Monitor and evaluate characteristics of supplemented salmon and steelhead

Project number 198909600

CBFWA Project Implementation Review Meeting Portland, Oregon

March 28, 2006

Paul Moran and Robin S. WaplesConservation Biology Division

Northwest Fisheries Science Center

National Marine Fisheries Service

Outline

• Critical uncertainties in recovery

• Previous achievements

• Future of genetic M&E in hatchery reform

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

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)

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

1. 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.

2. 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.

3. 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.

4. 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.

5. Park, L. K., and P. Moran. 1994. Developments in molecular genetic techniques in fisheries. Reviews in Fish and Fisheries Biology 4:272 299.

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. Ford, M. J. 1998. Testing models of migration and isolation among populations of chinook salmon (Oncorhynchus tshawytscha). Evolution 52:539-557.

12. Moran, P., D. A. Dightman, L. K. Park. 1998. Nonelectrophoretic genotyping using allele-specific PCR and a dsDNA-specific dye. Biotechniques 24:206-212.

13. 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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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.

19. 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.

20. 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].

21. 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.

22. Moran, P. 2003. New molecular methods represent a paradigm shift. SETAC Globe 4:42-43.

23. 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.

24. 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.

25. 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.

26. 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.

27. 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.

28. 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.

29. 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.

Papers, reports, book chapters, and abstracts—9 since 2003Papers, reports, book chapters, and abstracts—9 since 2003

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

Two strategies for genetic monitoring of hatchery supplementation

WashingtonMontana

OregonIdaho

Salmon River

Snak

eR

iverG

rand

eRon

deRiv

er

Imn

aha

R.

River

Clearwater

Middle

Fork

S. F

ork

Salmon

Riv

er

Columbia River

Snake

River

E. F

ork

Little Sheep Creek

Snake River Basin geneticmonitoring study area

Little Sheep Creek steelhead

• Mitigation/supplementation program• In operation for ~4 generations• Local broodstock• Sustained incorporation of wild

spawners• Accelerated rearing schedule

Parent tissue samples

X

Sample juvenile offspring, Aug. – Oct.

Trap intercepts migrating adults,March – May

Steelhead returning to Little Sheep Creek

Sample residents and out-migrating smolts

Mendelian inheritance

excluded non-excluded partially-excluded

(“match”)(“match”) (half-sib)(half-sib)

204 212

1000

2000

3000

32720-02132720-023

224212

1000

2000

204 212

1000

200032721-013500100015002000

32721-023500100015002000

32721-036

196 200 200 224

Candidate parents

Offspring

Steelhead reproductive success Steelhead reproductive success by hatchery/wild originby hatchery/wild origin

0.00

0.20

0.40

0.60

0.80

1.00

1.20

W H W H W H W H

2000 2001 2002 2003

Wild

Hatchery

Correlates of reproductive success

•mate choice/competition

•spawn time/location

•sperm competition/fecundity

•gamete/offspring viability

•egg-parr, parr-smolt, smolt-adult

•phenotypic traits

Estimation of selection gradientsModel is a modification of Smouse, Meagher and Kobak (J Evol Biol 12:1069-1077); Morgan and Conner (Evolution 55:272-281)

ftotal

fj

fj

fj

relative fitness of female j

relationship between fitness and traits

likelihood of observing offspring i

likelihood of observing offspring sample

traits

ttj

fttj

ft

fj zz

1

2log

jk

kjii mtotal

ftotal

mj

fkXL

,,,

iLL

Steelhead selection gradients

Length

Length

Larger females are more fit…

…but not so larger males

Early returning fish are more fit

Run timing

Distribution of offspring among sitesDistribution of offspring among sites

Least Squares Means

HH HW WH WWANCESTRY

2.0

5.8

9.6

13.4

17.2

21.0S

ITE

Pedigree studies at NWFSC

• Little Sheep Creek steelhead• Lostine River Chinook• Catherine Creek Chinook• Upper Grande Ronde Chinook• Wenatchee River Chinook• Minter Creek coho

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

• Relate reproductive success to specific quantitative genetic traits and rearing regimes in both hatchery and wild

• Pedigrees provide detailed characterization of micro-evolutionary processes

Reproductive success studies

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

Spatiotemporal variation in Salmon R. Chinook

I- 1 . 1 4 - 0 . 5 7 0 . 0 1 0 . 5 8 1 .1 5

I I

- 0 . 8 8

- 0 . 3 8

0 . 1 2

0 . 6 3

1 . 1 3

R a p id R iv e r H 0 0

R a p id R iv e r H 0 1

S e c e s h R 0 0S e c e s h R 0 1M c C a l l H

P o v e r t y F la t 0 0

P o v e r t y F la t 0 1

K n o x B r i d g e 0 0K n o x B r i d g e 0 1

S t o l l e M e a d 0 0

S to l l e M e a d 0 1

J o h n s o n C r 9 8J o h n s o n C r 0 0

B i g C r e e k L 9 8

B i g C r e e k L 0 2

B i g C r e e k U 9 8

B i g C r e e k U 0 1

M a r s h C r 0 0

M a r s h C r 0 1B e a r V a l C r 0 1

B e a r V a l C r 9 8

E l k C r 9 8

E l k C r 9 8

V a l l e y C r U 9 8

V a l l e y C r U 0 1

V a l le y C r L 9 8

V a l l e y C r L 0 1

S a l m o n R U 9 8

Middle Fork

South Fork

Mainstem

Little Salmon R.

RxC contingency test of steelhead allele frequencies

’ = 4.0 x 10-5

WallowaHatchery

Rattlesnake Cr.

Menatchee Cr.

Cottonwood Cr.

strays

Deschutes R.

Grande Ronde/Imnaha

P < 0.00004between sites

Paquin et al. unpubl.

52 populations, 16 loci

Pel98 Shi2 War2 Was99 Rou90 Aso3 Rat3 Men3 Cot2Tuc3 * * * * * NS * * *Wal95 NS * * NS * * NS NS NSPel98 NS NS NS NS NS * * *Shi2 NS * NS * * * *War2 * NS * * * *Was99 * * NS NS *

Traditional genetic monitoring

Geographic, temporal, and programmatic scale not possible with pedigree studies

Direct study of adaptation and domestication

• Quantitative genetics via natural pedigrees• Microsatellite markers linked to functional genes• Resident/anadromous, hatchery/wild, resistant/susceptible

Structural geneMicrosatellite marker

Fish chromosome

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