Inbreeding and inbreeding depression in hatchery steelhead Inbreeding and inbreeding depression in hatchery steelhead

K Naish, TR Seamons, M Dauer, T Quinn, L HauserUniversity of WashingtonSchool of Aquatic and Fishery Sciences

K Naish, TR Seamons, M Dauer, T Quinn, L HauserUniversity of WashingtonSchool of Aquatic and Fishery Sciences

AcknowledgementsAcknowledgementsFaculty

Paul Bentzen, Dalhousie U

Tom Quinn, UW

Lorenz Hauser, UW

Kerry Naish, UW

Jeff Hard, NMFS

Hatchery Crew

George Britter, WDFW

Rob Allan, WDFW

Dave Shores, WDFW

Kevin Flowers, WDFW

Jenny Allan

Merle Hash

Larry Sienko

Max Burleson

Lab and Field

Lyndsay Newton

Duy Mai

Will Atlas

Many others...

Funding

Weyerhaeuser

H. Mason Keeler Endowment

Hatchery Science Reform Group

National Science Foundation (DEB-9903914)

Bonneville Power Administration (2003-050-00)

Former Students

Greg Mackey

Jennifer McLean

Michael Dauer

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

To Willapa River (0.1 km)

Highway 6

•Spawned

•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

McLean et al. 2005. Cons. Biology, McLean 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

• 6602 hatchery fish over 14 return years• 5738 (2952 males and 2546 females)

were included in the pedigree (86.9% of all clipped fish)

Initiation year 1996 1997 1998 1999 2001 2002 2003 2004 2005 2006 2007 2008 2009199419951996

Return year

F0 return F1 return F2 return F3 return

Freshwater phaseMarine phase

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

12

12

12

12

B A C

D E

X

“Traditional” pedigree “Inbreeding” pedigree

Inbreeding in the hatchery

Delta F

RY0.0078 0.0313 0.0391 0.0469 0.0547 0.0625 0.0938 0.1250 0.2500 Nreturn

% Inbred

2002 7 293 2.392003 3 504 0.602004 1 1 19 743 2.832005 16 22 1 994 3.922006 76 42 966 12.222007 35 20 747 7.362008 22 30 2 1 7 12 587 12.612009 14 11 2 8 10 2 320 14.69

Full sibHalf sibHalf second cousins

Half firstcousins

First cousins

^ ^ ^ ^^

Increasingly inbred

Complexity in pedigrees

• A greater range of inbreeding classes can be detected with deeper pedigrees

Lowest FF2 0.125F3 0.03125F4 0.007813F5 0.001953F6 0.000488

Amount of inbreeding not unexpected given Ne

GenN

returnSex

N

spawnki σ2

i Ne_sex Ne _var Ne_both

F0 341 F 179 5.3 59.7 339.0 102.8 101.7M 161 3.7 41.3

F1 444 F 100 16.0 186.0 214.0 111.3 107.0M 115 13.5 265.6

F2 1577 F 212 4.6 54.8 443.1 93.9 100.9M 232 5.8 155.4

Avg. 515.6 304.2 303.7 102.2 103.1

Avg. no. offspring by sex

Variance in reproductive success by sex

^

Ne based on variance in sex ratio and reproductive success

v

Expected Ft in F3 = 0.0149Actual Ft in F3 = 0.0663 SD = 0.042

^

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

0

200

400

600

800

1000

1200

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

Total

Spawned (males + females)

Fraction of population spawned is low

Adults (count)

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.