990 ~~` 1993 .~ ~ · ~~ 1994 1989 · - 1988 Hi. 4142.6 4142.8 4143.0 FIGURE 6-4 Relative abundance of year classes of suckers in Upper I(lamath Lake, as inferred from fish recovered after mass mortality in 1997, in relation to water level during spawning interval when same year classes were produced. Source: USGS, unpublished data, 2001. tions. First, the present population, which is much smaller than the original population, may have adequate spawning area even when spawning area is reclucecI, simply because it puts less total clemancI on the spawning area. Thus, progressive recovery of the population couicI produce a bottleneck relatecI to spawning area in the future. Second, recruitment from spawning in streams may be more important than lake spawning uncler present cir- cumstances. These anti other possibilities cannot be clistinguishecI at present. Overall, maintaining full pool elevation for promotion of spawning, al- though intuitively appealing, is clifficult to clefencI scientifically. De~raciation of Snawning Areas cat ~ Some lacustrine spawning areas appear to be clegraclecI, as inclicatecI in Chapter 5. Where feasible, clegraclecI spawning areas shouicI be restored by introduction of aciclitional grave! in appropriate type anti size, removal of silt, or redirection of spring flows. It is unclear whether these actions will increase sucker spawning success, but they are not especially expensive anti may be beneficial. Potential diminution of clepth must be taken into ac- count if restoration involves the aciclition of new substrate. Also, factors other than clepth per se neecI to be stucliecI more extensively with respect to the suitability of spawning areas. Wave action anti other factors that have not yet been stucliecI might be relevant, for example.

228 FISHES IN THE KLAMATH RIVER BASIN While lakesicle spawning areas for suckers in Upper I(lamath Lake have been stucliecI extensively, tributary spawning areas have received relatively little attention. Where tributary spawning occurs, the morphometric fea- tures ancI substrate composition favoring the suckers shouicI be iclentifiecI, anti specific efforts shouicI be macle to offset any changes in these character- istics that may have occurred through anthropogenic mechanisms. In acicli- tion, potential adverse effects of suspenclecI loacI shouicI be iclentifiecI. Im- provement of appropriate conditions for spawning will likely require protection of riparian zones from grazing anti other disturbances, reduction in transport of suspenclecI loacI relatecI to lancI disturbance through agricul- tural anti other lancI-use practices, ancI restoration of wetiancI near chan- nels. Furthermore, it may be effective to protect specific spawning regions of tributaries from human presence in orcler to recluce the possibility of harassment ancI to increase public awareness of the importance of specific locations for successful spawning by suckers. Some tributaries ancI lakesicle spawning areas that are known to sup- port successful spawning by suckers may not require restoration but clo require vigorous protection because of their special value to the population. Even subtle changes, which might involve pumping of grounc~water in the vicinity of these spawning sites, lancI disturbance, recreational activities, poorly managed agricultural practices, ancI other human activities couicI easily clegracle or even eliminate these sources of sucker fry. Abandonment of Spawning Areas Some historical spawning areas have been abanclonecI for no apparent physical reason. Reestablishment of population components with natal af- finities to the areas shouicI be attempted. The clegree of benefit cannot be estimated from present information, but the work couicI be accomplishecI without great cost. Specific locations are as follows: 1. Harriman Springs in northern Upper I(lamath Lake was last used in 1974; spawning was also reported historically at Odessa Creek on the western shore (Ancireason 1975, USFWS 20021. Barkley Springs on the southeast shoreline of Upper I(lamath Lake was a previous spawning site but has not been used since the late 1970s (Perkins et al. 2000a), because Liking, poncling, ancI rerouting of water associated with the construction of Hagelstein Park in the 1960s apparently blockecI access of the fish to the site. Spawning substrate was aciclecI ancI water-control crevices clesignecI to inunciate the springs were constructed in 1995, but no spawning has yet been observed. 2. Spawning suckers were reported at a spring on Bare IslancI (in the northern portion of Upper I(lamath Lake east of Eagle Ricige) in the early

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 229 l990s, but spawning has not been observed at the site since then (Perkins et al. 2000a). 3. In the region of Agency Lake, spawning of suckers was observed in the late 1980s ancI early l990s in Crooked Creek, Fort Creek, Sevenmile Creek, Fourmile Creek, ancI Crystal Creek. The WoocI River has hacI the only recent spawning activity, most of it attributed to shortnose suckers. Aclults were last seen in the WoocI River in 1996, ancI larvae were last collectecI in 1992; no juveniles were founcI in 2000 (Simon ancI Markle 1997b, 2001; Cooperman ancI Markle 20031. 4. Aciclitional, indirect evidence of abanclonecI spawning sites in Upper I(lamath Lake itself has been obtained on the basis of lost fishing gear (Cooperman ancI Markle 20031. Shoreline surveys concluctecI cluring record low lake levels in 1994 revealecI fishing gear on the bottom at known spawning sites, such as Ouxy ancI Sucker Springs. Lost gear also was founcI at four unnamed, flowing spring sites between Mocloc Point ancI Sucker Springs. Failure to observe suckers spawning at these four sites cluring recent spawning surveys suggests that clirect removal or harassment lecI to the elimination of the spawning aggregations. The available evidence strongly suggests that lake ancI stream spawners mix only occasionally if at all ancI that spawning-site ficlelity causes an aban- clonecI spawning site to remain unused. Abandonment of apparently appro- priate spawning sites indicates that the use of a spawning site is a social tradition, that is, that fish learn about spawning sites by following or observ- ing other fish (e.g., Helfman ancI Schultz 19841. A goocI spawning site may remain unused by fish that show those characteristics if "teachers" are ab- sent, as has been clemonstratecI for reef-spawning wrasses in the Caribbean (Warner 1988, 19901. Use of abanclonecI sites might be renewed spontane- ously if populations of aclults become substantially more abundant. The possibility that sites are abanclonecI because of a break in tradition suggests a solution. Transplantation of spawning-reacly fish of both sexes to historically used sites, perhaps accompanied by confinement of the fish in cages for a brief acclimation period, might initiate use of the abanclonecI sites. Feasibility of this approach is suggested by Warner's (1988, 1990) manipulations, which involvecI transplantation of fish to locales that hacI been experimentally clepopulatecI, with subsequent establishment of site- specific, traclitional spawning groups by transplantecI inclivicluals. Males might be attracted to cagecI females in spawning-reacly condition; spawning readiness couicI even be inclucecI, if necessary, by hormone injection. Fish couicI be transplantecI from habitats that lack recruitment such as Tule Lake, the Lost River, or the I(lamath main-stem reservoirs assuming that spawning-reacly inclivicluals are available. If fish from Upper I(lamath Lake are used for such manipulations, they shouicI probably be young, first-time

