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2 EVALUATION OF THE BIOLOGICAL OPINION ON SHORTNOSE AND LOST RIVER SUCKERS

Populations of the shortnose and Lost River suckers currently are present within Upper Klamath Lake on the north side of the Klamath River drainage and within Clear Lake (which operates as a reservoir) and Gerber Reservoir on the Lost River to the southeast ( Figure 1). Small groups of individuals, some or all of which may be nonreproducing, are found elsewhere in the Klamath River drainage, including Tule Lake sump (USFWS 2001). Conditions in the lakes are relevant to the USFWS biological opinion because of its proposals for minimum lake levels that are intended to reduce mortality and improve spawning success, recruitment (addition of new individuals to the population), growth, and condition of the suckers.

The population sizes of endangered suckers in Upper Klamath Lake and elsewhere within the Klamath Basin are uncertain, but the abundances of these populations, which once were large enough to support commercial fisheries, are much lower than they were when agricultural development and water management began. Unfortunately, quantitative estimates of population sizes are not available. During the 1980s, qualitative evidence indicated that declines might have reduced the sucker populations in Upper Klamath Lake to just a few thousand old (greater than 10 years) fish (USFWS 1988). More recent estimates that were made possible incidentally by episodes of mass



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Page 11 2 EVALUATION OF THE BIOLOGICAL OPINION ON SHORTNOSE AND LOST RIVER SUCKERS Populations of the shortnose and Lost River suckers currently are present within Upper Klamath Lake on the north side of the Klamath River drainage and within Clear Lake (which operates as a reservoir) and Gerber Reservoir on the Lost River to the southeast ( Figure 1). Small groups of individuals, some or all of which may be nonreproducing, are found elsewhere in the Klamath River drainage, including Tule Lake sump (USFWS 2001). Conditions in the lakes are relevant to the USFWS biological opinion because of its proposals for minimum lake levels that are intended to reduce mortality and improve spawning success, recruitment (addition of new individuals to the population), growth, and condition of the suckers. The population sizes of endangered suckers in Upper Klamath Lake and elsewhere within the Klamath Basin are uncertain, but the abundances of these populations, which once were large enough to support commercial fisheries, are much lower than they were when agricultural development and water management began. Unfortunately, quantitative estimates of population sizes are not available. During the 1980s, qualitative evidence indicated that declines might have reduced the sucker populations in Upper Klamath Lake to just a few thousand old (greater than 10 years) fish (USFWS 1988). More recent estimates that were made possible incidentally by episodes of mass

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Page 12 mortality suggest, however, that the populations are considerably larger than they appeared to be in the 1980s, and that some recruitment to the adult age classes has occurred in most or all years of the last decade (see below). Population sizes might range from a few tens of thousands to the low hundreds of thousands (USFWS 2001) but still are much lower than they were originally. Aside from the decline in abundance over the long term, other indications of problems within the sucker populations include absence of spawning at a number of sites historically used for spawning, apparent increase in mass mortality of adults (“fish kills”), and weak recruitment in most years (USFWS 2001). The water quality of Upper Klamath Lake has changed substantially over the past several decades. The lake appears to have been eutrophic (rich in nutrients and supporting high abundances of suspended algae) prior to any anthropogenic influence (Kann 1998). Mobilization of phosphorus from agriculture and other nonpoint sources (Walker 2001), appears, however, to have pushed the lake into an exaggerated state of eutrophication that involves algal blooms reaching or approaching the theoretical maximum abundances. In addition, algal populations now are strongly dominated by the single blue-green algal species Aphanizomenon flos-aquae (cyanobacteria) rather than the diatom taxa that apparently dominated blooms before nutrient enrichment (Kann 1998, Eilers et al. 2001). Evidence indicates that changes in the water quality of Upper Klamath Lake have increased mass mortality among adult suckers. Under certain conditions, the bottom portion of the water column in the lake develops oxygen depletion, either no oxygen (anoxia) or lower than normal oxygen levels (hypoxia), and accumulates high concentrations of ammonia. Mixture of those bottom waters with the surface waters under the influence of changes in the weather likely causes mass mortality (Vogel et al. 2001). Although mass mortality has been recorded over the observed history of the lake, its frequency appears to have increased (Perkins et al. 2000). Major incidents were recorded for 1995, 1996, and 1997; low dissolved oxygen appears to have been the direct cause of mortality in these years (Perkins et al. 2000). Impaired water quality also might stress fry through high pH in surface waters resulting from high rates of photosynthesis, although exposures to the highest pH probably are too brief to cause mortality (Saiki et al. 1999). In addition, the present trophic state of the lake potentially poses a threat of mortality in winter, when anoxia can occur under the ice if oxygen demand is high. Although not yet observed, winter mortality could occur in the future (Welch and Burke 2001). Factors of concern other than water quality include the presence of exotic species capable of inducing types of predation and competition that are

