EFFECTS OF LOWERED FISHWAY WATER VELOCITY ON FISHWAY ENTRANCE SUCCESS BY ADULT PACIFIC LAMPREY AT BONNEVILLE DAM,

Technical Report 2010-4-DRAFT IDAHO COOPERATIVE FISH AND WILDLIFE RESEARCH UNIT EFFECTS OF LOWERED FISHWAY WATER VELOCITY ON FISHWAY ENTRANCE SUCCESS BY ADULT PACIFIC LAMPREY AT BONNEVILLE DAM, 2007-2009 Eric L. Johnson, Christopher C. Caudill, Tami S. Clabough, Matthew L. Keefer, and Michael A. Jepson University of Idaho Fish Ecology Research Laboratory Department of Fish and Wildlife And Mary L. Moser Northwest Fisheries Science Center NOAA Fisheries 2725 Montlake Blvd Seattle WA, 98112 For U.S. Army Corps of Engineers Portland District 2010

Acknowledgements Many people provided assistance for this study. M. Morasch, T. Dick, K. Tolloti and C. Morat installed and maintained radiotelemetry equipment. B. Ho, S. Lee and D. Queampts from the University of Idaho and H. Pennington, J. Roose, A. Batista and S. McCormick from the Pacific States Marine Fisheries Commission helped with field operations and data collection. B. Burke and K. Frick, National Marine Fisheries Service, provided database management. D. Joosten, University of Idaho, assisted with data management and interpretation. Funding for this project was provided by the U.S. Army Corps of Engineers, Portland District facilitated by D. Clugston. i

Table of Contents Acknowledgements... i Abstract... iii Introduction...1 Methods...3 Tagging and monitoring...3 Velocity modification...4 Entrance efficiencies and passage times...6 Data analysis...7 Results...9 Trapping, tagging and general patterns in lamprey passage behavior...9 First approach and entry: PH1, PH2, and spillway entrances...9 Total approach and entry: PH1, PH2, and spillway entrances...12 Entrance efficiency: Non treatment times at PH1, PH2, and spillway entrances...13 Fishway entrance velocity test...14 switching...14 First approach and entry: PH2 north and south entrances combined...14 First approach and entry: PH2 north fishway...15 First approach and entry: PH2 south fishway...15 Total approach and entry: PH2 north and south entrances combined...15 Total approach and entry: PH2 north fishway...16 Total approach and entry: PH2 south fishway...16 Passage ratio of the lower fishway at PH2...22 General patterns in passage times...24 Time-to-event analysis of passage times...25 Discussion...30 Evidence of treatment effects on performance metrics...30 Evidence of treatment effects on passage rate...32 Effects of standby conditions...33 Comparison to previous study results...33 Conclusions...34 References...35 Appendix A...39 Appendix B...49 ii

Abstract Operating fishways for multiple species is challenging because swimming ability differs among species and because many fishways were initially designed for commercially important species. Adult Pacific lamprey (Lampetra tridentata) do not easily enter fishways at Bonneville Dam and evidence from experimental fishway studies suggest that the high water velocities intended to attract adult salmonids can impede lamprey entry. In 2007-2009, we evaluated whether reduced water velocities (target of 1.2 m sec -1 ; 0.15 m of head) at the Bonneville Dam Powerhouse 2 (PH2) fishway openings improved entrance efficiencies and other passage performance metrics for radio-tagged adult lampreys compared to control water velocities (target of > 1.98 m sec -1 ; 0.46 m of head). We additionally evaluated potential effects of fishway velocities being reduced to near zero (i.e., standby mode when debris was floated off the trash racks) near fishway water intakes. Lampreys are primarily nocturnal and fishway velocities were manipulated only at night (~2200 h to 0400 h) to minimize potential negative effects on adult salmonid passage. Comparison of reduced, standby, and control velocities at PH2 fishway openings indicated that the reduced velocity treatment improved lamprey entrance efficiency (entrance:approach ratio) for tagged lampreys (PH2 north and south entrances combined). Entrance efficiencies (all entries and approaches pooled) were significantly different among treatments: 26-29% at reduced velocity, 13-20% at control velocity and 5-9% with standby conditions (P < 05). However, site-specific entrance efficiencies indicated significant improvements at PH2 north openings (P < 5) but not PH2 south openings (P = 0.11) in both years that the reduced velocity treatment was applied. The number of radio-tagged fish that approached PH2 openings per hour (approach rate) was consistently higher during the reduced-velocity treatments, suggesting that there was sufficient flow to attract adult lampreys. Entrance efficiencies and net numbers of entries suggested that operating the fishway units in standby mode negatively affected lamprey entry into PH2 fishway openings. Entrance efficiencies during the standby treatment were significantly lower than those during control or reduced velocity treatments (P < 05), with the exception between control and standby treatment in 2007 (P = 0.14). Cox proportional hazards regression models indicated that the rate of entry to PH2 fishways was highest during treatment periods (approach to entrance passage times were shortest) and that both treatment and control periods had higher passage rates than standby conditions. The combined 2007-2009 results suggest that some reduction in entrance velocity helped lampreys enter fishways, while zero attraction flow was probably a deterrent. Benefits of the reduced velocity treatment were variable across sites and years, suggesting further refinements may be possible. iii