230 FISHES IN THE KLAMATH RIVER BASIN spawners because fish with spawning experience are likely to abandon a new site for a site with which they are familiar. RegarcIless of the cause of spawning-site abandonment, loss of spawn- ing aggregations has several consequences for sucker recovery. If the aggre- gations at these sites represented genetically distinct groups of suckers, overall genetic diversity of the Upper I(lamath Lake populations probably has been reclucecI. Even without genetic distinctness, the uniqueness of circumstances at each site creates potential differences in survival of larvae originating at different sites. Multiple spawning sites have a bet-heciging effect on larval survival: the more spawning sites a population uses, the more resistant the population is to exceptional loss at any one site. Survival of Larvae ant! Juveniles Mortality of larval ancI juvenile stages of all fishes is high, even in populations that successfully saturate their environment. High mortality in the young stages of the life history of a given fish population cloes not necessarily indicate that these stages are a bottleneck that leacis to repres- sion of the population. Survival of larval ancI juvenile stages in a repressed population couicI be usefully compared with those in a vigorous popula- tion; a bottleneck at the larval ancI juvenile stages wouicI be inclicatecI by substantially lower survival rates in the repressed population than in the vigorous population. However, estimation of survival rates of young life- history stages of fish is extremely clifficult, ancI less clirect indicators often are the only recourse for assessment of these stages, as is the case for sucker populations of Upper I(lamath Lake. Morphological Anomalies in Young Fish Morphological anomalies which may indicate parasitism, dietary cle- ficiencies, or physiological stress cluring clevelopment suggest abnormal losses of young fish cluring clevelopment. Where fish are not uncler physi- ological stress clue to poor water-quality conditions, morphological anoma- lies selclom exceed 1% (I(arr et al. 19861. In Upper I(lamath Lake, however, the frequencies of anomalies among the larval ancI juvenile shortnose suck- ers averaged 8%' ancI among the Lost River suckers averaged 16% (Plunkett ancI Snycler-Conn 20001. The anomalies incluclecI deformities of the fins, eyes, spinal column, vertebrae, ancI osteocranium, as shown by Plunkett ancI Snycler-Conn (2000), who suspected chemical agents of human origin. These authors reviewed literature indicating high frequencies of anomalies in other fishes as well Fathead minnows ancI chub species) ancI in amphib- ians of the Upper I(lamath Lake basin. Harmful agents have not yet been iclentifiecI.

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 23 Skeletal deformities in young fish can affect their swimming perfor- mance anti inclirectly increase their vulnerability to predation anti impair their ability to escape unfavorable habitat conditions. Plunkett anti Snycler- Conn (2000, p. 2) suggest that the relatively high rate of anomalies in young suckers couicI result in "early elimination of anomalous 0-agecI suck- ers from Upper I(lamath Lake populations." Direct comparisons with popu- lations in Clear Lake anti Gerber Reservoir, where populations are appar- ently stable, wouicI be informative. Entrainment of Larvae ant! Juveniles Entrainment at anti lack of passage through I(lamath River clams anti other irrigation structures were aciclecI to the list of threats to the encian- gerecI suckers after the original listing (e.g., USFWS 1992a). Entrainment into irrigation anti power-cliversion channels is now recognized as being responsible for loss of "millions of larvae, tens of thousands of juveniles, anti huncirecis to thousands of aclult suckers each year" (USFWS 2002, Appendix C., p. 241. Sucker larvae appear at the south encI of Upper I(la- math Lake beginning in late April. Millions of young fish then are swept from Upper I(lamath Lake into the Link River, whence large numbers are drawn into the A Canal (USFWS 2002), from which they cannot escape. Speculation has clevelopecI about the source of the young fish that reach the Link River. They may come from known spawning sites along the northeastern portion of Upper I(lamath Lake, from such tributary streams as the Williamson River, or from unknown spawning sites farther south. Because all known spawning sites are in the northern portions of the lake, the critical question is whether currents in the lake are strong enough anti of proper alignment to cleliver larvae to the Link River 18 mi to the south. Some evidence indicates that larval anti juvenile fish entering the Link River originate in known riverine anti lake spawning areas. Prevailing wincis are from the northwest when larvae are present anti establish sub- stantial south-flowing currents, according to a numerical mocle! clevel- opecI by Philip Williams & Associates (PWA 20011. The Philip Williams mocle! suggests that it is very feasible for larvae proclucecI from the Wil- liamson anti Sprague system to enter the south encI of the lake within a few clays of swimup, the time at which larvae first leave the substrate for the water column (R. S. Shively, U. S. Geological Survey, I(lamath Falls, Oregon, personal communication, 20021. Whether entrainment is caused by natural movement of fish that wouicI historically have entered Lower I(lamath Lake or is an avoidance response to poor habitat or poor water- quality conditions is unknown. RegarcIless, given that these larvae likely originate in known spawning aggregations anti that any larvae leaving the lake to the south are permanently lost from the population, entrainment

232 FISHES IN THE KLAMATH RIVER BASIN of young fish is a potentially important contributor to failure of the popu- lations to grow. USER was scheclulecI to place fish screens at the A Canal in the summer of 2003. These screens function effectively with fish larger than 30 mm (USFWS 20021. Although retention of fish smaller than 30 mm couicI be achieved, the likelihoocI that very young, fragile fish wouicI survive im- pingement (along with algae ancI clebris) on the screens is low, ancI the chances of salvaging them successfully are even lower. luvenile fish may survive impingement but, unless they move against the current, will still be lost from source populations because fish screened from the A Canal will next pass through the Link River Dam ancI then enter other canals, be killecI by turbines, or join nonreproclucing populations downstream (Figures 1-2 ancI 1-41. Even so, the screening cloes prevent loss of subaclults, aclults, ancI some juveniles through the A Canal. USFWS (2002) recommencis coordination of intake at the A Canal with timing of juvenile movements, cleflection barriers that wouicI move juve- niles away from intake structures, location of intakes above the water- column strata in which young suckers usually swim, ancI salvage. These measures seem reasonable ancI shouicI be pursued. Salvage operations may be pointless, however, if emigration from the lake is an avoidance response to poor water quality. SalvagecI fish possibly couicI be moved to a hoicling facility with goocI water quality before return to Upper I(lamath Lake or couicI be transplantecI to other sites to establish new populations. Adequacy of Nursery Habitat for Larvae ant! Juveniles Upper I(lamath Lake has lost an estimated 66% of emergent marsh vegetation ancI submerged vegetation (USFWS 20021. Specific changes in- clucle the apparent loss of emergent vegetation in the region between the Williamson River mouth ancI Goose Bay that probably once was important larval habitat; vegetation shouicI be restored in this area as soon as possible. In general, cliking, draining, ancI water-level management have reclucecI emergent ancI submerged vegetation along shorelines by about 40,000 acres (USFWS 20021. Remaining marginal marshes around Upper I(lamath Lake are reclucecI, patchy, ancI often clewaterecI by micicIle to late summer as water level falls. Vegetation in shallow water is a consistent aspect of larval habitat ancI may be important to juvenile habitat as well (Chapter 51. Abundance of this habitat feature cluring the larval phase, which extends from April through luly, in Upper I(lamath Lake is in part relatecI to water depth. Higher water levels in Upper I(lamath Lake are associated with larger amounts of emer- gent vegetation (Table 6-21. Ignoring emergent vegetation, total shoreline area that is at least 1 ft creep at lake water levels of 4,142-4,143 ft accounts

