Hatchery and Supplementation Program 2013 Annual Report

Transcription

1 Hatchery and Supplementation Program 2013 Annual Report Lewis River Hydroelectric Projects FERC Project Nos. 935, 2071, 2111, 2213 Photograph by Jim Richardson, National Geographic Erik Lesko March 7, 2014 (30 day review DRAFT) i

2 Table of Contents 1.0 Introduction Winter Steelhead Broodstock Collection Merwin Trap In River Netting Cedar Creek Winter Steelhead Broodstock Collection Timing Genetic Analysis of Potential Broodstock Genetic Analysis of BWT Steelhead Returns to the Merwin Trap Spawning and Egg Take Rearing, Tagging and Release Rearing Tagging Release Monitoring and Evaluation Winter Steelhead Redd Surveys (Lower River) Abundance Distribution BWT steelhead returns to the Merwin Trap Ratio of wild steelhead to hatchery steelhead in the traps and netting Salmon Redd Surveys Upstream Transport of Winter Steelhead Screw trap Operations Mainstem Carcass Surveys Spring Chinook To be reported in the 2015 Annual H&S report data was reported in the 2012 annual report Coho Salmon To be reported in the 2015 Annual H&S report data were reported in the 2012 annual report Tributary Carcass Surveys (coho salmon) TO BE PROVIDED BY WDFW tributary data has not yet been provided by WDFW Tributary Carcass and Redd Surveys (coho salmon) To be reported in the 2015 Annual H&S report ii

3 4.0 Recommendations for ongoing management References APPENDICES Appendix A Wild Winter Steelhead Collection Log 2013 Appendix B Genetic Assignment Results from Lewis River Captures at Merwin Trap (MT) and In River Tangle Netting (TN) 2013 Appendix C Wild Winter Steelhead Spawning Log 2013 Appendix D Steelhead Redd locations, Lewis River, WA 2013 Appendix E Appendix F Smolt and Fry collections at the lower North Fork Lewis River screw trap deployed from April 18 through June 27, 2013 Fork Length measurements from a sample of fishes captured in the lower North Fork Lewis River Screw Trap, April 18 through June 27, 2013 TABLES Table 1 Summary information of winter steelhead program captures and distribution 2013 (excludes recaptures) Table 2. Spawning Crosses for the 2012 brood year of wild winter steelhead Table 3. Summary of rearing statistics for the 2013 brood year Table 4. Wild Winter Steelhead Abundance Downstream of Merwin Dam 2008 through 2013 based on redd counts Table 5. Redd distribution summary for reaches 1 through 5 including redds per mile Table 6. Summary information for the number of days released steelhead to recruit to the Merwin Trap after in river tangle net capture 2013 (n = 9) Table 7. Summary of Winter Steelhead transported and released upstream of Swift Dam Table 8. Collection summary for the rotary screw trap deployed downstream of Merwin Dam April 18 June 28, Table 9. Disposition of captured fish (excluding fry) including catch rates of BWT and non BWT rainbow form April 18 June 28, FIGURES iii

4 Figure 1. Frequency of winter steelhead captured at the Merwin fish trap between December 27, 2012 and May 13, 2013 (n = 752) Figure 2. Frequency of capture of unclipped winter steelhead from in river tangle netting between March 1, 2013 and May14, Figure 3. Actual collection (at Merwin trap and tangle netting) timing of steelhead used as broodstock compared to predetermined collection curve during the 2013 season... 6 Figure 4. Proportion of primary genetic assignment of potential steelhead broodstock sampled in 2013 and proportion of assignment values with at least a 5 percent assignment probability to specific river system Figure 5. Number and timing of winter steelhead (males and females) spawned at Merwin hatchery (n=19) in Figure 6. Observed mortality rate of fish ponded for brood years 2009 through Figure 7. Graphical representation of wild winter steelhead abundance downstream of Merwin Dam 2008 through 2013 based on redd counts Figure 9. Number of steelhead marked, released and recaptured through both the Merwin trap and tangle netting efforts Figure 10. Ratio of hatchery to wild steelhead recruitment by month to the Merwin trap Figure 11. Ratio of hatchery to wild steelhead captured during in river tangle netting effort (by period) in the North Fork Lewis River Figure 13. Number of smolts and fry captured on a daily basis and daily discharge from Merwin Dam during the deployment period of the lower river screw trap Figure 14. Daily capture of smolts and fry salmonids in the lower Lewis River screw trap April 18 through June 27, Figure 15. Daily capture by species of salmonids in the lower Lewis River screw trap April 18 through June 27, iv

5 1.0 Introduction The purpose of this report is to document results from field studies associated with implementation of the Hatchery and Supplementation (H&S) Program during Monitoring and evaluation (M&E) activities are planned in consultation with the Hatchery and Supplementation subgroup and incorporated into the Annual Operating Plan (AOP) each year. In 2013, several M&E activities were completed including: Transport of winter steelhead, spring chinook and early coho salmon upstream of Swift Dam Screw trapping efforts downstream of Merwin Dam Carcass and redd surveys downstream of Merwin Dam Broodstock collection and rearing program for wild winter steelhead Additional hatchery production of spring Chinook and coho salmon smolts This report is required by Section of the Lewis River Settlement Agreement which states: On an annual basis, the Licensees shall provide to the ACC for review and comment a report compiling all information gathered pursuant to implementation of the Hatchery and Supplementation Plan. The report also will include recommendations for ongoing management of the Hatchery and Supplementation Program. The ACC shall have 60 days to comment on the annual report. Within 60 days of the close of the comment period, the Licensees shall finalize the report after consideration of all comments. The Licensees shall also provide the comprehensive periodic review undertaken pursuant to Section below to the ACC. The Licensees shall provide final annual reports and the comprehensive periodic review to the Services during the development of any required ESA permit or authorization for hatchery operations, including NOAA Fisheries HGMP process. The report may be included as part of the detailed annual reports of the ACC activities required by Section