Introduction Populations of adult Pacific lamprey Lampetra tridentata in the Columbia River basin have declined steeply from historic levels (Close et al. 2002). Lamprey abundance, based on adult counts at hydroelectric dams has decreased four-to ten-fold during the past 40 years and declines have been especially evident in the interior basin (Close 2001). Daytime counts of adult Pacific lampreys at Bonneville Dam reached a record low in 2009 (Figure 1). As a result of these declines, petitions were recently submitted to list Pacific lamprey under the U.S. Endangered Species Act (USFWS 2004). Federal, state, and tribal agencies are currently drafting and/or implementing lamprey management plans (e.g., USACE Pacific Lamprey Passage Improvements Draft Implementation Plan: 2008-2018). Decreases in lamprey populations appear to be related to poor upstream migration performance at dams by adults, poor quality of spawning habitat, low emigration survival past dams as juveniles, and other factors including unfavorable ocean conditions and increased marine mammals predation rates (Mesa et al. 2003). Hydroelectric dams that can impede the upstream migration of adult Pacific salmon and steelhead (Oncorhynchus spp.) have also affected Pacific lamprey passage (Moser et al. 2002a, 2002b; Cummings 2007). Fishways at many dams in the Pacific Northwest were designed and are operated to facilitate passage by strong-swimming salmonids. These same fishways may not readily accommodate weaker, anguilliform swimmers like adult lampreys. Specifically, adult lamprey passage efficiencies at lower Columbia River dams are often < 50% (Moser et al. 2005; Keefer et al. 2009c) compared to adult salmon and steelhead passage efficiencies, which are typically > 90% (e.g., Keefer et al. 2004). Concerns about low lamprey passage efficiencies have led to recent development of passage structures specifically for Pacific lamprey (i.e., Lamprey Passage Structures [LPSs]) which have improved dam passage rates at the tops of Bonneville Dam fishways (Moser et al. 2006; in review). However, radiotelemetry and experimental fishway studies have shown that adult lampreys have difficulty entering fishway openings (Moser et al. 2002; Keefer et al. 2010a) and many may not reach LPS s. High water velocities at the entrances intended to attract adult salmonids and American shad (Alosa sapidissima) appear to restrict lamprey entry (Moser et al. 2002; 2005; Daigle et al. 2005). Fishway entrances often have water velocities that exceed 2.0 m sec -1, which are considerably higher than the critical adult lamprey swimming speed of 0.8 m sec -1 (Mesa et al. 2003), and are higher than velocities found to deter lamprey passage in experimental studies (> 1.2 m sec -1, Keefer et al. 2008). Delays in passage and the physiological fatigue experienced during fishway entry may be associated with a host of consequences that negatively affect upstream migration and spawning. Excess energy use or stress experienced by lampreys when using fishways could affect sexual maturation, disease susceptibility, and energetic budget (Mesa et al. 2003). These effects may be especially important because lampreys enter fresh water ~ 1 year before they spawn and they do not feed during their freshwater residency (Beamish 1980). Homing by lampreys has not been clearly demonstrated but if homing is a lamprey life history characteristic, it is plausible that strenuous swimming at passage obstructions may adversely affect lampreys ability to migrate 1

upstream, which may result in lampreys attempting to spawn in tributaries downstream from natal streams. Adult lampreys are predominantly nocturnal when passing dams during upstream migration (Moser et al. 2002; Daigle et al. 2005; Keefer et al. 2009a, 2009b). In contrast, salmon, steelhead, and shad pass primarily during the day (Keefer and Caudill 2008). These diel behaviors provide a unique opportunity to manipulate fishway operations to better accommodate multiple species with differing morphology, behavior, and swimming abilities. The primary objective of this study was to evaluate effects of reduced nighttime water velocity at fishway entrances on the entrance success and behavior of radio-tagged adult Pacific lampreys at Bonneville Dam, the first Columbia River dam adults encounter during upstream migration. Over three years, we monitored lamprey behavior during an experimental manipulation of fishway operations at Bonneville s Powerhouse 2 (PH2) to determine if the modified operation contributed to improved lamprey passage success. At night, velocities at fishway entrances were reduced using a randomized block design. Constraints on fishway operations resulted in three velocity treatments: control, treatment (two years) and a standby condition used to maintain fishway operational criteria. Specifically, we evaluated: 1) approach rates, 2) entrance efficiencies, 3) entrance times, 4) fishway retention, and 5) dam passage times for radio-tagged lampreys that approached and entered during each of three fishway velocity treatments. 400 Daytime Counts (1000's) 300 200 100 0 1940 1950 1960 1970 1980 1990 2000 2010 Figure 1. Historic counts of adult Pacific lamprey at Bonneville Dam (adapted from US Army Corps of Engineers Annual Fish Passage Reports, 1969, 1998 to 2003, and DART 2009, http://www.cbr.washington.edu/dart/dart/html). Lampreys were not enumerated during the period 1970-1997. 2

Methods Tagging and monitoring During June through August 2007-2009, we captured and radio-tagged 1,589 adult Pacific lampreys at Bonneville Dam (Table 1). Lampreys were captured at night using two traps in the Washington-shore fishway and a trap at the Washington-shore fishway entrance (see Moser et al. 2007). Trapping at night likely increased capture efficiency, because lampreys are more active during low light conditions (Almeida et al. 2002; Daigle et al. 2008). Night-time trapping also decreased the chance of interfering with adult salmonid passage and reduced salmonid smolt bycatch. Lampreys with a girth circumference > 9 cm (at the insertion of the first dorsal fin) were anesthetized in a 3 ml 50 L -1 solution of eugenol (the active ingredient in clove oil) until they lost equilibrium (Moser et al. 2002; Cummings 2007). Once under anesthesia, lampreys were placed ventral side up in a wetted, 12 cm diameter polyvinyl chloride (PVC) cradle with a sealed T-end. A portion of the pipe was cut away to allow access to the ventral surface of the animal for surgery. The PVC cradle and surgery tank was disinfected prior to use each day (15 min submersion in chlorinated water solution of 7.8 ml L -1 ). Sponges for the PVC cradle were replaced daily. Radio tags and surgical tools were sterilized in a solution of chlorahexaderm (7.8 ml L -1 ) and rinsed with de-ionized water before each use. A ~3 mm incision was made in the ventral side of the lamprey using a sterile scalpel slightly to one side of the ventral mid-line, aligned directly below the anterior edge of the first dorsal fin fold. A 14 cm long sterile catheter (Abbocath-T, Hospira Inc. Lake Forest, Illinois) was placed inside the body cavity and pushed through the musculature and skin creating a small hole approximately 5 cm posterior to the incision. The antenna of the radio tag was guided through the catheter until it emerged from the hole. The radio transmitter was then gently inserted into the intra-peritoneal cavity through the initial incision. A minimum of two simple, interrupted monofilament sutures were applied to close the incision (Ethicon 18, 3-0 coated vicryl braided sutures with a FS-2 cutting needle in 2007 and 2008 and Ethicon 27, 3-0 undyed monofilament sutures with a RB-1 cutting needle in 2009). In 2007, we used Lotek NTC-6-2 radio transmitters (30.1 mm length, 9.1 mm diameter, and 4.5 g in water) with a burst rate of 5 s and an expected tag life of 235 d (Lotek Wireless Inc. Newmarket, Ontario; Table 1). In 2008 and 2009, we used Lotek NTC-4-2L radio transmitters (18.3 mm length, 8.3 mm diameter, and 2.1 grams in water) with a burst rate of 8 s and an expected tag life of 127 d. Length (mm), weight (g), and girth (mm) were recorded for each tagged lamprey and we estimated muscle lipid content (% fat) of each with a non-invasive Distell fish Fatmeter (Distell Inc., West Lothian, Scotland). In 2008 and 2009, half of all lampreys were double-tagged with a half-duplex passive integrated transponder tag (HDX-PIT; 4 32 mm and 0.8 g, Texas Instruments, Dallas, Texas). After radio-tagged lamprey recovered from anesthesia (> 2 hrs, in aerated river water), they were released ~3 river kilometers (rkms) downstream from the dam in approximately equal proportions on both sides of the river (randomly assigned; Figure 2). Release sites were at Tanner Creek (Oregon shore, rkm 232.0) and the Hamilton Island boat ramp (Washington shore, rkm 232.3). 3