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS TABLE 6-2 Estimates of Larval Habitat Availability CalculatecI as Percentage of Lakeshore InunciatecI to a Depth of at Least 1 Ft for Lake Ecige anti Marsh Regions in Northeastern Upper I(lamath Lake that Contain Emergent Vegetation, anti Total Lake Shoreline RegarcIless of Vegetation 233 % Larval Habitat Available % Lake Shoreline Available Dunsmoor Reiser Chapin Reiser et al. 2001 Water Level, Lake (ft) et al. 2000 et al. 2001 1997 (All Shoreline) 4,143.0 - - - 85-100 4,142.8 Boa 4,142.0 boa I Cob _ 40-60 4,141.5 - 80b - - 4,141.2 - 80C - - 4,141.0 - - - 10-25 4,140.0 od 0 0 - aShoreline emergent vegetation. ball emergent vegetation. CMarsh edge habitat only. dAlmost completely unavailable. for at least 50°/O of the lake's perimeter, but this fraction cleclines rapicTly with reclucecT water levels. Very little emergent vegetation is available to larval suckers below a lake level of 4,141 ft.; emergent vegetation is essen- tially inaccessible below 4,140 ft (Reiser et al. 20011. Reiser et al. (2001) recommencT maintaining water levels above 4,142 ft at least until luly 15 to ensure access by larvae ancT juveniles, although the ciata on use of this habitat by juveniles are not clear. Because the majority of suckers in Upper I(lamath Lake now spawn in the Williamson ancT Sprague river system, use of habitat in the system by larvae couicT be important in determining production of larvae. Uncler cur- rent conditions (blockage of spawning migrations at Chiloquin Dam com- binecT with a highly mocTifiecT stream channel in the lower Williamson clelta), a higher proportion of larvae may be proclucecT in the lower Williamson than were proclucecT there historically. As a result, the larvae may pass from the river to the lake more quickly ancT with less temporal dispersion than was the historical norm. Cooperman ancT Markle (2000) founcT that larvae left the Williamson River in as little as a single clay ancT that 99°/O of larvae entering the lake hacT not yet clevelopecT a tail fin ancT so were not yet competent swimmers ancT feeders. The majority of larvae in the lower river samplecT by Cooperman ancT Markle (2000) hacT empty guts. Thus, many larvae may be entering Upper I(lamath Lake before they are reacly to feecT or to avoid preciators (comparisons with Clear Lake ancT Gerber Reservoir

234 FISHES IN THE KLAMATH RIVER BASIN populations wouicI be useful but are not available). Modifications to the lower Williamson have reclucecI plant cover, ancI thus possibly reclucecI foocI production ancI shelter from predators. The Nature Conservancy is restor- ing the lower Williamson to a more natural, meandering, multiple-channel configuration that supports clenser riparian ancI emergent vegetation. This project shouicI be completecI soon. Larvae clescencling from the Williamson system will fincI cover near the mouth of the river when vegetation ancI morphology have begun to recover, which may take some time. Physical conditions that may impair spawning ancI support of fry in the rivers above Upper I(lamath Lake have not been aclequately stucliecI. Changes in river channels have occurred as a result of removal of riparian vegetation, access of cattle to the streams, alteration of flows, ancI loacling of the stream with fines. All of these factors shouicI be clocumentecI ancI measures shouicI be taken to reverse them on grouncis that these changes are quite likely to interfere with successful spawning ancI larval survival. Hypotheses about the significance of lake-level changes ancI capacity of Upper I(lamath Lake to sustain larval suckers can be tested against infor- mation on the relative abundance of sucker larvae, as cleterminecI over the years 1995-2000. If interannual variation in lake levels is a dominant factor in the viability of larvae in the lake, years of higher lake level cluring the larval clevelopment period shouicI be marked by higher larval abun- ciance. To be of use in management, any beneficial effects of high water level shouicI appear as higher CPUE (catch per unit effort) of larvae. This is not the case, however (Figure 6-51. In fact, the amount of larval habitat in spring varies across years much less (about 2-foicI; compare Figure 6-5 with Table 6-2) than larval abundance per unit area (as inclicatecI by CPUE- 1 0-fold). Aciclitional testing is possible through use of information on relative abundance of year classes among fishes collectecI cluring episodes of mass mortality. If interannual variations in lake level correspond to relative cle- grees of repression of larval production, ancI this factor has a major effect on the populations, year classes proclucecI in years of especially low water levels in Upper I(lamath Lake shouicI be exceptionally weak. Once again, this is not the case (Figure 6-61. Lack of correspondence between larval abundance ancI indicators of year-class success basecI on either collection of larvae or collection of aclults cloes not contradict the idea that inunciatecI vegetation is critical habitat, that is, habitat that the suckers neecI in some unknown amount anti clistri- bution. It cloes call into question the idea that greater or smaller abundance of this habitat feature from one year to the next is regulating the popula- tions. Cooperman ancI Markle (2003) have argued that complicating fac- tors couicI mask an important relationship between water level in Upper I(lamath Lake anti production of larvae. From a scientific viewpoint, how-

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 30 - 25- ~4 C) 20- a~ ~ 15- <~ 10- 5- 235 · 1999 ~ 2000 ~ 1996 · 1997 1998 1995 ~ O- 1 1 1 1 1 4142.2 4142.3 4142.4 4142.5 4142.6 4142.7 4142.8 4142.9 4143.0 Mean April - July Water Level, Feet FIGURE 6-5 Relative abundance of larvae as determined by standardized sam- pling, shown in relation to mean water level of Upper I(lamath Lake during the main interval of larval development (April-Tuly). Source: Simon and Markle 2001. ever, the water-level hypothesis is not supported because it fails empirical tests for the presently available data. An argument for a complex relation- ship involving water level wouicT require empirical support, of which there is none. One potential line of investigation wouicT be to examine the cTiffer- ences in larval production of the two sucker species. The two species appear to be responding in similar ways to environmental change, but the ciata 40 - 35 - 30 - 25- 20- G au 15 - 10 - | · Shortnose Suckers 1991 | a; Lost River Suckers 1992 1990 . . . 1988 · 1994 · . ~ 1993 1987 1989 - 4140.0 4140.5 4141.0 4141.5 4142.0 4142.5 4143.0 Mean April - July Water Level, Feet FIGURE 6-6 Relative abundances of year classes of endangered suckers collected from Upper I(lamath Lake during the fish kill of 1997, shown in relation to mean water level over the interval of larval development for the same year classes. Source: USGS, unpublished data, 2001.