6 2.0 Winter Steelhead The winter steelhead program is composed of three elements: a broodstock capture program, spawning and rearing program and transportation program. The intent of the collection program is to collect an adequate number of native winter steelhead and spawn a portion of these fish at Merwin Hatchery. The goal is to increase the numbers of returning winter steelhead and transport these fish upstream of Swift Dam to spawn naturally in hopes of building a self sustaining run that in time requires no hatchery support. A summary of the numbers of fish collected and their distribution is provided in Table 1. Table 1 Summary information of winter steelhead program captures and distribution 2013 (excludes recaptures). Method Total Captures Transport Upstream Radio Tagged Spawned Mortality* BWT Release to River Release to River Lethally Removed Merwin Trap Tangle Netting Lewis River Trap 5 5 TOTAL * Mortality occurred at Merwin Hatchery 2.1 Broodstock Collection Broodstock collection relied on two methods: (1) trapping at Merwin Dam and (2) in river netting. Cedar Creek weir was not used to contribute any broodstock in Transportation of adult broodstock collected through in river netting was accomplished by holding fish in insulated coolers filled with fresh river water and use of rubber mesh nets to transfer fish from the coolers to oxygenated holding tanks on shore. Steelhead captured in the Merwin trap were transferred to the Merwin hatchery using fish transport trucks. No direct mortality was observed using either of these procedures. However, one mortality at the hatchery did occur after being held for two weeks at the facility. Data for all steelhead transported to the Merwin hatchery is provided in Appendix A Merwin Trap The first unclipped steelhead was collected at the Merwin trap on December 27, This fish was released but later genetic assignment indicated that its origin assigned to native Lewis River stock. The second fish captured on December 31, 2012 assigned to Lewis River hatchery winter and was released. In total, 21 unclipped adipose fin steelhead were collected from the Merwin fish during the period December 27, 2012 through May 13, Thirteen of these fish were suspected of being program fish that had lost their snout tag due to the presence of stubby dorsal fins. 2

7 These fish were released back to river and not held at the hatchery. The first broodstock retained from the trap was on March 18, Of the 8 potential broodstock steelhead captured at the trap, three (3) were spawned and five (5) were released back to river. Figure 1 illustrates the catch frequency of steelhead entering the Merwin trap during the collection period. 350 Number of Steelhead Captured BWT/HATCHERY (n=744) WILD (n=8) 0 Dec Jan Feb Mar Apr May Jun Month Figure 1. Frequency of winter steelhead captured at the Merwin fish trap between December 27, 2012 and May 13, 2013 (n = 752) In River Netting In river collection efforts began on March 1, 2012and continued through May 11, A PacifiCorp crew of two biologists went out once per week depending on river conditions. Six to eight pound test monofilament, 4 inch (stretch) mesh tangle nets were drifted in known and established steelhead holding areas. Once a steelhead became entangled in the drifting net it was pulled into the boat and freed from the net, then placed in an insulated cooler with fresh river water. Steelhead were then transported to the oxygenated holding tank at the Lewis River hatchery access area. 3

8 In total, 103 unclipped steelhead were captured through the tangle netting program (Figure 2). Of these fish, 67 were BWT fish that were either marked and released back to river (49), transported upstream (6) or released as kelts (12). Thirty one (31) were transported to Merwin hatchery as potential broodstock and the remaining wild fish were released as kelts (5). Residuals are not included in Figure 2, but a total of 28 residual (less than 500 mm) steelhead were captured during the tangle netting effort. 40 BWT (n=67) Wild (n=36) Number of Steelhead Captured March 1-15 March April 1-15 April May 1-15 Period Figure 2. Frequency of capture of unclipped winter steelhead from in river tangle netting between March 1, 2013 and May14, Cedar Creek No winter steelhead were transported from Cedar Creek to Merwin hatchery. Therefore, no winter steelhead captured from Cedar Creek were used as broodstock. However, a substantial influence from Cedar Creek stock is observed in the genotype of the broodstock (see Section 2.3). 4

9 2.2 Winter Steelhead Broodstock Collection Timing The ability to conform to predetermined collection curves presents several difficulties in the field. Specific issues continue to make broodstock collection problematic. These specific issues include the following: More fish (than stipulated in the collection curve) need to be captured each period to ensure assignment analysis will not reduce available broodstock below target levels Spawning maturity is a significant variable during spawning and adds uncertainty when deciding to retain or release broodstock. This is most notable in females rather than males. Capture efficiency is affected by river conditions which can change weekly if not daily Gender ratios need to be managed and maintained to ensure adequate number of crosses and limited multiple use of broodstock males Steelhead condition varies throughout the collection period with a larger percentage of fish being returned to river later in the collection window due to ripeness, and, Fecundity varies substantially from fish to fish and from year to year. Because of the many unknowns with collecting live fish in their natural environment, the collection curve is intended to be a guide for collection crews to help plan fish collection activities on a weekly basis. This planning helps to ensure that fish are collected across their spawning period and helps ensure genetic diversity among the available broodstock. The first steelhead retained for broodstock was on March 7, 2012 from tangle netting efforts. This fish was later spawned on April 10. Tangle netting efforts ended on May 11 to protect spawning steelhead in the river. The Merwin trap continued to operate and captured the last broodstock female (and 5 males) on May 14, Figure 3 provides the timing of actual captures of steelhead from all available methods as compared to the predetermined collection curve. According to the collection curve, a total of 50 steelhead are to be held for broodstock and spawned. In 2013, only 19 steelhead (8 females; 11 males) were spawned. The collection was also compressed within March and April. This is due in part to our inability to collect steelhead prior to March 1 which may be a result of very few fish available. Additionally, there are concerns about tangle netting in May when fish are actively spawning and the fish that are captured in May tend to be spawn outs and unavailable for broodstock. 5