Radio-tagged lamprey movements were monitored using an array of fixed-site receivers at Bonneville Dam and in the tailrace. Radio receivers at Bonneville Dam were equipped with digital spectrum processors (DSP s) to receive transmissions on multiple frequencies simultaneously. Radio receivers coupled with a scanning receiver and one or more underwater coaxial cable antennas were positioned at fishway entrances and inside fishways to detect fish as they approached a fishway entrance, entered a fishway, moved within a fishway, and/or exited a fishway. Telemetry data were downloaded from receivers weekly. Details of the telemetry array are given in Keefer et al. (2009a) Table 1. Radio transmitter specifications and the numbers of adult Pacific lampreys collected and radio-tagged at Bonneville Dam in 2007-2009, with mean lamprey length (SD) weight (SD), and girth (SD) at the insertion of the first dorsal fin. Variable 2007 2008 2009 Tag type NTC-6-2 NTC-4-2L NTC-4-2L Tag specification 30.1 9.1 mm 18.3 8.3 mm 18.3 8.3 mm Tag life 235 d 127 d 127 d Number tagged 398 595 596 Number trapped 1,155 1,204 964 Mean length (cm) tagged 65.7 (5.8) 66.1 (4.2) 66.8 (4.3) Mean length (cm) trapped 64.7 (5.5) 64.6 (4.7) 65.3 (4.6) Mean weight (g) tagged 466 (95) 464 (79) 473 (89) Mean weight (g) trapped 444 (98) 434 (89) 442 (92) Mean girth (cm) tagged 11.0 (0.9) 10.9 (0.8) 11.0 (0.9) Mean girth (cm) trapped 10.9 (0.9) 10.6 (0.9) 10.8 (0.9) Mean girth to Tag ratio 1 25.8 (2.1) 23.1 (1.9) 22.9 (1.8) 1 Calculated as the Pacific lamprey diameter (at the insertion of the first dorsal fin) divided by the transmitter diameter. Velocity modification Water velocities through fishway entrances were estimated using differences in elevation (head) between the inside of the fishway (e.g., the collection channel) and the tailrace. The three target head levels were 0.45 m (control), 0.15 m (treatment), and m (standby), corresponding to mean entrance velocities of > 1.96, 1.2, and m sec -1, respectively. Changes in head at fishway entrances were achieved by altering operation of two smaller turbine units (fish units) located in PH2 that provide water to the fishway collection channel. Velocities were reduced to near zero by placing fish units on standby mode to float debris off of the fish unit trash racks. Head treatments (control and reduced velocities only) were alternated in a randomized block design (Figure 3) and standby conditions occurred intermittently during the season as required by operations guidelines. Changes to the operation of fish units occurred at night (typically between 4

2200 and 0400 hrs) to minimize potential effects on adult salmonid passage. Changes from control head levels (0.45 m head) to treatment levels (0.15 m head) generally took < 15 min at the four main PH2 entrances. Two entrances at Powerhouse 1 (PH1) and two openings adjacent to the spillway (Figure 2) were run under control conditions throughout the experimental period; higher velocities were always available for tagged lampreys to use during periods when the reduced velocity treatment was applied at PH2 exclusively. Figure 2. Map of Bonneville Dam showing release locations (solid squares) and primary fishway entrance locations. Water velocities were manipulated at two openings each at Powerhouse 2 north (PH2 N) and Powerhouse 2 south (PH2 S). Normal velocities were always available at Powerhouse 1 (PH1) and at the Bradford Island and Cascades Island fishways adjacent to the spillway. 5

Normal Standby Normal Standby Normal Standby 1 June 1 July 1 Aug. 1 Sept. 1 Oct. Date Figure 3. Velocity modification treatments tested at PH2 fishways at night (approximately 2200 0400 hrs) from 1 June through 1 October in 2007 (open symbols), 2008 (gray symbols) and 2009 (black symbols). The sequence of one-day, low-velocity treatments within two-day periods was randomized. Periodically, fish units were placed on standby for minutes to hours on some nights to float debris off of trash racks, resulting in little to no flow at fishway entrances. Note reduced velocity treatments were not performed in 2008. Entrance rates, ratios and passage times We evaluated lamprey passage behavior for each treatment using two types of metrics: entrance rate and ratios (e.g., entrance efficiency) and estimates of passage time. Rates were calculated at events / unit time where units were approaches, entries, and exits. We calculated lamprey entrance efficiencies as the total number of lampreys that successfully entered a fishway entrance divided by the total number that approached that same entrance. To test for treatment effects, entries that occurred during a different treatment than the approach treatment were discarded, and consequently the estimated effect sizes may be conservative. Lampreys that approached a fishway entrance but did not enter during a treatment were included in the percent unsuccessful. Entrance efficiencies for the velocity experiment were calculated from 2200 to 0400 hrs for all approaches and entries pooled at each fishway entrance (i.e., total efficiency) as well as for only first approaches and entries. Note that entrance efficiencies reported here for 2007 differ slightly from those reported in Johnson et al. (2009) because dam operations (i.e., times when fish units were on standby to float trash of fish unit trash racks) were unknown at the time of that reporting. For this study, we also calculated the net number of entries (net entry ratio) by subtracting the total number of exits at each site. The net number of entries was divided by the total number of entries and multiplied by 100 to obtain a percent. The ratio was 6