236 FISHES IN THE KLAMATH RIVER BASIN suggest that the responses are not exactly the same. Differences relatecI to timing or place of spawning may be important. From a management perspective, the clifficulty with a water-level hy- pothesis that involves unknown complications is that observations of higher water levels at present offer no evidence that wouicI support maintenance of higher water levels. At the same time, the lack of a relationship between observed water levels ancI larval abundances cannot be taken as justifica- tion for broacler manipulation of water levels, which at some extreme couicI be notably harmful. Monitoring of larval abundance ancI year-class abundances as inferred from mass mortality indicate that the explanation for interannual variabil- ity at present lies in key factors other than the amount of shallow water or emergent vegetation. This conclusion shouicI energize the investigation of other habitat features. For example, restricted availability or poor concli- tion of tributary spawning areas couicI be critical. Interannual variability of year-class abundance as affected by clelivery of larvae from tributary spawn- ing areas wouicI be an obvious subject for further study. The known biology of the suckers indicates that particular depths are preferred at establishecI spawning locales ancI that flooclecI emergent vegeta- tion is primary larval habitat. The lack of relationship between water level in Upper I(lamath Lake ancI larval production or larval survival indicates that other factors, such as clegraclecI water quality or poor larval habitat, override the presumed benefits of clepth-relatecI habitat availability. Rec- ommencling maintenance of particular water levels to promote sucker re- covery has no clear scientific basis until the factors that override water clepth are better unclerstoocI anti, if possible, rectified. USFWS may retain an interest in water-level manipulations as justified by the neecI to minimize risk. Given limitations on the legitimate use of the neecI to minimize risk, however (Chapter 9), it might be clifficult for USFWS to justify more strin- gent limitations on water level as a general operating rule. One alternative is for USFWS to work with USER in testing various water-level combina- tions that can be achieved through such actions as experimental use of water-bank resources or by use of the excess water that may be available in some years. Overview of Larval ant! Juvenile Production As explainecI above, larvae were variably abundant in trawl catches throughout the 6-yr monitoring period 1995-2000. Catches were high in 1995, 1996, 1997, ancI 1999, ancI were relatively low in 1998 ancI 2000. No correlations are obvious between abundance of fish in spawning runs ancI larval abundance (Simon ancI Markle 2001, USFWS 2002) or between fish kills ancI larval abundance. Abundances of young of the year (YOY)

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 237 also have high year-to-year variation anti lack any cletectable relationship with abundance of spawners. The year 1999 was goocI for larvae ancI juveniles regarcIless of sampling locale or method (Simon anti Markle 2001, USFWS 2002), anti 1991 must have been favorable as well, as jucigecI from abundance of aclults (monitoring of larvae clicI not begin until 19951. As in most fish populations, abundance of young suckers in Upper I(lamath Lake cleclines progressively through each summer ancI fall (Simon ancI Markle 20011. Declines couicI be explainecI by offshore movement as the fish grow, high mortality, high emigration rates from the lake, or a combination of these. Abundance of juveniles in spring (age 1+ yr) appear to reflect a 90°/O overwinter mortality or emigration (Simon ancI Markle 20011. High inciclences of physical abnormalities in these fish (Plunkett ancI Snycler-Conn 2000) imply that mortality or export may repress recruitment of subaclults ancI aclults, although avoidance of sampling gear by postiarval fish creates clifficulties in interpretation. Some minimal number of spawners is necessary to produce a successful year class of larvae, but the lack of correlation between numbers of spawn- ers ancI abundances of larvae implies that abundant spawners are no guar- antee of high larval numbers ancI that, given the high fecundity of suckers, a small number of spawning fish may be sufficient to produce abundant larvae if conditions for larvae are goocI. Aclults Entrainment Fish that enter water-management structures typically cannot return to the habitat from which they came or enter another suitable habitat. For Upper I(lamath Lake, the A Canal has long been recognized as a source of entrainment for all life-history stages, inclucling aclults, whose loss may be especially significant because of the importance of large fish in maintaining the fecundity of the population (Chapter 51. ScheclulecI screening of the A Canal, which will be ineffective for small fish < 30 mm, will block entrain- ment of subaclult ancI aclult fish, ancI couicI thus reverse an important his- torical source of mortality. The benefits of this measure to the population are unknown. Entrainment of fish from Upper I(lamath Lake via the Link River still occurs through intake structures of the Link River Dam, which shouicI be screened (USFWS 20021. Mass Mortality Unlike most other imperilecI lakesuckers, suckers of Upper I(lamath Lake suffer from episodic mass mortality of reprocluctive-age fish. Although such

238 FISHES IN THE KLAMATH RIVER BASIN mortality probably inhibits recovery, fish kills are not new to Upper I(lamath Lake. Records indicate periodic kills ciating at least to the late 1800s; before the 1990s, large fish kills occurred in at least 1894,1928,1932,1966,1967, 1971, anti 1986 (USFWS 20021. Whether episodic mass mortality has always occurred in Upper I(lamath Lake is a matter of conjecture. The actual numbers anti sizes of fish killecI are clifficult to estimate because of sampling clifficulties, clifferential sampling effort, loss of small fish to bircis, anti loss of fish that clo not float after cleath. Mortality may reach tens of thousands in a severe episode (Perkins et al. 2000b). The effects of fish kills on spawning populations of suckers probably have been substantial. As much as 50°/O of the aclult populations may have cliecI in the 1996 fish kill; sizes of spawning runs indicate that the spawning popula- tions of both species were reclucecI by 80-90% from 1995 to 1998 (USFWS 2002; Chapter 51. The largest clocumentecI case of mass mortality occurred in 1971; it involvecI the loss of about 14 million fish, most of which were blue anti tui chubs. Water level may or may not have playecI a role in conditions leacling to the incident, but 1971 was the year of highest recorclecI water level since full operation of the I(lamath Project began in 1960. It is unclear whether the extent or frequency of mortality is greater now than earlier. Incidents of mass mortality in 3 consecutive recent years (1995, 1996, anti 1997) are a reason for special concern, but it is impossible to determine whether such episodes now are more frequent than in the past. It couicI be argued that mass cleaths of suckers is a natural phenomenon caused by very high abundances of algae that have always been characteris- tic of Upper I(lamath Lake. Or it couicI be argued, without particularly strong support, that mass mortality is more frequent or more severe than it used to be. It is not necessary, however, to resolve this point for ESA purposes. Because the abundances of the enciangerecI suckers have been cirastically reclucecI, any factor that leacis to a larger population shouicI be favored as a step toward recovery of the species, even if it involves a natural mortality mechanism. Thus, reducing mass mortality, whether natural or not, shouicI be counted as beneficial to the welfare of the species ancI shouicI be pursued. Conditions commonly associated with fish kills inclucle high tempera- ture, intense blooms of bluegreen algae, high inciclences of copepocI (Ler- naea) infestations (see Table 6-3), cysts, lesions, infection with Flavobacte- rium columnare (columnaris clisease), high pH, high concentrations of unionized ammonia, ancI low concentrations of clissolvecI oxygen (Perkins et al. 2000b, Chapter 31. Before kills, some fish apparently move to the Link River (Gutermuth et al. 1998), anti others (mainly recibancI trout) become concentrated in specific refuge areas, inclucling Pelican Bay, Odessa Creek, anti the Williamson River mouth. Refuges often contain springs that offer much better water quality than the lake itself (Bienz anti Ziller 19871.

