Inbreeding and inbreeding depression in hatchery steelhead

1. Inbreeding and inbreeding depression in hatchery steelhead K Naish, TR Seamons, M Dauer, T Quinn, L Hauser University of Washington School of Aquatic and Fishery Sciences

2. Acknowledgements Hatchery Crew George Britter, WDFW Rob Allan, WDFW Dave Shores, WDFW Kevin Flowers, WDFW Jenny Allan Merle Hash Larry Sienko Max Burleson Faculty Paul Bentzen, Dalhousie U Tom Quinn, UW Lorenz Hauser, UW Kerry Naish, UW Jeff Hard, NMFS Lab and Field Lyndsay Newton Duy Mai Will Atlas Many others... Former Students Greg Mackey Jennifer McLean Michael Dauer Funding Weyerhaeuser H. Mason Keeler Endowment Hatchery Science Reform Group National Science Foundation (DEB-9903914) Bonneville Power Administration (2003-050-00)

3. Negative genetic risks of hatchery supplementation • On hatchery fish • Loss of genetic diversity • Inbreeding • Domestication • On wild fish • Loss of genetic diversity • Introgression • Outbreeding depression • Loss of population structure Naish et al. 2008 Advances in Marine Biology

4. Spawned and killed at the hatchery • Spawned • Released as smolts • Return to hatchery To Willapa River (0.1 km) Highway 6 Forks Creek

5. WA State hatchery • Provides fish for recreational fisheries • No tribal or in-stream commercial harvest • Also rear • Chinook • Coho

6. Hatchery population is losing genetic diversity • Spawned a fraction of the population • Larger • Assortatively spawned large fish • Earlier • Earlier spawned fish had more surviving offspring • Variance in reproductive success is high • Higher in males • Low effective number of breeders McLean et al. 2005. Cons. Biology, McLean et al. 2008. Cons. Genetics

7. Data and approach • Pedigree • Inferred from genetic data • Inbreeding? • Inbreeding depression? • Change in traits correlated with fitness • Fork length, body weight, day of return, gonad mass, fecundity, egg size

8. Study design: hatchery fish Freshwater phase Marine phase F0 return F1 return F2 return F3 return Initiation year Return year 1996 1997 1998 1999 2001 2002 2003 2004 2005 2006 2007 2008 2009 1994 1995 1996 Molecular based pedigree 6602 hatchery fish over 14 return years 5738 (2952 males and 2546 females) were included in the pedigree (86.9% of all clipped fish)

9. Identifying inbred individuals in a pedigree 1 1 1 1 A C B 2 2 2 2 D E X “Traditional” pedigree “Inbreeding” pedigree F - “the probability that both alleles at a locus are identical by descent” F ranges from 0 to 1

10. Inbreeding in the hatchery ^ ^ ^ ^ ^ Half second cousins First cousins Half sib Full sib Half first cousins Increasingly inbred

11. Complexity in pedigrees A greater range of inbreeding classes can be detected with deeper pedigrees

12. Amount of inbreeding not unexpected given Ne Expected Ft in F3 = 0.0149 Actual Ft in F3 = 0.0663 SD = 0.042 Ne based on variance in sex ratio and reproductive success v ^ ^ Avg. no. offspring by sex Variance in reproductive success by sex

13. Breeding protocol • 1996 - 2003 • 5 x 5 (+-) in one bucket • Average of • 53 females • 58 males • 2004 - 2009 • 1 x 1 in one bucket • Average of • 85 females • 85 males

14. 1200 Total 1000 Spawned (males + females) 800 600 400 200 0 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Fraction of population spawned is low Adults (count) Year

15. Ways to improve • Increase fraction of population spawned • Decrease variance in family size • 2003 unintentionally transferred or killed all but one spawning date • Decrease variance in male reproductive success relative to female reproductive success • Water harden before combining • More labor and space intensive

16. Inbreeding depression in O.mykiss Decreased marine survival rates in inbred smolts released from two captive broodstocks. In culture, close inbreeding (F=0.25) leads to a rapid decline in fitness (Pante et al. 1993) Results repeated in a controlled release in Alaska (Thrower and Hard, 2009)