Paul Moran and Robin S. Waples Conservation Biology Division Northwest Fisheries Science Center

1. Monitor and evaluate characteristics of supplemented salmon and steelheadProject number 198909600CBFWA Project Implementation Review MeetingPortland, Oregon March 28, 2006 Paul Moran and Robin S. Waples Conservation Biology Division Northwest Fisheries Science Center National Marine Fisheries Service

2. Outline • Critical uncertainties in recovery • Previous achievements • Future of genetic M&E in hatchery reform

3. Goals of our study • Reproductive success of hatchery fish • Steelhead and rainbow trout • Significance of adaptive variation Addressing critical uncertainties in supplementation, recovery, and conservation genetics

4. Broad support for genetic M&E • Columbia River Basin Fish and Wildlife Program and Subbasin Plans • Wy Kan Ush Me Wa Kush Wit • FCRPS Biological Opinion and Updated Proposed Action (RPAs and UPAs)

5. Previous achievements • Support for management • Population structure for NMFS status reviews • Data for US v Oregon resolution • Migration rates and effective population size • Chinook mouth tumors • Interlaboratory data standardization • Reproductive success estimates • Methodological and biological results • Publications

6. Papers, reports, book chapters, and abstracts—9 since 2003 • Waples, R. S., D. J. Teel, and P. B. Aebersold. 1991. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River Basin. Annual Report of Research to Bonneville Power Administration, Portland, OR, 50 p. • Utter, F. M.,R. S. Waples, and D. J. Teel. 1992. Genetic isolation of previously indistinguishable chinook salmon populations of the Snake and Klamath Rivers: Limitations of negative data. Fish. Bull. (U.S.) 90:770-777. • Waples, R. S., O. W. Johnson, P. B. Aebersold, C. K. Shiflett, D. M. VanDoornik, D. J. Teel, and A. E. Cook. 1993. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River Basin. Annual Report of Research to Bonneville Power Administration, Portland, OR, 179 p. • Park, L. K., P. Moran, and R. S. Waples (editors). 1994. Application of DNA technology to the management of Pacific salmon. Proceedings of the workshop, 22-23 March 1993, Seattle, WA. U.S. Dept. Commerce, NOAA Tech. Memo. NMFS‑NWFSC-17, 178 p. • Park, L. K., and P. Moran. 1994. Developments in molecular genetic techniques in fisheries. Reviews in Fish and Fisheries Biology 4:272 299. • Waples, R. S., and C. Do. 1994. Genetic risk associated with supplementation of Pacific salmonids: Captive broodstock programs. Can. J. Fish. Aquat. Sci. 51 (Suppl. 1):310‑329. • Park, L. K., P. Moran, and D. Dightman. 1995. A polymorphism in intron D of the chinook salmon growth hormone 2 gene. Animal Genetics. 2(26):285. • Park, L. K., P. Moran, and D. Nickerson. 1994. Application of the oligonucleotide ligation assay (OLA) to the study of chinook salmon populations from the Snake River. In, L. K. Park, P. Moran and R. S. Waples (eds.). Application of DNA technology to the management of Pacific salmon. U.S. Dep. Commer., NOAA Tech. Memo NMFS NWFSC-17:91-97. • Park, L. K., P. Moran, and D. A. Dightman. 1996. A chinook salmon PCR‑RFLP marker in the p53 locus. Animal Genetics 27:127‑128. • Moran, P., D. A. Dightman, R. S. Waples, and L. K. Park. 1997. PCR-RFLP analysis reveals substantial population-level variation in the introns of Pacific salmon (Oncorhynchus spp.). Mol. Mar. Biol. Biotechnol. 