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS TABLE 6-3 Incidence (HO) of Various Indicators of Stress in Suckers of Upper I(lamath Lake Based on Visual Inspection Incidence, % 239 Lampreys Copepods Wounds Infections Eye Damage Emaciation Wounds Lost River Suckers, Live Fish, 2001 Lake spawning 40 22 4 0 1 River spawning 48 28 22 0 2 Lake non-spawning 51 18 8 1 2 Shortnose Suckers, Live Fish, 2001 Lake spawning 53 30 3 0 0 River spawning 38 51 16 0 1 Lake non-spawning 48 33 8 0 4 Fish Kill 1997 73a allased on Foott 1997 and Holt 1997 in USFWS 2002; incidence of Columnaris disease was 92% and 80%, respectively, during the 1996 and 1997 fish kills (USFWS 2002). Sources: Coen et al. 2002, Cunningham et al. 2002, Hayes et al. 2002. Mortality of fish during routine sampling with trammel nets also increases during the weeks preceding a fish kill (USFWS 20021. Although USFWS (2002) went to considerable lengths to examine the possible direct influence of high water levels in Upper I(lamath Lake on sucker welfare, the data now on hand contradict the hypothesis that water level is associated with fish kills (NRC 2002, Figure 3; Chapter 31. Fish kills have occurred in years of low, average, and above-average median August lake levels. Water level may affect the accessibility of refuges that are re- portedly used by large fish during periods of poor water quality and fish kills, but the data on this topic are largely anecdotal (see Buettner 1992 unpublished memo, USFWS 2002, Appendix C, and below). High incidences of parasites, bacterial infections, and other anomalies imply that stressful conditions exist in Upper I(lamath Lake for several weeks before the appearance of dead fish. Loftus (2001, cited in USFWS 2002) developed a "stress-day" index that accounts for multiple stress factors related to water quality. In 1990-1998, accumulated stress days were maximal in luly and August during the fish-kill years of 1995 and 1997. The stress-day index approach is useful in that it involves regular, coordinated monitoring focused on water quality, meteorology, fish condi- tion (parasite frequency, body condition, and so on), and attention to in- creased numbers of adults in the Link River or presumed refuges. When conditions and early warning signs converge, whatever remedial actions are . . . . . .

240 FISHES IN THE KLAMATH RIVER BASIN feasible should be taken, possibly including oxygen supplementation at spe- cific locales where suckers aggregate (Chapter 31. In some lakes, mass mortality of fish occurs under ice ("winterkill"), usually in association with low concentrations of dissolved oxygen. Win- terkill is not known to have occurred in Upper I(lamath Lake or in any other lakes occupied by endangered suckers. Thus, the relevance of win- terkill to Upper I(lamath Lake remains hypothetical, as do management actions that would minimize its likelihood or effect. Winter mortality (but not necessarily winterkill) has been postulated as the cause of a 90°/O reduction of first-year juvenile suckers in Upper I(la- math Lake from late fall to early spring and population reductions in other species (Simon and Markle 20011. Comparable data are needed on winter mortality in surrounding water bodies with better water quality (such as Clear Lake) to determine whether the 90°/O mortality figure is extreme. Concern over winterkill is justified, especially if water quality deterio- rates further or if an exceptionally cold winter results in an unusually long period of ice cover. Improvement in water quality in the lake probably would reduce the likelihood of winterkill, but may be infeasible over the short term. Winter monitoring of oxygen should be undertaken in any event (Chapter 31. Loss of Habitat Adult Lost River suckers and shortnose suckers prefer open water; they use flowing waters chiefly for spawning. Total lake habitat available to suckers throughout the I(lamath basin is a fraction of its original extent because of drainage and other water-management practices (Chapter 21. Even where it persists, habitat for adults may be compromised during late summer. Adult suckers appear to prefer water that is deep and turbid, and thus dark (USFWS 2002), but degraded water quality in summer appar- ently forces fish to use specific areas of shallow, clear water, such as the mouth of Pelican Bay in Upper I(lamath Lake. Factors Relevant to All Life-History Stages A number of factors, some of which have already been mentioned, are potentially relevant to all life-history stages, although further research may show them to be more relevant to some stages than to others. Most promi- nent is poor water quality, which is linked not only to mass mortality of adults but potentially to undocumented mortality of other stages and to stress, which in turn may be a cause of anomalies, parasitism, and disease in multiple life-history stages. A second complex of factors that may apply broadly across stages, but still in unknown ways, falls under the heading of

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 24 predation ancI competition, primarily from nonnative fishes. A final factor that cannot yet be attached to any particular life-history stage is hybricliza- tion, which may change populations genetically. Water Quality Suckers of Upper I(lamath Lake suffer from varied deformities, para- sites, lesions, cysts, ancI infections. The afflictions of aclult suckers inclucle eroclecI, cleformecI, ancI missing fins; lorclosis; pugheacI; multiple water- moicI infections; reciclening of the fins ancI body clue to hemorrhaging; cloucliness of the skin caused by low mucus production; loss of pigmenta- tion; external parasitic infection by copepocis ancI leeches; lamprey wounds; ulcers; gas emboli in the eyes; exophthalmia; cataracts; ancI a high incidence of gill, heart, ancI kiciney abnormalities after fish kills. Plunkett ancI Snycler- Conn (2000) reported bocly-anomaly rates of 8-16% in larval ancI juvenile suckers. luvenile suckers suffered infestation with copepocis ancI trema- todes of O-7% in 1994-1996 and 9-40% in 1997-2000; shortnose suckers generally show higher rates of infestation than Lost River suckers (USFWS 2002 basecI on Carison et al. 20021. Data on both species in Upper I(lamath Lake ancI at river spawning sites also indicate relatively high frequencies of abnormalities in aclults (Table 6-31. Spawning ancI nonspawning fish clo not show substantial differences in the incidence of such indicators, except that copepocI infestations appear to be higher in shortnose suckers ancI eye ciamage is higher in river-spawning fish of both species. The latter finding might reflect crowding of fish downstream of Chiloquin Dam or injuries to the fish as they attempted to negotiate the unsuitable fish lacicler at the clam. The wiclely used Inclex of Biotic Integrity (I(arr et al. 1986) incorpo- rates 1% as a threshoicI criterion for anomalies; sites with fish above this threshoicI receive the lowest metric scores for their ability to support a diverse biota. The appropriate threshoicI may vary geographically ancI by taxa, however. For the Willamette River, Hughes ancI Gammon (1987) iclentifiecI 6% as a threshoicI. Hughes et al. (1998) proposed a more general threshoicI of 2%. Most collections from all size classes of Upper I(lamath Lake suckers exceed these threshoicis. It is not known why Clear Lake, with its better water quality ancI apparently stable population, also is character- izecI by "heavy parasite loacis on suckers ancI other fish" (Snycler-Conn, personal communication cited in USFWS 2002' Appendix E, p. 381. Even if infections ancI afflictions clo not leacI clirectly or even inclirectly to cleath, they are likely to inhibit growth (e.g., M.R. Terwilliger et al., Oregon State University, Corvallis, Oregon, unpublishecI material, 2000) ancI reproduction ancI may compromise an incliviclual's ability to resist other sources of stress. Without better baseline ancI reference values for suckers in other water bodies in ancI out of the I(lamath basin, it is clifficult