calculated using all unique fishway entries and exits that occurred during a single treatment (control, reduced velocity, standby) at each fishway entrance site. We were also interested in examining how fish behavior at the site of the treatment (PH2 entrances) affected passage through the collection channel from PH2 south entrances, transition pool and into the weired section of the fish ladder. We examined individual telemetry records for all radio-tagged adults entering PH2 N and PH2 S entrances and classified each as having passed the transition pool and lower ladder, as indicated by detection on a series of antennas above the transition pool (receiver NBO). The data were used to test whether the frequency of successful approach to NBO differed among treatments using chi-square (χ 2 ) tests. For the fishway velocity experiment, passage times for radio-tagged lampreys were calculated for four segments at Bonneville Dam: (1) the time from release to first approach a fishway, which was categorized by treatment encountered during approach; (2) the time from first fishway approach to first fishway entry, defined as the time between the first detection at an antenna along the outside of a fishway entrance to the first detection on the inside of a fishway entrance, for those fish approaching and entering same entrance during same treatment; (3) the time from first fishway entry to transition pool entry, defined at the first detection at a antenna inside of a fishway entrance to the first detection at a antenna near the fish ladder-tail water interface; and (4) total dam passage time, calculated from the first record on an antenna inside the fishway entrance to the last record at a top-of-ladder site. comparisons for first entry to transition pool and total dam passage time metrics were categorized by treatment condition encountered at time of entry. Again, classification of passage time by treatment was problematic because individual lampreys could experience more than one treatment (see Caudill et al. 2006 for a parallel example), and any treatment effects would likely be underestimated for fish taking longer than a day to pass the dam. Cox proportional hazards regression (PHReg; Hosmer and Lemeshow 1999) circumvents this problem, as explained below. Data analysis We used two statistical approaches to test for treatment effects on lamprey behavior and entrance efficiency. First, we tested for differences in the frequencies of fish passing under each of the three treatment conditions (reduced velocity, control, and standby) using chi-square (χ 2 ) tests. Entrance efficiencies among Bonneville velocity treatments were compared using Pearson s χ 2 tests. We used a Yates continuity correction to adjust computed χ 2 values to compensate for one degree of freedom (Zar 1999). Traditional ANOVA approaches were not appropriate for estimating effects on passage time because fish frequently encountered more than one treatment condition. Therefore, we used proportional hazards regression (PHReg, SAS 2008), a form of time-event analysis (Fox 1993; Allison 1995; Hosmer and Lemeshow 1999; Castro-Santos and Haro 2003), which explicitly incorporated the temporal changes in treatments and other environmental covariates. For example, some lampreys were detected at underwater antennas outside a fishway but not detected inside the fishway until the fishway treatment had changed ( switching, Caudill et al. 2006). PHReg is semi-parametric, and differs considerably from typical linear models where the 7

mean response of the population is of interest. PHReg estimates the probability or hazard of an event, such as the passage of a dam segment by an individual, occurring within a small time interval, given: 1) the event had not occurred prior to the time interval, and 2) a set of predictor variables (covariates) such as spill level, water temperature, or treatment at the beginning of the time interval. The probabilities of passage are expressed as hazard or odds ratios, and are familiar from the outcomes of medical trials. We modeled passage hazard in relation to changes in fishway flow while statistically accounting for variation in other environmental factors and fish traits. We tested for treatment effects on passage hazard using a model that included the time-varying covariates of time of day, velocity treatment, water temperature, and river discharge (Figure 4). We tested for treatment effects using a categorical variable coding the treatment as either control, reduced, or standby as outlined above. Temperature was included as a covariate because of its known effects on fish energetics and behavior (e.g., Brett 1995) including lamprey migration speed (Keefer et al. 2009c). We also included lamprey length as a fish trait because length was positively associated with passage success in a larger analysis (Keefer et al. 2009c). Hourly spill, discharge, and temperature data were downloaded from the Columbia River Data Access in Real Time archive (DART 2007-2009). Results Trapping, tagging and general patterns in lamprey passage behavior A total of 1,589 adult lampreys were radio-tagged and released during the three study years, with 769 (48%) at Tanner Creek and 820 (52%) at the Hamilton Island boat ramp. Mean lamprey size was similar among years, but the tag-to-lamprey girth ratio was lower in 2008 and 2009 than in 2007 as a result of using smaller diameter transmitters in the later two years. Median time in anesthesia (total surgery time) ranged from 9:50 (2008) to 10:46 (2007) min. Annual percentages of released lampreys recorded at Bonneville Dam fishway antennas ranged from 68% in 2007 to 79% in 2009. Annual percentages known to have passed the dam ranged from 21% (2007) to 31% (2009) (Table 2). The annual percentages of lampreys tagged that first approached the dam where site and location were known ranged from 65% (2007 and 2008) to 75% (2009) and the percentages of all tagged fish that first entered a fishway where site and location was known ranged from 32% (2008) to 43% (2007 and 2009). First approach and entry: PH1, PH2, and Spillway entrances Across years, the majority of lampreys made their first approach and first entrance at PH2 fishway openings followed by PH1 and the spillway (Figure 5). At PH2, lamprey used the PH2 south openings more than the PH2 north openings. The percentages of lampreys that entered the same fishway as they first approached were 61-92% at PH1 fishways, 33-55% at PH2 north fishways, 67-75% at PH2 south fishways and from 67-88% at the spillway (see Table 3 for details on PH2 fishways). 8

Discharge (kcfs) 500 400 300 200 100 A) 2007 2008 2009 0 250 B) 200 Spill (kcfs) 150 100 50 0 25 C) 20 Temperature (C) 15 10 5 0 10-May 30-May 19-Jun 09-Jul 29-Jul 19-Aug 09-Sep 29-Sep Date Figure 4. Mean daily total discharge (A), spillway discharge (B), and water temperature ( C) at Bonneville Dam from 10 May to 30 September, 2007-2009. 9