10 Collection Curve 2013 Actual Broodstock Captures Number of Steelhead Jan 21-Feb 28 Mar 1-15 Mar Apr 1-15 Apr May 1-15 May Collection Period Figure 3. Actual collection (at Merwin trap and tangle netting) timing of steelhead used as broodstock compared to predetermined collection curve during the 2013 season 2.3 Genetic Analysis of Potential Broodstock The Hatchery and Supplementation subgroup agreed to use a genetic assignment level of 50 percent or greater to the NF Lewis River or Cedar Creek stock(s) to identify acceptable broodstock. Additionally, steelhead captured after April 1 with 50 percent or greater assignment to the Cascade Strata are also considered acceptable broodstock. The only exception to this rule is for fish showing hatchery assignment at levels greater than 5 percent. These fish would not be incorporated into the broodstock despite any assignment of 50 percent or greater to the NF Lewis River wild winter steelhead stock or Cascade Strata. A total of 38 unclipped steelhead (non BWT) were analyzed and assigned a probability percentage. Figure 4 provides a summary of those results using only the greatest probability 6

11 (primary). Appendix B provides the results for each individual unclipped steelhead captured at the Merwin trap, through tangle netting and at the Cedar Creek weir Primary Assignment (n =38) Assignment > 5 percent (n=77) Proportion LR WILD Cedar Creek LR Hatchery Kalama Wild Kalama Summer Kalama Hatchery Grays R Coweeman Green River Elochoman Hatchery East Fork Lewis River System Figure 4. Proportion of primary genetic assignment of potential steelhead broodstock sampled in 2013 and proportion of assignment values with at least a 5 percent assignment probability to specific river system. By evaluating assignment probabilities greater than five percent, a clearer understanding of the contribution of each stock to the Lewis River basin is possible. This method captures not only fish with the primary probabilities but also fish that have a strong mixture of assignment to other basins. Figure 4 provides the proportion of all stocks identified through genetic assignment analysis with assignment probabilities greater than 5 percent. By including all stocks with at least a five percent probability Cedar Creek and the North Fork Lewis stock remain the strongest contributor to fish captured in the North Fork Lewis River with over 50 7

12 percent of the fish captured having assignment to these two streams. It is important to note that primary assignment is also heavily biased to these two stocks. The third highest contributor was Lewis River hatchery stocks from early returns to the Merwin hatchery 2.4 Genetic Analysis of BWT Steelhead Returns to the Merwin Trap Gary Winans to provide 2.5 Spawning and Egg Take A total of 8 females were spawned with 11 males through 8 spawning crosses. These fish represent the 2013 broodstock and are summarized in Table 2. All fish were spawned during a 4 days during the period April 10 to May 6, 2013 (Figure 5). The target goal of 25 females and 25 males was not reached for either females or males. Fecundity was above average (5,355 per female); however, this average is biased by two females that had estimated fecundity of 8,336 and 8,670 each. Estimated egg take (42,839) was less than program goals of 80,000. Eggs reaching the eyed stage from the 2013 brood egg take was 28,071 resulting in a projected release of 24,000 smolts in spring of 2014 substantially less that program target release of 50,000. Appendix C provides the spawning log for 2013 indicating fecundity, crosses, eyed egg take and estimated egg loss. 8

13 6 5 Females Males Number of Spawners April 10 April 18 April 29 May 6 Spawn Date Figure 5. Number and timing of winter steelhead (males and females) spawned at Merwin hatchery (n=19) in

14 Table 2. Spawning Crosses for the 2012 brood year of wild winter steelhead Females Males Spawn Cross DNA No. Primary Assignment Percent Assignment Primary Assignment DNA No. 4/10/ MT 5 Cedar Lewis R MT 4 91 Lewis R TN 5 4/18/ TN 19 Lewis R Cedar TN 7 98 Lewis R TN 13 3 TN 3 Lewis R Lewis R TN Cedar TN Cedar TN 26 4 TN 15 Lewis R Lewis R TN Cedar TN Cedar TN 26 4/29/ TN 21 Cedar Lewis R TN Cedar TN Cedar TN 26 6 TN 10 Lewis R Kalama TN Cedar TN 22 7 MT 7 Cedar Kalama TN Cedar TN 22 5/6/ TN 28 Lewis R Coweeman TN Lewis R TN 31 10

15 2.6 Rearing, Tagging and Release Of the 28,071 fry ponded, 13.8 percent (3,896) succumbed to natural mortality. Mortality caused by Flexibacter columnaris was very low (0.5%) and not a significant factor. This is in contrast to 2011 when F. columnaris infections caused significant mortality (49%). Despite low pond mortality, the 2014 release is expected to be less than half of the target goal of 50, Rearing Table 3. Summary of rearing statistics for the 2013 brood year GENERAL STATISTIC Egg Take 36,555 Eyed Eggs 28,071 Total Ponded 28,071 Food Conversion.92:1 MORTALITY Total Egg Loss 8,484 Total Pond Loss 4,167 Due to natural causes 3,896 Due to feed related issues 0 Due to disease (Columnaris) 143 Due to disease (BCW) 0 Overall Loss (egg and pond) 12,651 Shortage / Adjustment 1,504 RELEASE Projected Smolt Release (survival) 22,900 Release Date (Start Volitional) 5/1/2014 Release size 7 Fish/LB 11