242 FISHES IN THE KLAMATH RIVER BASIN to state categorically that the incidence of anomalies is extraordinary, but fielcI researchers who work with fish selclom observe affliction rates ap- proaching those founcI in Upper I(lamath Lake. Nonincligenous Species as Predators ant! Competitors Eighteen of the 33 fish taxa in the upper I(lamath basin are nonnative (Chapter 51. The nonnatives dominate numerically in many habitats ancI probably influence native species, inclucling the enciangerecI suckers, through predation ancI competition. Competition is particularly clifficult to quantify in nature (Fausch 1988, 19981. Thus, it is not often possible to invoke competition as a major cause of problems in a population, ancI it also is clifficult to moderate competition even where it can be clemonstratecI. In contrast, predation on native fishes by nonnative fishes is easily clemon- stratecI; it can have devastating effects on native fishes (e.g., Fuller et al. 19991. In Upper I(lamath Lake, introclucecI fathead minnows may prey on larval suckers, as shown in laboratory enclosures (Dunsmoor 1993, cf. Ruppert et al. 1993), although the applicability of the laboratory studies to conditions in nature is uncertain. luvenile ancI aclult yellow perch ancI juvenile largemouth bass consume larvae, as may Sacramento perch, most other centrarchicI sunfishes, ancI the two buliheacI species present in Upper I(lamath Lake. luvenile ancI aclult largemouth bass also couicI feecI on juve- nile suckers, although aclult suckers reach a body size that provides them refuge from fish predators. Comparisons of Upper I(lamath Lake with other lakes in this regard couicI be useful. With the exception of Sacramento perch, Clear Lake apparently has been spared significant introductions of nonnative fishes, ancI its populations appear to be stable. A species list for Gerber Reservoir is not reaclily available. The presence of numerous ancI diverse nonnative fishes in the I(lamath system complicates recovery efforts. Nonnative species typically clo well in clisturbecI systems (Moyle ancI Leicly 19921. Given that attempts to recluce abundances of nonnative fishes usually are unsuccessful, the best tactics for decreasing the success of these invaders are to discourage future introcluc- tions (especially of preciators), to restore water quality if possible, ancI to prevent movement of nonnative fishes within the basin. Selective control of nonnative species has been pursued in some environments (Ruzycki et al. 2003), however, ancI shouicI not be rulecI out entirely for Upper I(lamath Lake. Hybridization ant! Introgression Hybridization results in wasted spawning ancI loss of genetic diversity through elimination of rare alleles. Introgression (backcrossing of hybrids

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 243 with parental species) can harm a rare species, as apparently has hap- penecI to the enciangerecI lune sucker, Chasmistes liorus liorus, which hybridizes readily with the more abundant Utah sucker, Catostomus ardlens (Echelle 19911. The original ESA listing document for I(lamath suckers (53 FecI. Reg. 27130 f19881) cited apparently high rates of hy- briclization among the three Upper I(lamath Lake sucker species, espe- cially between shortnose suckers ancI I(lamath largescale suckers, ancI cited hybridization as a potential contributor to loss of genetic integrity ancI clecline of species. Apparent hybrids, as inclicatecI by morphological intermediacy, are commonly found in the Williamson River downstream of Chiloquin Dam ancI in sucker populations of Clear Lake, where crosses between Lost River suckers ancI I(lamath largescale suckers are most fre- quently suspected (e.g., Cunningham et al. 2002; Moyle 2002; D. Markle, Oregon State University, Corvallis, Oregon, personal communication, 20021. Recent anatomical studies of hybridization, however, imply that it is a rare occurrence. Among spawning fish captured in Upper I(lamath Lake in 2001' 0.2% of fish from shoreline spawning sites, 4°/O from the lower Williamson River, ancI 6% occupying the area below Chiloquin Dam were apparent hybrids (Cunningham et al. 2002' Hayes et al. 2002' lanney et al. 20021. In contrast, one-thircI of fish caught at Chiloquin Dam in 2000 appeared to be anatomically intermediate. Morphological studies may overestimate hybridization; allozyme frequency ancI nuclear genetic ciata indicate that recent hybridization is rare, that nominal spe- cies are all valid, ancI that little genetic divergence has occurred among populations within species (D. Buth, University of California at Los Ange- les, Los Angeles, California, personal communication, 2002; Dowling 2000; T. Dowling, Arizona State University, Tempe, Arizona, personal communication, 20021. Microsatellite ciata indicate, however, that the three species present in the Lost River (largescale, shortnose, ancI Lost River suckers) are significantly different from suckers in Upper I(lamath Lake ancI the upper Williamson River (G. Tranah, Harvard School of Public Health, Boston, Massachusetts, personal communication, 20021. Overall, morphological ciata indicate that hybridization has occurred, but current genetic analyses reveal that Lost River suckers ancI shortnose suckers are distinct ancI that the identity of the species has not been eroclecI by extensive hybridization. High priority should be attached to further genetic analysis that will give more information on hybridization ancI on the genetic structure of currently isolated populations. Before the I(lamath Project was completed, all sucker habitats were subject to interchange of fish (Chapter 21. Dams ancI irrigation canals isolated populations to an extent that could ultimately affect the genetic diversity of the species. None of the primary clams in the I(lamath basin allow passage of suckers. Efforts to protect the species with regard to

244 FISHES IN THE KLAMATH RIVER BASIN range fragmentation shouicI focus on habitat protection ancI improvement of all subpopulations ancI on construction of laciclers of proven effective- ness or removal of barriers to improve exchange among subpopulations. Other Issues Relevant to Recovery Other Natives ant! the Paraclox of Persistent Enclemics Shortnose ancI Lost River suckers apparently are more susceptible to clegraclecI habitat conditions or other factors, such as preciators, than any of the 14 other native species. Blue chub ancI tui chub clo appear in some fish kills, sometimes in large numbers, but their populations remain large in Upper I(lamath Lake, as clo populations of I(lamath Lake scuipins ancI recibancI trout. Even the I(lamath largescale suckers in the upper I(lamath basin ancI I(lamath smaliscale suckers in the lower basin seem not as af- fectecI by anthropogenic change as Lost River ancI shortnose suckers, al- though the I(lamath largescale sucker is listecI as a species of special concern in California (Moyle 20021. IntroclucecI species, such as yellow perch ancI fathead minnow, appear to be unaffected by poor water quality. Sacra- mento perch, which have been greatly reclucecI throughout their native range (Moyle 2002), apparently are cloing well in the I(lamath basin. Ex- planations for the exceptional vulnerability of shortnose ancI Lost River suckers couicI be appliecI to recovery efforts. One line of evidence is relatecI to physiological tolerances among species, but this information is limitecI. Falter ancI Cech (1991) found that shortnose suckers were less tolerant of elevatecI pH than were I(lamath tui chub ancI I(lamath largescale suckers (Chapter 51. Aciclitional comparative studies of physiological responses to water-quality clegraciation in the I(lamath basin are neeclecI. Overall, more ancI better information is neeclecI on the biology ancI population status of nonsucker species in the upper basin (Chapter 51. Because all native I(lamath fishes are enclemics, any significant cleclines in their populations couicI trigger ESA actions. Al- though research efforts clirectecI specifically at native fishes other than the listecI suckers wouicI be clesirable, information on them can be collectecI in conjunction with studies of suckers. Some of the species can be used as indicators of water quality ancI habitat conditions ancI wouicI provide insight into the welfare of the enciangerecI suckers, especially where cliffer- ences in physiological tolerance can be clemonstratecI. Comparisons be- tween enciangerecI I(lamath suckers ancI other catostomicI species in the I(lamath basin ancI between I(lamath suckers ancI lake suckers elsewhere couicI provide aciclitional, invaluable insight into solutions to problems in the I(lamath basin.