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Page 13 evolutionarily foreign to these endemic species. Hybridization occurs but the degree of threat associated with it is unknown; the native suckers probably showed some interbreeding prior to human intervention (Markle et al. 2000). In addition, access of the suckers to historically significant spawning areas has in many cases been blocked or the spawning areas themselves have been physically degraded to such an extent that they cannot serve their former roles (USFWS 2001). Overfishing or habitat degradation might have eliminated portions of the population that were using specific spawning areas and although fishing no longer occurs, these subpopulations cannot be regenerated without manipulation of existing stocks in combination with habitat restoration. Suckers of all sizes are entrained by water-management structures (USFWS 2001). Although screening of these structures has long been recognized as an important means of reducing mortality of the endangered suckers, it has not yet been accomplished. Also, interaction of multiple stresses may increase vulnerability of the endangered suckers to disease, degrade their body condition, and cause them to show a high incidence of anatomical abnormalities. The USFWS biological opinion states that the Klamath Project contributes directly to mortality and adverse environmental conditions for the endangered suckers. On this basis, USFWS presents a reasonable and prudent alternative (RPA) consisting, in summary, of requirements for minimum lake levels, interagency coordination and adaptive management, screening to prevent entrainment of fish, creation of improved passage facilities, steps toward improvement of habitat and water quality, and additional studies. The RPA is intended to avoid jeopardizing listed species either directly or through adverse modification of critical habitat (50 CFR 402.02). With the exception of the recommendation on lake-level maintenance, there is good scientific or technical support for all the requirements listed in the RPA. Interagency coordination and adaptation of management are advisable, especially because the information base is evolving rapidly and because annual optimization of strategies for using water is an obvious need. Given the documented loss of suckers to entrainment and the blockage of their access to spawning waters at known locations (USFWS 2001), requirements of the RPA calling for mitigation of these problems also seems highly defensible. Potential for improvement of habitat and water quality must be viewed as incremental rather than comprehensive, but even incremental improvements offer the prospect of increasing the viability of the sucker populations and thus seem justified. Recommendations on water level are more difficult to evaluate, however.

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Page 14 Image: jpg ~ enlarge ~ • Dry Water Years, USBR proposed º Critical Dry Water Years, USBR proposed — Mean, 5 Dry Water Years, 1960–1998 –– Mean, 2 Critical Dry Water Years, 1960–1998 Δ USFWS Biological Opinion FIGURE 2 Overview of monthly levels for Upper Klamath Lake proposed by USBR through its biological assessment of 2001, USFWS through its biological opinion of 2001, and observed conditions for the years 1960–1998. Hydrologic categories used by USBR in its proposals (dry years or critical dry years) are explained in the text. Mean depths, excluding wetlands, corresponding to water levels are approximately as follows (feet): 4,137=3.5; 4,138=4.0; 4,139=4.8; 4,140=5.7; 4,141=6.6; 4,142 =7.6 (Welch and Burke 2001). Figure 2 shows the water levels given by USFWS in its RPA (2001) as well as two other lake-level regimes (USBR recommended and historical). The USFWS requirements are given as absolute minimums (i.e., they do not vary from one type of water-level year to another). In contrast, assessment