16 Number Ponded May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr Month Figure 6. Observed mortality rate of fish ponded for brood years 2009 through Tagging All fish were tagged with blank wire snout tags in December A total of 22,900 fish were tagged Release All fish will be volitionally released on May 1, 2014 at the Merwin boat launch. Volitional release will continue until June 1, Any fish remaining in the ponds on June 1, 2014 will be forced out and released downstream of the County Bridge in Woodland, WA. Projected average release size in 7 per pound. A total release number of 22,900 smolts is projected. 12

17 3.0 Monitoring and Evaluation 3.1 Winter Steelhead Redd Surveys (Lower River) Abundance Abundance estimates are derived by using a multiplier on the total number of redds observed. This method assumes an equal sex ratio. Table 4 provides abundance estimates for years 2008 through The redd count is based on 0.81 females per redd and a sex ratio of 1:1 (Freymond and Foley 1986). However, it is unlikely that the actual sex ratio of females to male spawning steelhead is precisely 1:1. Using steelhead returns to the Merwin Trap we can calculate the sex ratio observed and apply this ratio to the annual estimate. This may be a more accurate estimate of female to male ratio in the river because of the large numbers captured in the trap and is unbiased in terms of capture efficiency. Using trap data collected for 2013, a total of 761 steelhead were trapped. These include mainly BWT steelhead, but also include steelhead held for broodstock and steelhead released because of stubby dorsal fins and no wire tag in their snout. Of this total, 449 were male and 312 were female. Therefore, for every female we assume that there are 1.43 males (instead of 1) that make up the population. As a result, the population estimate is higher than assuming the 1:1 ratio. Both estimates are provided in Table 4 and Figure 7 for 2013 and will continue to be reported this way in the future. The number of redds per female will also need to be verified at some point to improve the accuracy of this estimate. Table 4. Wild Winter Steelhead Abundance Downstream of Merwin Dam 2008 through 2013 based on redd counts. Number of Redds observed Corrected Abundance Estimate Year Abundance Observed sex ratio Estimate (females to males) :

18 Abundance Estimate Abundance Estimate (based on trap ratio) Total Number of Redds Survey Year Figure 7. Graphical representation of wild winter steelhead abundance downstream of Merwin Dam 2008 through 2013 based on redd counts Distribution A summary of redd distribution is provided in Table 5. Reach number 5 has the most redds, but also has the most habitat at 7.71 miles (not including the section downstream of Eagle Island). Redd density is highest in reach number 2 at 166 per mile. The relatively large number of redds in this reach is attributable to a small but heavily used spawning area approximately 0.75 miles downstream of Merwin Dam. It is not fully known why this area is used so extensively by steelhead but is consistent from year to year. Redd locations are illustrated in Appendix D. Reach breaks coincide with WDFW reach breaks used for fall Chinook sampling. 14

19 Table 5. Redd distribution summary for reaches 1 through 5 including redds per mile Reach Reach Length (miles) Redds Redd per Mile Total number of redds = 456 Average redds per mile = BWT steelhead returns to the Merwin Trap During the course of in river netting, PacifiCorp biologist double floy tagged captured blank wire tagged steelhead and then released them immediately. A total of 49 fish were marked with double floy tags. Of these, nine recruited to the Merwin trap and seven were recaptured through in river netting. Based on the number of recaptures back to the Merwin trap the recapture rate was calculated to be percent (Table 5). This value is less than anticipated, but is not representative of the new trap design and enhanced attraction flow regimes that will be initiated in the spring of Average recruitment time to the trap after release from in river netting was 22 days. This value was highly variable (σ = 18.47) with a range of 4 to 65 days and confidence interval of 10 to 35 days (95%CL). The time and number of fish marked released and subsequently recaptured through tangle netting or through the Merwin trap is shown in Figure 9. Table 6. Summary information for the number of days released steelhead to recruit to the Merwin Trap after in river tangle net capture 2013 (n = 9) Metric Days Mean ± (95 CL) Median 16 Standard Error 6.16 Standard Deviation Range 4 to 65 Number Marked 49 Recruitment to trap 9 Range for the population to Recapture Rate 18.30% 15

20 35 30 Marks (n=49) Trap Recaptures (n=9) Tangle Net Recaptures (n=7) Number of Steelhead Mar 1-15 Mar Apr 1-15 Apr May 1-15 Period Figure 8. Number of steelhead marked, released and recaptured through both the Merwin trap and tangle netting efforts Ratio of wild steelhead to hatchery steelhead in the traps and netting Program return fish are treated as hatchery fish despite their genotype assignment to wild stocks. The ratio of program fish returns and hatchery fish to wild origin stocks is an important measure to monitor because high numbers of hatchery fish spawning with wild fish may adversely affect the native stock. Additionally, inbreeding between program fish is a concern that will be addressed during the 2014 sampling season and reported in the 2014 annual report along with estimation of effective population size. For 2013, two metrics were monitored: returns to the Merwin trap and ratio of hatchery fish captured during in river tangle netting. Tangle netting captures provides a direct measure of 16

21 the proportion of hatchery to wild fish when done during spawning or in areas where spawning is occurring. This differentiation between holding and spawning steelhead was not made in 2013 but will be in 2014; however, the information gained from both the trap data and netting efforts provided insight into the proportion of hatchery and wild fish in the river and to some extent the proportion of hatchery to wild fish on the spawning grounds (phos) when netting occurs in known spawning areas. Figures 10 and 11 provide the proportion of hatchery fish entering the Merwin trap and through tangle netting. Fish entering the Merwin trap were almost all program fish (hatchery). There were only 8 fish that were of wild origin. In other words, for every fish of wild origin there were approximately 93 hatchery fish. For tangle netting, the ratio was better but still exceeded limits of less than 5 percent hatchery (or 1 hatchery fish to 19 wild) fish on the spawning grounds. The ratio of in river captures was 67 hatchery to 36 wild or for every wild fish there were 1.86 hatchery fish implying a phos of 65 percent. 350 Number of Steelhead Captured BWT/HATCHERY (n=744) WILD (n=8) 0 Dec Jan Feb Mar Apr May Jun. Month Figure 9. Ratio of hatchery to wild steelhead recruitment by month to the Merwin trap