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS Captive Propagation 1 1 1 ,_ ~ 1 245 Cantive Propagation is a controversial means of protecting enciangerec! species. Successful propagation can leac! to complacency about the concli- tion of natural populations anc! to clelay in the correction of the original causes of clecline, but it also can serve as insurance against catastrophes. Although I(lamath suckers have not reached the point where captive propa- gatlon IS necessary, many conservation practitioners recommenc against waiting until there is no alternative to captive Propagation. because bv then . 1 1 1 ~ , , genetic resources are climinishec! anc! problems with rearing methods may be disastrous. The I(lamath Tribe has established a sucker hoicling anc! rearing facility (the I(lamath Tribes Native Fish Hatchery) at Braymill near Chiloquin. The facility has been used for physiological anc! behavioral studies anc! for fertilization anc! larva-rearing trials (e.g., Dunsmoor 1993; L. I(. Dunsmoor, I(lamath Tribes, Chiloquin, Oregon, personal communication, September 3,20021. The facility could serve as the core of a captive-propagation effort if populations continue to clecline. Methods aireacly clevelopec! there can be used, perhaps with advice based on successful propagation of cui-ui at the David I(och Cui-ui Hatchery in Sutcliffe, Nevada, if captive propagation proves necessary. Critical Habitat Critical habitat, as clefinec! by the ESA (Chapter 9), was not iclentifiec! for the I(lamath suckers at the time of original listing, anc! has yet to be completed for either enciangerec! species, although a ciraft proposal ap- pearec! in 1994 (59 FecI. Reg. 61744 F199411. On the basis of established ESA criteria (for example, water quantity anc! quality; physical habitat appropriate for spawning, rearing, anc! feeding; anc! protection from precia- tion anc! climatic stress), USFWS iclentifiec! six critical-habitat units (CHUB) in the basin: Clear Lake anc! its watershed, Tule Lake, the I(lamath River, Upper I(lamath Lake anc! its watershed, the Williamson anc! Sprague Riv- ers, anc! Gerber Reservoir anc! its watershed. All except Gerber Reservoir are habitat units for both sucker species; Gerber Reservoir contains only shortnose suckers, but Lost River suckers presumably could live there. The ciraft critical-habitat determination (59 FecI. Reg. 61744 F19941) anc! its recommendations should be reviewed anc! revised in light of recent finclings. The process of identifying critical habitat for both species needs to receive higher priority anc! should be more specific. In designating Upper I(lamath Lake a CHU, USFWS (59 FecI. Reg.61744 F19941) clic! not identify specific areas of particular value. The CHU approach could be expanclec! to inclucle the needs of specific life-history stages, for example, east coast springs for spawning, Williamson River mouth anc! nearby shorelines as a

246 FISHES IN THE KLAMATH RIVER BASIN nursery region, Mocloc Point anti Goose Bay as staging areas before spawn- ing, anti west coast bays as postspawning aggregation areas (see Chapter 51. Buettner (1992) identified sites that have the greatest potential as adult refuges at low lake levels on the basis of their size, proximity to the main lake, relative water quality, ancI density of submerged vegetation. The issue of water-quality refuges neecis more stucly relative to critical habitat. If the postulatecI patterns can be verified anti the location anti use of these appar- ent water-quality refuges can be confirmed, they might be clesignatecI as critical habitat anti consiclerecI for special protection. Although there is only weak pressure for clevelopment in the I(lamath basin, the human population of the area has grown, anti future growth is likely (Chapter 21. Proposals for new construction or use of the lake should take into account possible adverse effects on suckers. For example, an article in SAIL magazine for luly 2002 iclentifiecI HowarcI Bay, Pelican Bay, anti Harriman Springs as clesirable destinations for boaters. HowarcI Bay apparently is a preferred aggregation area for postspawning shortnose suck- ers (Coen et al. 20021; Pelican Bay was identified by Buettner (1992) as a refuge for suckers cluring the fish kills of luly 1971 anti August 1986 anti was consiclerecI the best sucker refuge site on the west shoreline when lake levels cirop; anti Harriman Springs is a former spawning site. Increased boat traffic, clevelopment, grounc~water pumping, or other activities may aciversely affect these sites. LESSONS FROM COMPARATIVE BIOLOGY OF SUCKERS Of the 63 species of suckers in the woricI, 61 are endemic to North America. Among the few known extinctions of freshwater fishes in North America, suckers figure prominently. Previously abundant, sometimes wicle- spreacI species have clisappearecI, inclucling the harelip sucker (Lagochila lacera) anti the Snake River sucker (Chasmistes muriei). Fully 35% of sucker species are imperilecI (Warren anti Burr 1994), and eight have fed- eral enciangerecI or threatened status (50 CFR 17.11 F199911. Populations of large suckers in general anti lake suckers in particular have cleclinecI largely because of anthropogenic factors. Although there is an obvious neecI for concern about these very American fishes, comparative ciata indicate that they can survive long periods of interrupted recruitment anti can recover from these remarkable hiatuses in reproduction if factors causing clecline are reclucecI. For example, clecline has occurred in other lake suckers: cui-ui experienced no known recruitment from 1950 to 1969; lune suckers hacI experienced at least 15 yrs without recruitment by the micicIle 1980s, anti that probably continued into the l990s; some populations of razorback suckers (Xyrauchen texanus) experienced 20-30 yr without re- cruitment; anti Utah suckers (Catostomus ardens) did not reproduce suc- cessfully between the micicIle 1960s anti the early 1990s.

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 247 Despite extenclecI interruptions in breeding, several species of suckers have responclecI successfully to recovery programs. Cui-ui successfully spawn in the Truckee River because of enhanced flows ancI are propagated in a hatchery managed by the Paiute Tribe, from which they are regularly trans- plantecI into Pyramid Lake, where they are abundant (USFWS 1992b). Ef- forts to promote recovery of lune suckers have been uncler way since the early l990s anti appear to have been successful; they inclucle water-allocation agreements, refuge-population establishment, ancI captive breeding ancI re- lease (USGS 19981. The robust rec~horse, Moxostoma robustum, a large sucker thought to have undergone population cleclines in Atlantic slope cirain- ages, is now propagated anti plantecI anti has shown successful recaptures in three southeastern rivers (Jennings et al. 1998; C. lennings, U. S. Geological Survey, Athens, Georgia, personal communication, 20021. An extensive re- covery program for razorback suckers instituted in 1988 inclucles captive rearing anti transplantation, habitat acquisition ancI protection, ancI control of nonincligenous species; success has been mixed (Minckley et al. 1991, Mueller ancI Marsh 19951. This general picture of clecline, public concern, multifacetecI efforts at recovery, anti evidence of success can suggest actions that might be successful with the I(lamath basin sucker species. All four living lake suckers (shortnose sucker, Lost River sucker, cui-ui, anti rune) are relatively large anti long-livecI (Chapter 51. High tolerance of poor water quality implies that the fishes evolvecI in habitats that periocli- cally experience extremes of water quality. Long life in these suckers may reflect an evolutionary history that incluclecI harsh conditions that often resultecI in reproductive failure, perhaps for many consecutive years. Excep- tional longevity is a cause for optimism in that it allows the fish to recover from population cleclines once conditions favorable to survival are restored (Scoppettone anti VinyarcI 1991). Age distributions in Upper I(lamath Lake suckers, as refiectecI in the fish- kill data, show apparent resilience in I(lamath species (e.g., Cooperman anti Markle 20031. Heavy fishing pressure resultecI in low numbers of oicI suckers until 1987, when the fishery was eliminatecI. Numbers of aclults later increased sharply (Figure 5-41. The rapicI increase demonstrates the positive effect of closing the fishery. More important, the increase shows that even after pro- longecI population cleclines brought about by overfishing, a relatively small number of large, highly fecund inclivicluals can produce many young anti help to restore a population (Cooperman ancI Markle 20031. Even slight improve- ments in conditions favorable to suckers in Upper I(lamath Lake, its tributar- ies, anti surrounding water bodies couicI contribute to recovery. CONCLUSIONS Despite elimination of fishing for the shortnose anti Lost River suckers in 1987, these two listecI species have failecI to show an increase in overall