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Page 15 proposals of the USBR are framed for categories of water-level year. Categories shown in Figure 2 are characterized as critically dry (lowest 4%) and dry (approximately 12% of years just wetter than the critically dry ones). The span of lake level records that the USBR chose to use in its analysis (1960–1998) reflects the full interval of operations for the completed Klamath Project. Even earlier records are available, extending back to the creation of Link River Dam in 1919 ( Figure 3), but the interval between 1919 and 1960 would not be typical from the viewpoint of current project operations. Records prior to 1919, extending back to 1905, also are available ( Figure 3); they show higher maximum and minimum lake levels than have been typical of Upper Klamath Lake since closure of the dam. In addition, operation of the Klamath Project has created a higher amplitude of intraannual variation in lake level and a change in seasonality of intraannual change in lake level as compared with the original condition of the lake (USFWS 2001, III. 2., page 38). While the operating interval between 1960 and 1998 is very useful for judging the degree of variability that can be expected in lake levels over a long period of years with the Klamath Project in place, the possibility for use of lake-level data in environmental analysis is limited to a much shorter interval. Interaction between lake level and environmental variables or indicators of the welfare of the endangered fish is dependent on concurrent information for lake level, environmental conditions, and fish. While information of a sporadic or anecdotal nature is available over as much as 100 years, routinely collected data on environmental characteristics and fish are available only since 1990 or later. Thus, while the long-term lake level record seems to invite statistical analysis of the welfare of fish in relation to lake level, the information at hand is actually limited to a period often years or less. This limitation explains the focus of this report and of the USFWS biological opinion on data extending over approximately the last ten years. All three lake-level regimes (USFWS RPA, USBR recommended and historical) reflect seasonality that is partly inherent in the runoff reaching Upper Klamath Lake and partly a by-product of water withdrawals. The degree of seasonality in the USFWS RPA is considerably lower, however, than the seasonality of the other two regimes depicted in Figure 2, and minimum levels are highest overall for the USFWS RPA. The USBR proposed minimums are below the mean lake levels for the historical operating regime in each of the two dry-year categories, because the USBR used the lowest recorded monthly lake levels as its proposed minimums for each category. From the viewpoint of lake levels, water years are almost independent of each other because the lake has little capacity for interannual storage. The USBR proposal would allow more drawdown of lake level than has been characteristic in the past. Although the lake levels proposed by USBR

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Page 16 Image: jpg ~ enlarge ~ FIGURE 3 Historical record of level at the end of September for Upper Klamath Lake. Source: USBR. have been observed over the past 40 years, the use of these 40-year minimums as year-to-year minimums indicates that drawdown to the 40-year minimums would be possible in any year of future operations if USBR'S proposals were accepted. If USBR chose to operate the project by using greater average drawdown than has been observed over the past 40 years, the result would be substantially lower mean lake levels in each of the hydrologic categories. Control of lake levels as a means of advancing the welfare of the endangered suckers raises more difficult scientific issues than the other requirements listed by the USFWS in its RPA. The recommendation for water-level control is based on concerns related to habitat (shoreline spawning areas and emergent vegetation), and water quality (low oxygen in summer, need for deep-water refugia in summer and fall, and possibility of adverse conditions under ice cover). Impairment of water quality, primarily through eutrophication of Upper Klamath Lake, is a cause of mortality and stress for sucker populations. As indicated above, the present scientific evidence for this association is credible. An essential premise of the lake-level recommendations is that the adverse water-quality conditions known to stress or kill the endangered suckers are associated with the lowest water levels within the recent historical range of levels (since 1990, when consistent documentation first began). Presumption of this connection, which is essential to the arguments for specific lake levels

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Page 17 proposed in the RPA, is inconsistent with present information on Upper Klamath Lake. Control of phosphorus in Upper Klamath Lake offers the potential of suppressing population densities of algae, thus improving water quality in the lake (Welch and Burke 2001). No relationship between lake levels and population densities of algae (as shown by chlorophyll) is evident, however, in the 9-year water-quality monitoring record that has been fully analyzed ( Figure4). Thus, the idea of relieving eutrophication through phosphorus dilution caused by higher lake levels is not consistent with the irregular relationship between chlorophyll and lake level. Also, lake level fails to show any quantifiable association with extremes of dissolved oxygen or pH (see data presented by Welch and Burke 2001). For example, the most extreme pH conditions recorded for the lake over the past 10 years occurred in 1995 and 1996, which were years of intermediate water level, and not in 1992 and 1994, when water levels were lowest. (These two years had the lowest recorded water levels since 1950.) Furthermore, a substantial mass mortality occurred in 1971, the year of highest recorded water levels since 1950 (USFWS 2001), and within the last ten years, mortality of adults was highest in 1995, 1996, and 1997, none of which were years of low water level. The absence of notable adult mortality in any year of low water during the 1990s might in fact suggest an association the reverse of the one postulated in the biological opinion, although the evidence is statistically inconclusive. The USFWS itself has found no association of mass mortality with lake levels (USFWS 2001, III.2.70). Intensified eutrophication now affects the characteristics of the lake every year, and thus may constitute a threat to the suckers regardless of interannual variation in water level. Higher water levels are potentially supported on the grounds of improved survival of fry or juveniles rather than suppression of adult mortality. Higher water levels could reduce the likelihood that spawning areas around the lake would be dewatered and could be favorable to fry or juveniles. Abundance of juvenile suckers has been monitored since 1991 on the basis of seining (Simon et al. 2000a). This information, which must be used cautiously because it is not quantitative, indicates low abundances of juveniles in the drought years 1992 and 1994 but not in drought year 1991. Abundances also were low in non-drought years 1997 and 1998. Simon et al. (2000a) have reported generally declining abundance during the non-drought interval 1995–1998. They have also shown (Simon et al. 2000a, b) that the abundance of age 1+ suckers consistently has been very low, suggesting a bottleneck at this life stage, but interpretation of the data is complicated by very low effi