22 40 BWT/Hatchery (n=67) Wild (n=36) Number of Steelhead Captured March 1-15 March April 1-15 April May 1-15 Period Figure 10. Ratio of hatchery to wild steelhead captured during in river tangle netting effort (by period) in the North Fork Lewis River Salmon Redd Surveys NOTE* Mainstem redd survey data for spring Chinook and coho for surveys conducted in 2012 are reported in the 2013 annual H&S report. Redd surveys conducted in 2013 will be reported in the 2015 annual report. The delay in reporting these data is due to the completion timing of surveys and reporting deadlines which does not allow time for complete analysis of the data. 3.5 Upstream Transport of Winter Steelhead In 2013, a total of 741 blank wire tagged steelhead were transported upstream of Swift Dam (Table 7). A total of 100 transported steelhead also received a surgically implanted radio transmitter for distribution studies in the upper basin. Distribution and detection data along biological data each of these fish is provided in the Monitoring and Evaluation report as an appendix to the ACC/TCC annual report. 18

23 This year represents the second year of transportation activities and is a substantial improvement from The goal of the H&S program is to transport a minimum of 500 winter steelhead each year. This year we exceeded that target by 241 (Table 7). Table 7. Summary of Winter Steelhead transported and released upstream of Swift Dam. YEAR Number Number fitted with radio Transported transmitters Screw trap Operations In 2013, screw trapping was conducted near the golf course using one 8 foot diameter screw trap from April 18 through June 28, In total, 12,035 fish were captured (1,211 smolts) in the screw trap during the collection period (Table 8). Of these, 829 smolts were marked and transported upstream for recapture and trap efficiency testing (Table 9). Unfortunately, only 5 recaptures were reported from the marked release group. Due to the low recapture rate (0.6%), estimates of efficiency do not provide any value because there is no confidence in the estimates. Efforts to improve efficiency (and ultimately abundance estimates) are planned for PacifiCorp will place an additional trap at the golf course as well as have the option of moving the trap(s) to other locations in the river. Also, to improve confidence of our estimates we will plan to mark all captured smolts and release upstream of the trap. If capture rates are smaller than anticipated, the company through consultation with the H&S subgroup may use marked hatchery releases as surrogates for low numbers of captured smolts in the screw trap. Because of low recapture rates, results for 2013 are provided as a summary of fish captured, timing, fork lengths, species composition and other related capture data. Capture data are provided in Appendix E and length data for a sample of captured fishes are provided in Appendix F. A substantial portion of the fish captured in the trap were chinook fry and accounted for 87 percent of the total catch. Chinook fry were followed by coho smolts (821), rainbow (292) and cutthroat (25) in terms of abundance. In addition one chum fry and one pacific lamprey (137 mm) were captured. 19

24 Catch rates varied widely over the period of deployment. Figure 13 provides total capture with respect to flow. There is no significant relationship between flow and total catch rate (Pearson correlation test, P > 0.05) over the duration of trap deployment. This applies to smolts and fry when treated as individual groups. Table 8. Collection summary for the rotary screw trap deployed downstream of Merwin Dam April 18 June 28, Species Life Stage No Collected Period of collection Mean Length (FL, mm) MIN (mm) MAX (mm) σ Coho Smolts 893 4/18 6/ Fry 110 4/18 6/22 Rainbow Smolts 293 4/19 6/ Fry 211 5/31 6/28 Chinook Fry 10,501 4/18 6/28 Cutthroat Smolts 25 4/28 5/ Chum fry 1 16 May 40 Lamprey fry 1 26 Jun 137 TOTAL 12,035 Table 9. Disposition of captured fish (excluding fry) including catch rates of BWT and non BWT rainbow form April 18 June 28, Total Released upstream 829 Rainbow 280 Coho 528 Cutthroat 21 Recaptures 5 (0.6%) Total Released Downstream 309 Rainbow 12 Cutthroat 4 Coho 293 Non Clipped Rainbow 264 BWT 208 Non BWT 58 20

25 Merwin Discharge (cfs) Number of Fish Captured 800 Merwin Discharge (cfs) No. of Fish Apr 19 May 03 May 17 May 31 Jun 14 Jun 28 Date Figure 11. Number of smolts and fry captured on a daily basis and daily discharge from Merwin Dam during the deployment period of the lower river screw trap The timing of catch rates varied between smolts and fry. Figure 14 shows that smolt capture rates peaked in early May and dropped off substantially towards the end of May. Fry capture rates peaked in late May and may have been related to high flow events during this time frame, however this was not tested. In addition, another peak of fry capture rate is observed during the first half of June when flows had subsided. In general larger smolt sized fish were captured earlier in the season and fry captures increased later (Figure 14). This very well may be indirectly related to flow as lower flows may allow larger fish to evade the trap. Also, this relationship does not appear to be species specific (Figure 15), but more a function of natural emigration or hatchery release timing. 21

26 Smolts Fry Number of Fish Apr 18 May 02 May 16 May 30 Jun 13 Jun 27 Time (Day) Figure 12. Daily capture of smolts and fry salmonids in the lower Lewis River screw trap April 18 through June 27,