Table 2. Numbers of adult Pacific lampreys released downstream from Bonneville Dam and numbers and percentages of those released that were recorded in the tailrace and at dam fishways, that passed the dam, and that were recorded on their first approach at a fishway opening and first fishway entry. 2007 2008 2009 Passage metric n % n % n % Released 398 595 596 Recorded at tailrace 368 92.5 569 95.6 549 92.1 Recorded at dam 271 68.1 444 74.6 470 78.9 Known to pass dam 83 20.8 146 24.5 177 31.0 Recorded first fishway approach 1 260 65.3 385 64.7 444 74.5 Recorded first fishway entrance 1 169 42.5 190 31.9 254 42.6 1 only includes known time and location of approach and entry Table 3. Locations first fishway entry by radio-tagged lampreys, by the location of their first fishway approach site at PH2, 2007-2009. Lampreys that had known approach and entry locations but unknown approach and entry times were included. First First entry site All sites Approach PH1 Spillway PH2 Same approach site South North South North South North Total & entry 2007 PH2 S 1 1 4 0 41 8 55 74.5% PH2 N 0 1 7 2 41 25 76 32.9% 2008 PH2 S 1 2 3 1 44 15 66 66.7% PH2 N 1 3 10 6 51 38 109 34.7% 2009 PH2 S 0 1 3 2 56 20 82 68.3% PH2 N 0 1 7 6 54 82 150 54.7% Entrance efficiencies (treatment and non treatment hours combined) for first entrances were similar across all entrances, with the exception of PH2 north openings, which had much lower than average entrance efficiency in 2007-2008 (Figure 5). During the treatment hours (22:00-04:00), first entrance efficiencies were lowest at PH2 north entrances (range 1.8% - 10.5%) followed by PH2 south entrances (range 23.2% - 30.7%) and were highest at PH1 north entrances (range 64.3% - 66.7%; Table 4). Entrance efficiencies at south spillway entrances (Bradford Island) were 50% across years and those at the north spillway ranged from 33-62%. Across years, spillway entrance efficiencies were always higher than at PH2, generally higher than those at PH1 south entrances, but typically lower than PH1 north. 10

Proportion of first fishway approaches 0.5 0.4 0.3 0.2 0.1 A) 2007 2008 2009 Proportion of first fishway entrances 0.5 0.4 0.3 0.2 0.1 B) First fishway entry:approach efficiency 1.0 0.8 0.6 0.4 0.2 C) PH1 S PH1 N B-Branch Casc Is PH2 S PH2 N Unk Site Figure 5. Distribution of first fishway approaches (A) and first fishway entrances (B) recorded for radio-tagged adult Pacific lampreys at Bonneville Dam through 30 September, 2007-2009. Panel (C) shows entrance efficiency (entry/approach) by site (day and night combined). The unknown site (Unk) was for fish recorded in the transition pools at PH1 and PH2 without clear fishway approach and/or entry records. Note different y-axes. 11

Table 4. Distributions of first known fishway approach and entry events (top) and all known fishway approach and entry events (bottom) for radio-tagged lampreys, with the estimated entrance efficiencies during experimental periods (22:00-04:00). PH1 S = Powerhouse 1 south, PH1 N = Powerhouse 1 north, Spillway S = B-Branch Bradford Island, Spillway N = Cascade Island, PH2 S = Powerhouse 2 south, and PH2 N = Powerhouse 2 north. Sample sizes given in parentheses. First approaches 2007 PH1 S PH1 N Spillway S Spillway N PH2 S PH2 N Approaches 28 14 26 10 33 67 Entries 14 9 13 5 9 7 Exits 3 1 8 1 6 2 Efficiency 5% 64.3% 5% 5% 27.3% 10.4% 2008 Approaches 74 12 28 9 56 112 Entries 23 3 14 3 13 2 Exits 14 0 5 1 5 2 Efficiency 31.1% 25.0% 5% 33.3% 23.2% 1.8% 2009 Approaches 73 9 38 21 75 133 Entries 23 6 19 13 23 14 Exits 5 0 7 6 17 5 Efficiency 31.5% 66.7% 5% 61.9% 30.7% 10.5% All Approaches 2007 PH1 S PH1 N Spillway S Spillway N PH2 S PH2 N Approaches 46 (36) 25 (22) 76 (59) 19 (18) 435 (105) 430 (120) Entries 21 12 38 10 108 50 Exits 3 1 18 3 50 14 Efficiency 45.7% 48.0% 5% 52.6% 24.8% 11.6% 2008 Approaches 178 (103) 22 (20) 83 (71) 37 (31) 370 (160) 854 (216) Entries 53 10 34 9 76 47 Exits 21 1 12 1 21 13 Efficiency 29.8% 45.5% 41.0% 24.3% 20.5% 5.5% 2009 Approaches 109 (84) 27 (24) 110 (84) 82 (48) 554 (199) 842 (238) Entries 37 13 51 32 165 114 Exits 7 1 13 10 60 28 Efficiency 33.9% 48.1% 46.4% 39.0% 29.8% 13.5% Total approach and entry: PH1, PH2, and Spillway entrances During treatment hours total entrance efficiencies (total number of approaches and entries pooled for all lampreys) were consistent with entrance efficiencies for first approaches (Table 4). Entrance efficiencies were consistently lowest at PH2 north entrances (range = 5.5-13.5%) followed by PH2 south entrances (range = 20.5-29.8%) and were highest at PH1 north entrances (range = 45.5-48.1%; Table 4). Entrance efficiencies were 41.0-5% at Bradford Island, 24.3-52.6% at Cascades Island and 29.8-45.7% at PH1 south entrances (Table 4). 12