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Page 18 ~ enlarge ~ FIGURE 4 Relationship of chlorophyll a and median August lake level in Upper Klamath Lake between 1991 and 1998. Chlorophyll data are averages reported by Welch and Burke (2001). Recruitment and mortality data are from USFWS (2001). ciency for catching fish older than one year. Overall, the study of young fish shows no clear pattern associated with lake level. The most reliable current information on recruitment is through analysis of age-class structure of adult suckers (USFWS 2001, III. 2., page 43). This data record is not consistent with the underlying assumptions of proposals for maintenance of higher water levels. The strongest recruitment (as inferred from relative abundances of adult year classes) observed over the last ten years was for 1991 ( Figure 5), which falls within the lowest 15% of lake levels since 1950. Furthermore, as shown by the continuing strength of the 1991 year class in 1995 and beyond, the year class showed good survival through the dry years of 1992 and 1994. While the use of emergent vegetation by fry is cited as a reason for maintaining high water levels, the combination of high recruitment in 1991 and low recruitment in other years (as inferred from year class data) casts doubt on the importance of this factor, at least within the operating range of the 1990s. Overall, the presumed causal connections between lake levels and recruitment of the sucker populations in Upper Klamath Lake do not have strong scientific support at present.

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Page 19 Image: jpg ~ enlarge ~ FIGURE 5 Estimated age frequency distributions using opercles from Lost River suckers and shortnose suckers collected from 1997 fish kill in Upper Klamath Lake, Oregon. Estimates did not include all suckers collected, but were calculated using only suckers from which a length measurement (fork length) was obtained. Data are truncated from 1987 to 1994, additional information exists on other year classes of suckers. Source: USGS, unpublished data, 2001. Mortality possibly could be caused by multiple factors that interact with lake level. For example, mortality of suckers is influenced by changes in water column stability; an extended period of stability leading to decline of oxygen near the bottom can be followed by sudden mixing of the entire water column associated with a change in weather (high wind velocity). Thus, interpretation of information on lake level is complicated by the influence of weather. There is no evidence as yet, however, that the significance of undesirable mixing events is higher when lake levels are low than when they are high. As a result, mixing as a cause of water quality conditions leading to mortality cannot be interpreted at this time in terms of lake level. Despite a monitoring record of substantial length, there is no clear evidence of a connection between the lake levels and the welfare of the two sucker species in Upper Klamath Lake. Lake levels cannot be reduced, how

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Page 20 ever, below those observed in the past 10 years without risk of adverse occurrences that are not described in the detailed monitoring record (1990-present; analyses complete through 1998). A negative association between the welfare of the species and the lake level could emerge if lake levels are reduced below those of recent historical experience. The absence of any empirical connection between the observed lake levels and the welfare of the endangered suckers cannot be taken as justification for continuous or frequent operation of the lake at the lowest possible levels, given that the effects of operating the lake at lower levels are undocumented. Thus, while the observational record contradicts important underlying assumptions of the RPA, it does not provide an endorsement for the lake levels proposed in the USBR biological assessment, which, if implemented, could take interannual mean lake levels well below those of recent historical observation. The potential benefits of higher lake levels in Clear Lake, Gerber Reservoir, and Tule Lake sump are more difficult to evaluate, because the record of analysis and observation for these water bodies is not as extensive as that for Upper Klamath Lake. These lakes have not suffered notable mass mortality in association with low lake levels, but Clear Lake populations showed poor body condition following severe drawdown in the early 1990s. The USFWS provides reasonable support for lake levels in Clear Lake no lower than the recent drought-related minimum (1992–1993:4,519 feet). The RPA reasonably adds a margin of two feet (4,521) to allow for water loss in the absence of withdrawals under drought conditions.