6:318-330. • Ford, M. J. 1998. Testing models of migration and isolation among populations of chinook salmon (Oncorhynchus tshawytscha). Evolution 52:539-557. • Moran, P., D. A. Dightman, L. K. Park. 1998. Nonelectrophoretic genotyping using allele-specific PCR and a dsDNA-specific dye. Biotechniques 24:206-212. • Waples, R. S. 1998. Separating the wheat from the chaff: Spatial and temporal patterns of genetic differentiation in marine species. J. Heredity 89:438-450. • Ford, M. J., P. J. Thornton, and L. K. Park. 1999. Natural selection promotes divergence of transferrin among salmonid species. Molec. Ecol. 8:1055–1061. • Ford, M. J. 2000. Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among chinook salmon (Oncorhynchus tshawytscha) populations. Molec. Ecol. 9:843-855. • Moran, P. 2002. Current conservation genetics: building an ecological approach to the synthesis of molecular and quantitative genetic methods. Ecology of Freshwater Fish 11:30-55. • Moran, P. and J. Baker. 2002. Inhibitory compounds reduce PCR efficiency in genotyping archived fish scales. Transactions of the American Fisheries Society 131: 109–119. • Waples R. S., M.J. Ford, D. Schmitt. 2002. Empirical results of salmon supplementation in the Pacific Northwest: A preliminary assessment. pp. xxx, in, T. Bert, ed. Ecological and Genetic Implications of Aquaculture Activities. Kluwer Academic Publishers. In press. • Waples, R. S. 2002. Definition and estimation of effective population size in the conservation of endangered species. In: Beissinger, S. R. and D. R. McCullough, (eds.), pp. 147-168. Population Viability Analysis. University of Chicago Press, Chicago, IL. • Waples, R. S.  Salmonid insight into effective population size.  Pp. xxx in A. P. Hendry and S. C. Stearns, eds.  Salmonid perspectives on evolution.Oxford University Press [In press]. • Moran, P. 2003. Genetic structure of Oncorhynchus mykiss populations in the Grande Ronde River, Imnaha River, and adjacent regions of the Snake River basin. Final report submitted to the U.S. fish and Wildlife Service, Lower Snake River Compensation Plan Office, Boise, Idaho, in partial fulfillment of Contract No. 14110-1-H070. 28p. + Appendices. • Moran, P. 2003. New molecular methods represent a paradigm shift. SETAC Globe 4:42-43. • Johnson, O., K. Neely, and R. S. Waples. 2004. Lopsided fish in the Snake River Basin: Fluctuating asymmetry as a way of assessing the impact of hatchery supplementation in chinook salmon, Oncorhynchus tshawytscha. Env. Biol. Fish. 69:379-393. • Lundrigan, T.A., P. Moran, D. J.Teel, A. R. Marshall, S.F. Young, and D.L. Bottom. 2004. Conservation and genetic stock identification: A study investigating the stock-specific distribution and performance of juvenile Chinook salmon in the Columbia River estuary. N. Pac. Anadr. Fish. Comm. Tech. Rep. 5: 70-71. • Waples, R. S. 2004. Salmonid insight into effective population size. Pp. 295-314 in A. P. Hendry and S. C. Stearns, eds. Evolution illuminated: Salmon and their relatives.Oxford University Press, Oxford, UK. • Waples, R. S., D. J. Teel, J. Myers, and A. Marshall. 2004. Life history divergence in chinook salmon: historic contingency and parallel evolution. Evolution 58:386-403. • Winans, G.A., M.Z. Paquin, D.M. VanDoornik, D. Rawding, B. Baker, A. Marshall, P. Moran, and S. Kalinowski. 2004. Genetic stock identification of steelhead in the Columbia River basin: An evaluation of different molecular markers. N. Am. J. Fish Manag. 24:672–685. • Moran, P., D.J. Teel, E.S. LaHood, J. Drake, and S. Kalinowski. 2006. Standardizing multi-laboratory microsatellite data in Pacific salmon: An historical view of the future. Ecol. Freshwater Fish accepted. • Narum, S. R., S. Boe, P. Moran, and M. Powell. 2006. Small scale genetic structure and variation in steelhead trout of the Grande Ronde River, Oregon, U.S.A. Trans. Amer. Fish. Soc. accepted.