27 1000 Number of Fish (smolts and fry) Coho Chinook Rainbow Cutthroat 0 Apr 22 May 06 May 20 Jun 03 Jun 17 Jul 01 Date (days) Figure 13. Daily capture by species of salmonids in the lower Lewis River screw trap April 18 through June 27, Mainstem Carcass Surveys NOTE* Mainstem and tributary carcass survey data for spring Chinook and coho are collected from the fall of each year and surveys extend to January. This schedule does not provide sufficient time to analyze and report data from the previous year into the following year reporting schedule deadline. Therefore reporting for mainstem and tributary surveys of coho and spring Chinook lag one year from the survey period. For example, survey data collected in the fall of 2013 and early 2014 will not be reported until the 2015 report is released Spring Chinook To be reported in the 2015 Annual H&S report data was reported in the 2012 annual report 23

28 Coho Salmon To be reported in the 2015 Annual H&S report data were reported in the 2012 annual report Tributary Carcass Surveys (coho salmon) TO BE PROVIDED BY WDFW tributary data has not yet been provided by WDFW Tributary Carcass and Redd Surveys (coho salmon) To be reported in the 2015 Annual H&S report 4.0 Recommendations for ongoing management Improvements in the way we handle and rear steelhead from wild winter broodstock continues to be improved upon. Mortality of both adults and rearing juveniles has declined from previous years. Also, rearing conditions have improved as recommendations from the H&S subgroup have been implemented. The test use of circular tanks (as opposed to ponds) will continue to be evaluated to determine if survival may be increased as is supported by several studies. During 2013, the HS subgroup invited regional experts in the field of genetics to discuss options for limited the founder effects from our broodstock collection program. Of particular concern is the number of wild broodstock females that are used in the hatchery rearing program. For 2013, only 8 females were spawned. The long term effects of this are not fully known, but the potential for adverse effects such as inbreeding, loss of genetic diversity and reduction in effective population sizes of native Lewis River winter steelhead stocks is perhaps the most concerning aspect of the program. Monitoring and evaluation activities have struggled to achieve desired precision and accuracy guidelines particularly for estimates of abundance for both adult escapement and recruitment estimates. The H&S subgroup will continue to look for ways to improve precision and accuracy of our monitoring and evaluation activities. 5.0 References Freymond, B., and S. Foley Wild steelhead spawning escapement estimates from Boldt Case rivers Washington Department of Game. Fish Management Division. Rep. No Olympia,WA. Hilborn, R., B. G. Bue, and S. Sharr Estimating spawning escapement for periodic counts: a comparison of methods. Canadian Journal of Fisheries and Aquatic Sciences 56:

29 Hill, R. A Optimizing aerial count frequency for area under the curve method of estimating escapement. North American Journal of Fisheries Management 17: Hood, G. M Pop Tools version URL Kinsel, C., P. Hanratty, M. Zimmerman, B. Glaser, S. Gray, T. Hillson, D. Rawding, and S. VanderPloeg Intensively Monitored Watersheds: 2008 Fish Population Studies in the Hood Canal and Lower Columbia Stream Complexes. FPA 09 12, Washington Department of Fish and Wildlife, Olympia, Washington. 25

30 Appendix A Wild Winter Steelhead Collection Log

31 # Trap Date Capture Method Gender Fork Length (cm) Pit Tag # DNA Sample # Primary Genetis Assignments Probabilites Disposition * Comments 1 12/27/2012 Merwin Trap M A230 MT 1 LR Wild.9479 R 2 12/31/2012 Merwin Trap M A1EA MT 2 LR Hatchery (Winter).7938 R 3 1/10/2013 Merwin Trap M 66 OF6A MT 3 LR Wild.456 R wanded positive in trap but not at hatchery. Returned to river (Lesko) 4 3/4/2013 Tangle Net M 77 9E1F TN 1 LR Wild.7199 SO Spawnout 5 3/4/2013 Tangle Net M 82 9E4B TN 2 LR Hatchery (summer) Lethally Removed L /12/2013 Tangle Net F 56 9E4E TN 3 LR Wild.8161 S potentially spawned w / male TN 16, 24, /12/2013 Tangle Net F 68 9E38 TN 4 LR hatchery.9842 SO Spawnout 8 3/18/2013 Merwin Trap M A231 MT 4 LR Wild.7306 S Spawned w / Female # MT 5 9 3/21/2013 Tangle Net M 92 9E45 TN 5 LR Wild.907 S Spawned w / Female # MT /21/2013 Tangle Net F 76 9E58 TN 6 Kalama (winter).5457 R 11 3/21/2013 Tangle Net M 49 9E5A TN 7 LR Cedar.8764 S Spawned w / Female # TN /25/2013 Merwin Trap F A21E MT 5 LR Cedar.9477 S Spawned w / Male # MT 4, TN /28/2013 Tangle Net F 74 E4F4 TN 8 EFLewisR.5125 R 14 3/28/2013 Tangle Net F 65 E559 TN 9 LR Cedar.4847 LR Wild.3344 LRhatW.1135 R 15 4/1/2013 Tangle Net F 88 90FC TN 10 LR Wild.9376 S Spawned w / male TN 20, /1/2013 Tangle Net F 84 9E01 TN 11 Kalama (summer).5932 R 17 4/1/2013 Tangle Net F 79 9E3E TN 12 LR Cedar.8789 SO Spawn Out 18 4/8/2013 Tangle Net M 86 9E5E TN 13 LR Wild.9856 S Spawned w / Female # TN /8/2013 Tangle Net M 89 9E67 TN 14 LR Cedar.8406 SO Spawn Out 20 4/8/2013 Tangle Net F 67 9E75 TN 15 LR Wild.9746 S Spawned w / male TN 16, 24, /8/2013 Tangle Net M 71 9E41 TN 18 Coweeman.7341 S spawned w/ female TN /8/2013 Tangle Net F 83 9E18 TN 19 LR Wild.615 S Spawned w / Male # TN 7, TN /8/2013 Tangle Net M 46 9E26 TN 20 KalamaW.5068 S spawned w / female TN 10, MT /8/2013 Merwin Trap M A23B MT 6 LR Cedar.5661 R No BWT tag with Stubby Dorsal 25 4/15/2013 Tangle Net M 80 9E47 TN 16 LR Wild.3364 LR Cedar Spawned w / female TN 3,15,21 S /15/2013 Tangle Net M 69 9E16 TN 17 LRhatW.8176 R 27 4/15/2013 Tangle Net F 70 9E59 TN 21 LR Cedar.762 S Spawned w / male TN 16, 24, /15/2013 Tangle Net M 73 9E29 TN 22 LR Cedar.9577 S spawned w / female TN 10, MT /19/2013 Tangle Net M 69 9E52 TN 23 LR Merwin.7732 R 30 4/19/2013 Tangle Net M 82 9E02 TN 24 LR Cedar.7811 S Spawned w / female TN 3,15, /19/2013 Tangle Net M 51 9E57 TN 25 LR Merwin.8185 M Mortality 4/29/ /22/2013 Tangle Net M 98 9E10 TN 26 LR Cedar.9175 S Spawned w / female TN 3,15, /22/2013 Tangle Net M 93 9E2B TN 27 LR Cedar.8522 R 34 4/29/2013 Merwin Trap F A218 MT 7 LR Cedar.9608 S Spawned w / male TN 20, /29/2013 Tangle Net F 83 9E22 TN 28 Coweeman.5039 LR Spawned w/ male TN 18, TN 31 S Merwin /29/2013 Tangle Net F 83 9E05 TN 29 LR Wild.6491 SO Spawnout 37 4/29/2013 Tangle Net M 80 9E43 TN 30 LR Wild.7887 R 38 4/29/2013 Tangle Net M 73 9E0C TN 31 LR Wild.9827 S Spawned w/ female TN /13/2013 Merwin Trap M A1FF MT 8 R * R = Released; SO = Spawnout; S = Spawned; L = Lethally Removed; M = Mortality APPENDIX A A 1