248 FISHES IN THE KLAMATH RIVER BASIN abundance. Apparently stable populations with regular recruitment ancI the presence of all life-history stages at appropriate abundance are found only in Clear Lake ancI Gerber Reservoir. Thus, the listecI suckers at these two locations require special degrees of protection, both in the lakes themselves ancI in tributary waters where the suckers spawn. The two listecI suckers are present in Upper I(lamath Lake, where they reproduce ancI show the full spectrum of age classes indicating successful maturation of at least some inclivicluals. This population has not increased in abundance, however, because of episodes of mass mortality affecting large fish ancI possibly other factors as well. Populations at other locations (the main-stem reservoirs, the main stem of the Lost River, ancI Tule Lake) are of very low abundance ancI consist primarily of aclults; no full represen- tation of age classes is present at these locations. Suckers have been elimi- natecI entirely from the micicIle portion of the main stem of the Lost River, from Lower I(lamath Lake, ancI from Lake of the Woocis. Small irrigation clams ancI the larger Chiloquin Dam across the main stem of the Sprague River impede the movement of suckers attempting to spawn in the tributaries to Upper I(lamath Lake. Elimination of Chiloquin Dam couicI greatly expand any potential spawning area, although channel ancI riparian improvements to the upper Sprague might be necessary to achieve the full benefit of clam removal. Spawning of suckers in tributaries to Upper I(lamath Lake is successful in producing fry, but the spawning areas clo not receive special protection ancI are poorly stucliecI. Physical restoration of tributary spawning areas is a matter of high priority anti will involve exclusion of livestock anti other measures clesignecI to promote conditions that favor spawning of the suck- ers. Physical restoration near the mouth of the Williamson River as it enters Upper I(lamath Lake is also important. Water level in Upper I(lamath Lake shows no relationship to water- quality conditions that result in mass mortality of aclult suckers or other potentially adverse water-quality conditions. In aciclition, water level shows no relationship to year-class strength or to abundance of fry or juveniles over the years cluring which stanciarclizecI sampling is available. Thus, main- tenance of water levels above recent historical levels in orcler to increase the abundance of suckers by maximizing the area of habitat where young suckers are founcI is not supported by the currently available evidence. Water levels lower than recent historical levels couicI have unclocumentecI adverse effects ancI therefore are inacivisable. Experimental maintenance of specific water levels couicI be incorporated into a management plan, how- ever, through agreements between USFWS ancI USER, if USFWS sees merit in further studies of water-level control. The two listecI suckers spawn in specific lakesicle areas of Upper I(la- math Lake, typically in association with the presence of springs. Some

DECLINE AND RECOVERY OF KLAMATH BASIN SUCKERS 249 spawning areas have been abanclonecI entirely, possibly because of the elimi- nation, through fishing, of specific groups of fish that habitually used these areas. Some spawning areas show signs of anthropogenic clegraciation. Se- lective restoration of these areas anti manipulation of stocks to encourage bonding of specific groups of suckers to the unused sites couicI be beneficial in spreading the reproductive risk of the sucker populations. Suckers of all ages in Upper I(lamath Lake historically have been en- trainecI into the A Canal, which is the main supply conduit for USBR's I(lamath Project. Screening of this source of mortality is scheclulecI for summer of 2003, but it cannot be expected to prevent mortality of very small fish. Refinement of the operation of the screens as recommenclecI by USFWS (2002) might recluce the mortality of very young fish. The Link River Dam intake units remain unscreened, ancI thus remain a source of mortality for fish of all ages. Suckers of Upper I(lamath Lake ancI at other locations where suckers are present in the upper basins share their habitat to varying degrees with nonincligenous species, some of which are known to prey upon or compete with young suckers. Elimination of nonincligenous species over very large systems such as Upper I(lamath Lake is beyond the current state of the art, but programs clesignecI to prevent aciclitional introductions ancI prevent the spreacI of presently nonincligenous species wouicI be highly acivisable. Be- cause the actual effect of the nonincligenous species on the suckers is poorly known, it is clifficult to jucige the importance of this factor basecI on current . , . Information. Hybridization among sucker species was an original concern of consicI- erable importance to the listing of the suckers. Subsequent studies have reclucecI the level of this concern, but it wouicI be acivisable to have more information on the genetic identities of suckers at various locations in the upper basin. Captive propagation is a possibility ancI couicI be concluctecI on a pat- tern that has been clevelopecI for populations of relatecI suckers at other locations. Captive propagation is probably clisacivantageous at present, however, in that it tencis to undermine incentives for return of the popula- tions to a self-sustaining basis, which may still be possible in the I(lamath basin. Continued clecline of the population sizes or loss of any major sub- populations wouicI indicate a neecI for captive propagation. The long life-history of suckers requires extenclecI observation as a means of judging population trencis. Benefits of restoration actions will not necessarily be evident until the fish benefiting from these actions have achieved spawning capability. Similarly, the negative effects of mortality focused on large fish may become evident only graclually, but couicI extin- guish entire subpopulations.

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In 1988 the U.S. Fish and Wildlife Service listed two endemic fishes of the upper Klamath River basin of Oregon and California, the sucker and the Lost River sucker, as endangered under the federal Endangered Species Act (ESA). In 1997, the National Marine Fisheries Service added the Southern Oregon Northern coastal California (SONCC) coho salmon as a threatened species to the list. The leading factors attributed to the decline of these species were overfishing, blockage of migration, entrainment by water management structures, habitat degradation, nonnative species, and poor water quality.

Endangered and Threatened Fishes of the Klamath River Basin addresses the scientific aspects related to the continued survival of coho salmon and shortnose and Lost River suckers in the Klamath River. The book further examines and identifies gaps in the knowledge and scientific information needed for recovery of the listed species and proves an assessment of scientific considerations relevant to strategies for promoting the recovery of those species.

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