7. Two strategies for genetic monitoring of hatchery supplementation • Gene frequency monitoring design: • Change in allele frequencies through time among hatchery, natural, and wild populations • Reproductive success design: • Pedigrees in natural populations and hatchery broodstocks

8. Little Sheep Creek Snake River Basin geneticmonitoring study area

9. Little Sheep Creek steelhead • Mitigation/supplementation program • In operation for ~4 generations • Local broodstock • Sustained incorporation of wild spawners • Accelerated rearing schedule

18. Steelhead returning to Little Sheep Creek X Trap intercepts migrating adults, March – May Parent tissue samples Sample juvenile offspring, Aug. – Oct. Sample residents and out-migrating smolts

19. Candidate parents 3 0 0 0 3 2 7 2 0 - 0 2 3 3 2 7 2 0 - 0 2 1 2 0 0 0 2 0 0 0 1 0 0 0 1 0 0 0 2 0 4 2 1 2 2 1 2 2 2 4 2 0 0 0 2 0 0 0 3 2 7 2 1 - 0 3 6 3 2 7 2 1 - 0 1 3 2 0 0 0 3 2 7 2 1 - 0 2 3 1 5 0 0 1 5 0 0 1 0 0 0 1 0 0 0 1 0 0 0 5 0 0 5 0 0 2 2 4 2 0 0 2 0 4 2 1 2 1 9 6 2 0 0 Mendelian inheritance excluded non-excluded partially-excluded (“match”) (half-sib) Offspring

20. 1.20 1.00 0.80 Wild Hatchery 0.60 0.40 0.20 0.00 W H W H W H W H 2000 2001 2002 2003 Steelhead reproductive success by hatchery/wild origin

21. Correlates of reproductive success • mate choice/competition • spawn time/location • sperm competition/fecundity • gamete/offspring viability • egg-parr, parr-smolt, smolt-adult • phenotypic traits

22. Estimation of selection gradients Model is a modification of Smouse, Meagher and Kobak (J Evol Biol 12:1069-1077); Morgan and Conner (Evolution 55:272-281) relative fitness of female j relationship between fitness and traits likelihood of observing offspring i likelihood of observing offspring sample

23. Steelhead selection gradients Larger females are more fit… Length …but not so larger males Length

24. Early returning fish are more fit Run timing

25. Distribution of offspring among sites

26. Pedigree studies at NWFSC • Little Sheep Creek steelhead • Lostine River Chinook • Catherine Creek Chinook • Upper Grande Ronde Chinook • Wenatchee River Chinook • Minter Creek coho

27. Reproductive success in NE Oregon Chinook captive broodstock programs Preliminary results show progeny of captive fish similar to wild in Lostine River and Catherine Creek

28. Reproductive success studies • Relate reproductive success to specific quantitative genetic traits and rearing regimes in both hatchery and wild • Pedigrees provide detailed characterization of micro-evolutionary processes

29. Conventional gene frequency monitoring studies • Allele frequency changes through time among hatchery, natural, and wild populations • Infer short-term reproductive success superimposed on long-term evolutionary divergence

30. Spatiotemporal variation in Salmon R. Chinook

31. RxC contingency test of steelhead allele frequencies 52 populations, 16 loci a’ = 4.0 x 10-5 Wallowa Hatchery strays Rattlesnake Cr. Menatchee Cr. P < 0.00004 between sites Deschutes R. Cottonwood Cr. Grande Ronde/Imnaha Paquin et al. unpubl.

32. Traditional genetic monitoring Geographic, temporal, and programmatic scale not possible with pedigree studies

33. Direct study of adaptation and domestication • Quantitative genetics via natural pedigrees • Microsatellite markers linked to functional genes • Resident/anadromous, hatchery/wild, resistant/susceptible Structural gene Microsatellite marker Fish chromosome

34. Future role of genetic M&E • Artificial propagation with reform remains central to recovery planning • Current genetic methods provide powerful tools for real-time M&E of hatchery reform