32 APPENDIX B: Genetic Assignment Results from Lewis River Captures at Merwin Trap (MT) and In River Tangle Netting (TN) 2013

33 DNA Sample Primary (A) P(A) Secondary (B) P(B) Tertiary (C) P(C) # TN 1 LR Wild 0.72 LRCedar 0.22 Cowman 0.04 TN 2 LR Hatcher (S) 0.73 Kalama summer 0.14 LR Wild 0.10 TN 3 LR Wild 0.82 KalamW 0.09 Cowman 0.03 TN 4 HR Hatchery (W) 0.98 KalmFHat 0.01 TN 5 LR Wild 0.91 LRCedar 0.07 Kalama Winter 0.01 TN 6 Kalama Winter 0.55 LRMerwin 0.27 LR Cedar 0.16 TN 7 LR Cedar 0.88 LRMerwin 0.05 Green R 0.03 TN 8 EFLewisR 0.51 LRMerwin 0.44 MillCr 0.03 TN 9 LR Cedar 0.48 LRMerwin 0.33 LR Hatchery( W) 0.11 TN 10 LR Wild 0.94 GarysR 0.04 LR Cedar 0.02 TN 11 Kalama Summer 0.59 LR Wild 0.33 EFLewisR 0.02 TN 12 LR Cedar 0.88 LR Wild 0.07 LR Hatchery (W) 0.03 TN 13 LR Wild 0.99 LR Cedar 0.01 TN 14 LR Cedar 0.84 LR Wild 0.11 EFLewisR 0.02 TN 15 LR Wild 0.97 Cowman 0.02 TN 16 LR Wild 0.34 Kalama Winter 0.32 LR Cedar 0.31 TN 17 LR Hatchery (W) 0.82 ElochHat 0.06 LR Cedar 0.04 TN 18 Cowman 0.73 Grays R 0.17 GermCr 0.05 TN 19 LR Wild 0.62 LR Cedar 0.22 Grays R 0.09 TN 20 Kalama Winter 0.51 LR Wild 0.21 Green R 0.19 TN 21 LR Cedar 0.76 Kalama Summer 0.16 LR Wild 0.03 TN 22 LR Cedar 0.96 LR Wild 0.03 Cowman 0.01 TN 23 LR Wild 0.77 LR Cedar 0.20 Kalama Winter 0.02 TN 24 LR Cedar 0.78 LR Wild 0.20 SandyR 0.01 TN 25 LR Wild 0.82 LR Cedar 0.17 GermCr 0.00 TN 26 LR Cedar 0.92 Green R 0.05 LR Wild 0.01 TN 27 LR Cedar 0.85 LR Wild 0.09 ElochHat 0.04 TN 28 Cowman 0.50 LR Wild 0.42 LR Cedar 0.07 TN 29 LR Wild 0.65 LR Cedar 0.35 TN 30 LR Wild 0.79 LR Cedar 0.19 Green R 0.01 TN 31 LR Wild 0.98 LR Cedar 0.02 MT 1 LR Wild 0.95 Kalama winter 0.05 MT 2 LR Hatchery (W) 0.79 LR Cedar 0.11 Kalama Hatchery 0.08 MT 3 LR Wild 0.46 GraysR 0.39 LR Cedar 0.10 MT 4 LR Wild 0.73 LR Cedar 0.26 MT 5 LR Cedar 0.95 LR Wild 0.05 MT 6 LR Cedar 0.57 LR Wild 0.39 Kalama Winter 0.03 MT 7 LR Cedar 0.96 LR Wild 0.03 Cowman 0.01 APPENDIX B B 1

