Inbreeding and inbreeding depression in hatchery steelhead K

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

Acknowledgements Hatchery Crew 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. . . George Britter, WDFW Rob Allan, WDFW Dave Shores, WDFW Kevin Flowers, WDFW Jenny Allan Merle Hash Former Students Larry Sienko Greg Mackey Max Burleson Jennifer Mc. Lean Michael Dauer Funding Weyerhaeuser H. Mason Keeler Endowment National Science Foundation (DEB-9903914) Hatchery Science Reform Group Bonneville Power Administration (2003 -050 -00)

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

Spawned and killed at the hatchery • Spawned To Willapa River (0. 1 km) Highway 6 • Released as smolts • Return to hatchery

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

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 Mc. Lean et al. 2005. Cons. Biology, Mc. Lean et al. 2008. Cons. Genetics

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

Study design: hatchery fish • Molecular based pedigree Initiation year 1994 1995 1996 Return year 1996 1997 1998 1999 2001 2002 2003 2004 2005 2006 2007 2008 2009 F 0 return F 1 return F 2 return F 3 return Freshwater phase Marine phase • 6602 hatchery fish over 14 return years • 5738 (2952 males and 2546 females) were included in the pedigree (86. 9% of all clipped fish)

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

Inbreeding in the hatchery Delta F RY 2002 2003 2004 2005 2006 2007 2008 2009 0. 0078 0. 0313 0. 0391 0. 0469 0. 0547 0. 0625 0. 0938 0. 1250 0. 2500 Nreturn 22 14 ^ Half second cousins 1 16 76 35 30 11 ^ Half first cousins 1 2 2 1 7 8 ^ First cousins Increasingly inbred 7 3 19 22 42 20 12 10 ^ Half sib 1 2 ^ Full sib 293 504 743 994 966 747 587 320 % Inbred 2. 39 0. 60 2. 83 3. 92 12. 22 7. 36 12. 61 14. 69

Complexity in pedigrees • A greater range of inbreeding classes can be detected with deeper pedigrees F 2 F 3 F 4 F 5 F 6 Lowest F 0. 125 0. 03125 0. 007813 0. 001953 0. 000488

Amount of inbreeding not unexpected given Ne Expected Ft in F 3 = 0. 0149 Actual Ft in F 3 = 0. 0663 SD = 0. 042 Ne based on variance in sex ratio and reproductive success v Gen N F 0 return 341 F 1 444 F 2 1577 Avg. 515. 6 Sex F M F M N spawn 179 161 100 115 212 232 304. 2 ki σ2 i Ne_sex Ne _var Ne_both 5. 3 3. 7 16. 0 13. 5 4. 6 5. 8 59. 7 41. 3 186. 0 265. 6 54. 8 155. 4 339. 0 102. 8 101. 7 214. 0 111. 3 107. 0 443. 1 93. 9 100. 9 303. 7 102. 2 103. 1 ^ Avg. no. offspring by sex ^ Variance in reproductive success by sex

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

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

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

Inbreeding depression in O. mykiss • 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) Decreased marine survival rates in inbred smolts released from two captive broodstocks.