Entrance Efficiency: Non treatment times at PH1, PH2, and spillway entrances During non-experimental hours (04:00-22:00), first and total passage efficiencies were generally lower than during test periods, probably reflecting the effects of daylight on lamprey activity. Fish that first approached at PH1 north and Bradford Island fishways entered at a higher rate than those that first approached at PH1 south or either of the PH2 fishways (Table 5). Relatively higher non-experimental entrance efficiencies in 2008 at PH2 entrances were likely related to the higher frequency standby operations. Table 5. Distributions of known first fishway approaches and entries (top) and all known fishway approaches and entries (bottom) with the estimated entrance efficiencies for radio-tagged lampreys at Bonneville Dam in 2007-2009 during non-experimental hours (04:00-22:00 only). PH1 S = powerhouse 1 south, PH1 N = powerhouse 1 north, Spillway S = B-Branch Bradford Island, Spillway N = Cascade Island, PH2 S = powerhouse 2 south, and PH2 N = powerhouse 2 north. Sample sizes given in parentheses. First Approaches PH1 S PH1 N Spillway S Spillway N PH2 S PH2 N 2007 Approaches 5 0 9 7 29 36 Entries 0 0 4 2 1 1 Exits 0 0 0 1 1 0 Efficiency 0% 0% 44.4% 28.6% 3.4% 2.8% 2008 Approaches 16 5 14 9 20 37 Entries 3 3 6 2 0 1 Exits 1 0 1 0 0 1 Efficiency 18.8% 6% 42.9% 22.2% 0% 2.7% All Approaches 2009 Approaches 19 5 16 14 13 33 Entries 3 1 6 6 3 1 Exits 0 0 2 2 2 0 Efficiency 15.8% 2% 37.5% 42.9% 23.1% 3.0% 2007 PH1 S PH1 N Spillway S Spillway N PH2 S PH2 N Approaches 26 (14) 10 (4) 40 (27) 22 (20) 911 (97) 434 (102) Entries 1 3 8 9 66 8 Exits 0 0 1 3 29 2 Efficiency 3.8% 3% 2% 40.9% 7.2% 1.8% 2008 Approaches 153 (53) 21 (14) 80 (55) 51 (38) 253 (106) 512 (129) Entries 20 8 26 12 68 31 Exits 8 2 7 0 25 10 Efficiency 13.1% 38.1% 32.5% 23.5% 26.9% 6.1% 2009 Approaches 73 (36) 8 (7) 90 (58) 138 (47) 215 (84) 318 (122) Entries 8 2 27 37 61 18 Exits 1 0 8 14 30 12 Efficiency 11.0% 25.0% 3% 26.8% 28.4% 5.7% 13

Fishway entrance velocity test Fishway velocity reductions to 0.15 m head (treatment nights) at fishway entrances occurred 47% (2009) and 48% (2007) of the nights from 1 June through 30 September (Figure 3). velocities (target 0.45 m at fishway entrances) occurred 46% (2007), 65% (2008) and 42% (2009) of the nights. Standby operations occurred 6% (2007), 35% (2008), and 11% (2009) of the nights. Switching In 2007, 55 lampreys approached a PH2 south fishway entrance. Of these, 41 (75%) entered at PH2 south, 8 (14%) entered a PH2 north fishway, and 6 (11%) entered a non-ph2 fishway. Twelve lampreys entered a fishway during a different treatment than the one they first encountered when they approached the fishway (24% treatment switching); most of these (92%) approached during control velocity and entered during a reduced velocity treatment. Seventy-six fish approached the PH2 north entrances and 25 (33%) of these also entered PH2 north entrances, while 41 (54%) entered PH2 south entrances and 10 (13%) entered non-ph2 fishways. Eighteen percent (12/66 that approached and entered PH2) entered during a different treatment with most of these lampreys (75%) approaching during control velocity and entering during a reduced velocity treatment. In 2008, 66 fish approached a PH2 south fishway. Of these, 44 (67%) entered a PH2 south fishway and 15 fish (23%) entered a PH2 north fishway, and 7 fish (10%) entered a non-ph2 fishway. Five entries (of the 59 total fish that entered a PH2 fishway) occurred during different treatments (8% treatment switching) with most fish (83%) approaching during standby velocity and entering during control velocity. Of the 109 fish that approached a PH2 north fishway, 38 (35%) entered a PH2 north fishway, 51 (47%) entered a PH2 south entrance, and 20 (18%) entered a non-ph2 fishway. Thirteen fish (15% of the 89 fish that entered a PH2 fishway) switched treatments and all entered during a control velocity night after approaching during standby operation. In 2009, 82 lampreys approached PH2 south fishways. Of these, 56 (68%) entered a PH2 south fishway, 20 (24%) entered a PH2 north fishway, and 6 (7%) entered a non-ph2 fishway. Twelve percent (9 of 76 that entered PH2) entered during a different treatment. In contrast to previous years, the 9 fish that approached and entered during different treatments, (33%) approached during a control or standby treatment and entered during a reduced flow treatment. Of the 150 fish that approached the PH2 north fishway, 82 (55%) entered a PH2 north fishway and 54 (36%) entered a PH2 south fishway. Eighteen percent (24/136 that entered a PH2 south fishway) of the fish entered during a different treatment, and most of these (63%) approached during a control or standby treatment and entered during a reduced velocity treatment. We examined fishway approaches and entries at multiple scales. Below, we present results for first approaches and entries across all four PH2 fishway entrances. We also examined results for the north and south entrance locations separately, though samples sizes were smaller. We then present parallel analyses for all approach and entrance event records combined. First approach and entry: PH2 north and south entrances combined The first fishway approach rate (number of approaches per hour) at PH2 fishway entrances was generally highest 14

during the standby treatment (range = 0.26-0.45 approaches per hour) and lowest during the control treatment (range = 0.11-0.21; Table 6). The approach rate during the reduced velocity treatment was slightly higher than during the control operations across years. Entrance rate was the highest during treatments in 2007 and 2009. Entrance rate increased to a greater degree than approach rate during treatment periods compared to control periods, though entrance efficiency did not differ among velocity treatments in any year for first fishway attempts (Pearson s χ 2 : P 0.18; Table 6). Exit rate also increased during treatment periods though net entry ratios stayed relatively constant because of increased entry rate during treatment periods. The proportion of lampreys that exited the fishway did not differ among treatments in any year (Pearson s χ 2 : P 0.20; Table 6). First approach and entry: PH2 north fishway Entrance efficiencies for fish making first approaches during control velocities were 7.7% (2007), 0% (2008), and 11.1% (2009; Table 7). Entrance efficiencies during standby operations were 0% (2007), 4.4% (2008), and 0% (2009). Entrance efficiencies were highest for lampreys that approached during a reduced velocity treatment, and were 15.6% (2007) and 13.6% (2009), though these rates were not significantly higher than efficiencies during control operations in either 2007 or 2009 (Table 7). However, in 2007 the power for this test was low power because sample sizes were small (i.e. at least 20% of expected values in the chi-square test were < 5; Table 7). First approach and entry: PH2 south fishway Fewer lampreys first approached at PH2 south fishway entrances compared to PH2 north entrances, but entrance efficiencies at this site were higher than those at PH2 north entrances across treatments. Entrance efficiencies for fish that first approached during control velocities were 3% (2007), 28.6% (2008), and 21.4% (2009; Table 7). Point estimates of entrance efficiencies were highest for fish that approached during reduced velocity treatments at 31.3% (2007) and 48.4% (2009) and efficiency was significantly higher during the reduced versus control velocity treatment in 2009 (Pearson s χ 2 = 4.46, P = 3), but not in 2007 (Pearson s χ 2 = 5, P = 0.71). In 2007 the statistical power of this test was low. Point estimates of entrance efficiency at PH2 south entrances during the standby treatment were lower than during either control or reduced velocity treatments at 12.5-14.3% all years (Table 7). Pairwise comparisons between standby entrance efficiencies and either control or treatment entrance efficiencies were non-significant (P > 5), likely due to small sample sizes. Total approach and entry: PH2 north and south entrances combined Total fishway approach rates were highest during standby operation (range = 2.6-5.0 approaches per hour) and lowest during control operation (range = 0.7-1.3, Table 8). Approach rates during the reduced velocity treatments were intermediate (range = 1.2-1.8). The total number of approach attempts made by an individual during any treatment was generally less than < 7-10 with those approaching during standby operation having the highest number of approach attempts (Figure 6). Across treatments and years most lampreys (60-80%) only made one fishway entry and very few fish made > 2 entries (Figure 7). Consistent with trends in first entrances, total entry rate increased considerably under treatment conditions compared to control conditions (Table 8), and the relatively larger increase in entry rate than approach rate resulted in higher total entrance efficiencies during reduced 15

