Lewis River Bull Trout: A Synthesis of Known Information J. Michael Hudson1, Jeremiah Doyle2, Jamie Lamperth3, Robert Al-Chokhachy4, Greg Robertson5, Tom Wadsworth3 1 U.S. Fish and Wildlife Service, Columbia River Fish and Wildlife Conservation Office 2 PacifiCorp 3 Washington Department of Fish and Wildlife 4 U.S. Geological Survey, Northern Rocky Mountain Science Center 5 U.S. Forest Service, Gifford-Pinchot National Forest April 4, 2019 1 [THIS PAGE INTENTIONALLY LEFT BLANK] 2 Table of Contents I. Introduction ..................................................................................................................................... 8 II. Study Area ........................................................................................................................................ 8 a. Subbasin Description ......................................................................................................... 8 b. Bull trout populations and life-history types present in the Lewis River subbasin ......... 10 c. Habitat ............................................................................................................................. 10 i. Stream Temperature .................................................................................................................... 10 ii. In-stream Habitat ........................................................................................................................ 11 d. Fishery management ........................................................................................................ 12 III. Demographic characteristics ........................................................................................................ 13 a. Abundance ....................................................................................................................... 13 i. Estimates of abundance from mark/resight in Swift reservoir .................................................... 13 ii. Estimates of abundance from redd counts in Cougar Creek and P8 ........................................... 15 b. Effective population size ................................................................................................. 17 i. Estimates of effective number of breeders (Nb) ......................................................................... 17 c. Sex ratio ........................................................................................................................... 19 d. Age structure ................................................................................................................... 19 e. Age at maturity ................................................................................................................ 19 IV. Vital Rates ...................................................................................................................................... 21 a. Survival ........................................................................................................................... 21 b. Growth ............................................................................................................................. 22 c. Fecundity ......................................................................................................................... 23 V. Spatial Distribution ....................................................................................................................... 23 a. Length-frequency of bull trout in tributaries ................................................................... 23 b. eDNA ............................................................................................................................... 24 c. Occupancy and distribution ............................................................................................. 25 VI. Movement patterns ........................................................................................................................ 28 a. PIT monitoring ................................................................................................................ 28 b. Radiotelemetry ................................................................................................................ 32 c. Screw traps ...................................................................................................................... 34 VII. Genetic diversity ............................................................................................................................ 36 VIII. Limiting factors ............................................................................................................................. 37 3 a. Evaluation of three proposed management scenarios to enhance three potential bull trout nursery habitats accessible to Lake Merwin and Yale Lake, Lewis River ...................... 38 b. Lake Merwin and Swift Creek Reservoir tributary streams: bull trout limiting factors analysis ............................................................................................................................ 39 c. Lewis River bull trout habitat restoration project identification assessment .................. 42 IX. Data gaps and Research Monitoring and Evaluation (RME) needs ......................................... 48 X. Acknowledgments .......................................................................................................................... 49 XI. Literature cited .............................................................................................................................. 49 Table of Tables Table 1. Estimates of annual bull trout (>360 mm FL) staging at the head of Swift reservoir in the upper Lewis River ..................................................................................................................... 15 Table 2. Number of age-0 bull trout collected by spawn year and spawning tributary to estimate effective number of breeders (Nb) ............................................................................................ 18 Table 3. Estimates of the effective number of breeders (Nb) with 95% confidence intervals (in parentheses) from bull trout spawning tributaries on the Lewis River in southwest WA. ........ 18 Table 4. Number of juvenile bull trout captured and length statistics of the captured fish by year and trap location. Length was measured from each captured bull trout. Eagle Cliff is the Lewis River near the head of Swift Reservoir. ......................................................................... 35 Table 5. Initial sample sizes from each tributary, number of full sibling families detected, adjusted sample sizes, and estimates of genetic diversity including the mean number of alleles per locus (A), allelic richness (AR), expected heterozygosity (Hexp), and observed heterozygosity (Hobs) for bull trout collected from three Lewis River tributaries. .................... 36 Table 6. Pairwise estimates of genetic variation (pairwise FST) among bull trout collected from three Lewis River tributaries. Estimates are based on 16 microsatellite loci. .......................... 36 Table 7. Initial bull trout habitat ranking categories. .............................................................................. 40 Table 8. Factors likely preventing the occurrence of an established bull trout population in the four streams with marginal or optimal habitat potential. .................................................................. 41 Table 9. List of habitat variables used to develop a redd occurrence model for bull trout in the upper Lewis River subbasin, WA. The variables were summarized at 100 m reaches. ........... 43 4 Table 10. Parameter estimates and scaled odds ratios for the global model relating bull trout redd occurrence to physical habitat variables in the upper Lewis River subbasin, WA. Log- 2 2 2 transformed (loge(x+1)) values of Boulder (m ), Fines (m ), and Pool (m ) were used in model. ........................................................................................................................................ 44 Table 11. Parameter estimates and odds ratios for the bull trout redd occurrence model with the lowest AICc score. .................................................................................................................... 45 Table of Figures Figure 1. Spatial distribution of adfluvial bull trout, the only life history that has been documented in the Lewis River basin based on field sampling over the past four decades (1979 – 2016). Map inset shows the Lewis River basin (white polygon in southwest WA) in relation to the distribution of bull trout (dark stream lines) in the coterminous United States. ......................... 9 Figure 2. Location and number of years of available stream temperature data in the upper Lewis River basin. ............................................................................................................................... 11 Figure 3. Location and number of years of data available from USDA-Forest Service stream inventory surveys. ..................................................................................................................... 12 Figure 4. Annual estimates of bull trout (>360 mm) staging at the head of Swift reservoir in the upper Lewis River (bars represent the 95% confidence intervals). ........................................... 14 Figure 5. Annual cumulative bull trout redd counts from Cougar Creek. ^shortened