34 Appendix C Wild Winter Steelhead Spawning Log 2013

35 Spawn Date Female DNA # Male DNA # Female Fork Length (cm) Total Egg Weight w/ovarian (g) Estimate Eggs/Female Eyed Egg Eggs/LB Eyed Eggs On Hand Dead Eggs Actual Eggs/Female 4/10/2013 MT 5 MT 4, TN % 4/18/2013 TN 19 TN 7, TN % 4/29/2013 TN 3 TN 16, 24, % 4/29/2013 TN 15 TN 16, 24, NA NA % 4/29/2013 TN 21 TN 16, 24, % 4/29/2013 TN 10 TN 20, % 4/29/2013 MT 7 TN 20, % 5/6/2013 TN 28 TN 18, % TOTAL AVERAGE % Percent of Egg Loss APPENDIX C C 1

36 Appendix D Steelhead Redd locations, Lewis River, WA 2013

37 Steelhead Redd Locations, Lewis River, WA 2013 Surveys Path: G:\work\common\MikeIchisaka\lewis\Lewis_Redds\Lewis_redds mxd 2/7/2013 Steelhead 2013 I Miles 1:13,000 WASHINGTON Map Sheet 1 of 3 Lewis River MERWIN Map Location I

38 Steelhead Redd Locations, Lewis River, WA 2013 Surveys Path: G:\work\common\MikeIchisaka\lewis\Lewis_Redds\Lewis_redds mxd 2/7/2013 Steelhead 2013 I Miles 1:13,000 WASHINGTON Map Sheet 2 of 3 Lewis River MERWIN Map Location I

39 Steelhead Redd Locations, Lewis River, WA 2013 Surveys Path: G:\work\common\MikeIchisaka\lewis\Lewis_Redds\Lewis_redds mxd 2/7/2013 Steelhead 2013 I Miles 1:13,000 WASHINGTON Map Sheet 3 of 3 Lewis River MERWIN Map Location I

40 Steelhead Redd Locations, Lewis River, WA 2013 Surveys Path: G:\work\common\MikeIchisaka\lewis\Lewis_Redds\Lewis_redds mxd 2/7/2013 Steelhead 2013 I Miles 1:13,000 WASHINGTON Map Sheet 1 of 3 Lewis River MERWIN Map Location I

41 Steelhead Redd Locations, Lewis River, WA 2013 Surveys Path: G:\work\common\MikeIchisaka\lewis\Lewis_Redds\Lewis_redds mxd 2/7/2013 Steelhead 2013 I Miles 1:13,000 WASHINGTON Map Sheet 2 of 3 Lewis River MERWIN Map Location I

42 Steelhead Redd Locations, Lewis River, WA 2013 Surveys Path: G:\work\common\MikeIchisaka\lewis\Lewis_Redds\Lewis_redds mxd 2/7/2013 Steelhead 2013 I Miles 1:13,000 WASHINGTON Map Sheet 3 of 3 Lewis River MERWIN Map Location I

43 APPENDIX E. Smolt and Fry collections at the lower North Fork Lewis River screw trap deployed from April 18 through June 27, 2013

44 CO CK RB CT CHUM Lamprey smolt fry smolt fry smolt fry smolt fry smolt fry smolt fry SMOLTS FRY TOTAL 4/18/ /19/ /20/ /21/ cone pulled cone pulled cone pulled cone pulled cone pulled cone pulled /28/ /29/ /30/ /1/ /2/ /3/ /4/ /5/ /6/ /7/ /8/ /9/ /10/ /11/ /12/ /13/ /14/ /15/ /16/ /17/ /18/ /19/ /20/ /21/ /22/ /23/ /24/ /25/ /26/ /27/ /28/ /29/ /30/ /31/ /1/ /2/ /3/ APPENDIX E E 1

45 6/4/ /5/ /6/ /7/ /8/ /9/ /10/ /11/ /12/ /13/ /14/ /15/ /16/ /17/ /18/ /19/ /20/ /21/ /22/ /23/ /24/ /25/ /26/ /27/ /28/ APPENDIX E E 2

46 Appendix F Fork Length measurements from a sample of fishes captured in the lower North Fork Lewis River Screw Trap, April 18 through June 27, 2013

47 COHO SMOLTS RAINBOW SMOLTS CUTTHROAT OTHER 1 4/18/ /19/ /28/ /18/2013 CO /18/ /20/ /30/ /16/2013 CHUM /18/ /20/ /1/ /25/2013 PCL /18/ /21/ /1/ /18/ /21/ /2/ /18/ /21/ /2/ /19/ /21/ /2/ /20/ /30/ /4/ /20/ /2/ /7/ /20/ /2/ /9/ /20/ /2/ /9/ /20/ /3/ /10/ /20/ /4/ /10/ /20/ /6/ /10/ /20/ /7/ /10/ /21/ /7/ /10/ /21/ /7/ /15/ /21/ /8/ /15/ /21/ /8/ /18/ /28/ /8/ /20/ /28/ /9/ /20/ /28/ /10/ /23/ /28/ /10/ /23/ /28/ /10/ /24/ /28/ /11/ /31/ /28/ /11/ /30/ /11/ /30/ /11/ /30/ /11/ /30/ /11/ /30/ /11/ /1/ /11/ /2/ /11/ /2/ /11/ /2/ /11/ /3/ /11/ /3/ /11/ /3/ /11/ /6/ /11/ /6/ /11/ /6/ /11/ /6/ /11/ /6/ /11/ /6/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ Appendix F F 1

48 COHO SMOLTS RAINBOW SMOLTS CUTTHROAT OTHER 57 5/7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /7/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /8/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /9/ /11/ /10/ /11/ /10/ /11/ /10/ /11/ /10/ /11/ /10/ /11/ /10/ /12/ /10/ /12/ /10/ /12/ /10/ /12/ /10/ /12/ Appendix F F 2