velocity treatments in all study years (Pearson s χ 2 :13.1, P < 01, 2007; χ 2 :36.0, P < 01, 2008; χ 2 :8.5, P = 04, 2009). Results for total exit rates also increased during treatment conditions and were compensated by increased entrance rates, and consequently the percentage of lampreys that exited the fishway into the tailrace did not differ among treatments in any year (Pearson s χ 2 : P = 0.42, 2007; P = 0.39, 2008; P = 0.42, 2009); resulting net entry ratios were similar among treatments (Table 8). Total approach and entry: PH2 north fishway Proportionately more lamprey approaches were followed by entries during the reduced velocity treatment, ranging from 21.1% (2007) to 21.3% (2009), than during control operation treatment, which ranged from 4.6% (2007) to 12.6% (2009) (Pearson s χ 2 = 14.7, P < 01, 2007; χ 2 = 7.4, P = 07, 2009; Table 9) or during standby operations which ranged from < 1% (2007) to 3.9% (2009) (Pearson s χ 2 = 24.8, P < 001, 2007; χ 2 = 36.9, P < 001, 2009; Table 9). Entrance efficiencies during standby velocities at PH2 north fishways were significantly lower compared to control operations during 2008 (Pearson s χ 2 = 19.7, P < 001) and 2009 (Pearson s χ 2 = 12.3, P < 01) but not in 2007 (Pearson s χ 2 = 2.9, P = 9). No significant differences were observed in the percentage of lampreys that exited the fishways (net entry ratio) during treatment and control operations, but the power for these tests was low. Total approach and entry: PH2 south fishway Total entrance efficiencies were consistently about 8% higher during reduced velocity treatments (29.9%, 2007; 40.6%, 2009) than during control velocities (21.6%, 2007; 32.7%, 2009) at PH2 south. However, these differences were not statistically significant (Pearson s χ 2 = 2.54, P = 0.11, 2007; χ 2 = 2.44, P = 0.11, 2009; Table 9). Efficiency at PH2 south entrances during standby operations were 17.5% (2007), 12.0% (2008), and 14.3% (2009). Efficiency during standby was significantly lower than during control velocity (Pearson s χ 2 = 5.6, P = 2, 2007; χ 2 = 17.9, P < 01, 2008; χ 2 = 16.0, P < 001, 2009). Adult lampreys frequently exited the fishway after entry and fishway net entry ratios did not differ among treatments in any year (Pearson s χ 2 = 0.49, P = 0.48, 2007; χ 2 = 0.57, P = 0.45, 2008; χ 2 = 2, P = 0.89, 2009). 16

30 25 A) treatment control standby 20 15 10 5 0 30 25 B) control standby 20 Frequency 15 10 5 0 35 30 25 C) treatment control standby 20 15 10 5 0 0 5 10 15 20 25 30 # Approaches Figure 6. Frequency histograms showing the total numbers of fishway approaches made by individual radio-tagged lamprey at PH2 fishway openings during each treatment in 2007 (A), 2008 (B), and 2009 (C). 17

1.0 0.8 A) treatment control standby 0.6 0.4 0.2 1.0 0.8 B) control standby Frequency 0.6 0.4 0.2 1.0 0.8 C) treatment control standby 0.6 0.4 0.2 0 1 2 3 4 5 6 7 8 9 10 # Entrances Figure 7. Frequency histograms showing the total numbers of entrances made by individual radiotagged lamprey at PH2 fishway openings during each treatment in 2007 (A), 2008 (B), and 2009 (C). 18

Table 6. Numbers of first fishway approach, entry, and exit events, and estimated entrance efficiencies (total number of entries / total number of approaches) for lampreys that approached and entered PH2 during the same treatment, and net entry ratio (calculated using all unique fishway entries and exits that occurred during a single treatment (control, reduced velocity, standby) at each fishway entrance site for radio-tagged lampreys at PH2 (north and south fishways combined). Also included are the total number of hours each treatment was conducted at night (22:00-04:00) and the approach, entrance, and exit rates (total numbers per hour) for each treatment at Bonneville Dam, 2007-2009. Entrance efficiencies among velocity treatments were compared using Pearson s χ 2 tests. Only P values reported are pairwise comparisons between treatment and control (2007 and 2009) and control versus standby (2008). Appr/ Entry/ Entrance Exits/ Net Year Condition Hours Approach hour Entry P hour Efficiency Exits P hour Entry Ratio 2007 348 48 0.14 10 0.59 29 20.80% 6 0.36 17 40% 331 36 0.11 5 15 13.90% 1 03 80% Standby 47 16 0.34 1 21 0.60% 1 21 0% Total 726 100 0.14 16 22 16.00% 8 11 50% 2008 - - - - - - - - - - - 475 102 0.21 10 0.82 21 9.80% 3 0.2 06 70% Standby 251 66 0.26 5 20 7.60% 4 16 20% Total 726 168 0.23 15 21 8.90% 7 10 53.30% 2009 338 97 0.29 24 0.18 71 24.70% 15 0.82 44 37.50% 304 73 0.24 11 36 15.10% 6 20 45.50% Standby 84 38 0.45 2 24 5.30% 1 12 50% Total 726 208 0.29 37 51 17.80% 22 30 40.50% 18

Table 7. Total number of first fishway approach, entry, and exit events, and estimated entrance efficiencies for lampreys that approached and entered same site during same treatment (total number of entries/total number of approaches), and net entry ratio (calculated using all unique fishway entries and exits that occurred during a single treatment (control, reduced velocity, standby) at each fishway entrance site for radio-tagged lamprey at PH2 (north and south fishways separated). Also included is the approach rate (total number of approaches/total number of hours) for each treatment at Bonneville Dam, 2007-2009. Entrance efficiencies among velocity treatments were compared using Pearson s χ 2 tests. Only P values reported are pairwise comparisons between treatment and control (2007 and 2009) and control versus standby (2008). Appr/ Year Location Condition Approach hour Entry P Efficiency Exits 2 Net Entry Ratio 2007 PH2 South 16 5 5 0.71 1 31.3% 4 2% 10 3 3 3% 1 66.7% Standby 7 0.15 1 14.3% 1 0% Total 33 5 9 27.3% 6 33.3% PH2 North 32 9 5 0.60 1 15.6% 2 6% 26 8 2 7.7% 0 100% Standby 9 0.19 0 0% 0 - Total 67 9 7 10.4% 2 71.4% 2008 PH2 South - - - - - - - 35 7 10 0.37 1 28.6% 3 7% Standby 21 8 3 14.3% 2 33.3% Total 56 8 13 23.2% 5 61.5% PH2 North - - - - - - - 67 0.14 0 0% 0 - Standby 45 0.18 2 0.31 1 4.4% 2 0% Total 112 0.15 2 1.8% 2 0% 2009 PH2 South 31 9 15 3 48.4% 11 26.7% 28 9 6 21.4% 5 16.7% Standby 16 0.19 2 12.5% 1 5% Total 75 0.10 23 30.7% 17 26.1% PH2 North 66 0.20 9 0.69 13.6% 4 55.6% 45 0.15 5 11.1% 1 8% Standby 22 0.26 0 0% 0 - Total 133 0.18 14 10.5% 5 64.3% 1 Small sample size resulted in least 20% of expected values < 5 2 No statistic reported since at least 20% of expected values < 5 19

Table 8. Total numbers of fishway approach, entry, and exit events, and estimated entrance efficiencies for fish that approach and entered PH2 during same treatment (total number of entries/total number of approaches), and net entry ratio (calculated using all unique fishway entries and exits that occurred during a single treatment (control, reduced velocity, standby) at each fishway entrance site for radio-tagged lamprey at PH2 (north and south fishways combined). Also included are approach, entrance, and exit rates (total numbers per hour) for each treatment at Bonneville Dam, 2007-2009. Entrance efficiencies among velocity treatments were compared using Pearson s χ 2 tests. Only P values reported are pairwise comparisons between treatment and control (2007 and 2009) and control versus standby (2008). Appr/ Entries/ Entrance Exits/ Net Year Condition Hours n Approach hour Entry P hour Efficiency Exits P hour Entry Ratio 2007 348 99 430 1.2 110 <01 0.316 25.60% 47 0.42 0.135 57.30% 331 59 219 0.7 29 88 13.20% 10 30 65.50% Standby 47 25 216 4.6 19 0.404 8.80% 7 0.149 63.20% Total 726 183 865 1.2 158 0.218 18.30% 64 88 59.50% 2008 - - - - - - - - - - - - 475 182 582 1.2 90 <01 0.189 15.50% 23 0.39 48 74.40% Standby 251 133 642 2.6 33 0.131 5.10% 11 44 66.70% Total 726 315 1224 1.7 123 0.169 10% 34 47 72.40% 2009 338 155 567 1.8 163 04 0.482 28.70% 51 0.42 0.151 68.70% 304 133 392 1.3 80 0.263 20.40% 21 69 73.80% Standby 84 79 437 5 36 0.429 8.20% 16 0.190 55.60% Total 726 367 1,396 2 279 0.384 20% 88 0.121 68.50% 20

Table 9. Total numbers of fishway approach, entry, and exit events, and estimated entrance efficiencies for fish that approached and entered same site during same treatment (total number of entries/total number of approaches), and net entry ratio (calculated using all unique fishway entries and exits that occurred during a single treatment (control, reduced velocity, standby) at each fishway entrance site for radio-tagged lamprey at PH2 (north and south fishways separated). Also included is the approach rate (total number of approaches/total number of hours) for each treatment at Bonneville Dam, 2007-2009. Entrance efficiencies among velocity treatments were compared using Pearson s χ 2 tests. Only P values reported are pairwise comparisons between treatment and control (2007 and 2009) and control versus standby (2008). Appr/ Year Location Condition n Approach hour Entry P Efficiency Exits P Net Entry Ratio 2007 PH2 South 74 221 0.64 66 0.11 29.9% 33 0.48 5% 42 111 0.34 24 21.6% 10 58.3% Standby 24 103 2.20 18 17.5% 7 61.1% Total 105 435 0.60 108 24.8% 50 53.7% PH2 North 78 209 0.60 44 001 21.1% 14 0.94 1 68.2% 45 108 0.33 5 4.6% 0 100% Standby 22 113 2.40 1 0.8% 0 100% Total 120 430 0.59 50 11.6% 14 72.0% 2008 PH2 South - - - - - - 110 178 0.37 53 <001 29.8% 16 0.45 69.8% Standby 90 192 0.76 23 12.0% 5 78.3% Total 160 370 0.51 76 20.5% 21 72.4% PH2 North - - - - - - 154 404 0.85 37 <001 9.2% 7 2 1 81.1% Standby 118 450 1.79 10 2.2% 6 4% Total 216 854 1.18 47 5.5% 13 72.3% 2009 PH2 South 104 219 0.65 89 0.11 40.6% 31 0.89 65.2% 89 153 0.50 50 32.7% 18 64.0% Standby 62 182 2.17 26 14.3% 11 57.7% Total 199 554 0.76 165 29.8% 60 63.6% PH2 North 137 348 1.03 74 07 21.3% 20 0.86 1 73.0% 114 239 0.79 30 12.6% 3 9% Standby 67 255 3.04 10 3.9% 5 5% Total 238 842 1.16 114 13.5% 28 75.4% 1 At least 20% of expected values < 5 21