020313 genetic pedigree of chinook transported above cougar dam
DESCRIPTION
Presented at the 2013 Willamette Fisheries Science Review in Corvalllis, OregonTRANSCRIPT
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Total Lifetime Fitness and Cohort
Replacement Rate for Chinook Salmon Outplanted
above Cougar Dam, South Fork McKenzie River
Dave P. Jacobson1, Nick Sard1, Michael J. Hogansen2, Kirk Schroeder2,
Marc A. Johnson2, Kathleen G. O’Malley1 and Michael A. Banks1
• 1 Oregon State University, Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment
Station, Hatfield Marine Science Center, 2030 SE Marine Science Drive, Newport, Oregon 97365
• 2 The Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, 28655 Highway 34,
Corvallis, Oregon 97333
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Objectives
• Determine the proportion of unmarked
Chinook collected at the Cougar trap-and-
haul in 2012 that could be assigned as
progeny of 2007-2009 outplants
• Estimate total lifetime fitness of 2007
outplants and investigate sources of variance
• Estimate cohort replacement rate and
genetic effective population size
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Total Lifetime Fitness
The number of adult spawners produced by an
individual
For our study:
The number of unmarked adult Chinook
collected at Cougar Dam that could be
confidently assigned as progeny of a previous
outplant
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Cohort Replacement Rate (CRR)
The number of adults in one generation divided
by the number of adults in the generation that
produced them
For our study:
The number of adult females in one generation
divided by the number of adult females in the
generation that produced them
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Effective Population Size
The average size of a population in terms of
the number of individuals that contribute
genes equally to the next generation
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Adult Return Years
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Methods
• Genotyped outplants at 11 microsatellites
• Performed a likelihood-based parentage
analysis
• CERVUS
•Explanatory variables: Outplant date, outplant site, sex, number of mates
• Generalized Linear Models (GLM)
•R
•Genetic Effective Population Size
•LDNE1
1Waples and Do 2008
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Assignments by sex
Results – 2012 Adult Returns
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Assignments to cohort
Results – 2012 Adult Returns
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Age class assignments
5 year old 4 year old Unknown
Results – 2011 and 2012 Adult Returns
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2011
September 1st
6/23 7/18 8/12 9/06
Date
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2012
September 1st
5/29 7/18 9/06 10/26
Date
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Seasonality of
Assignment Rate
Collected Assigned Proportion that
Assigned
Before 01 September 331 259 0.78
After 01 September 169 32 0.19
Total 500 291 0.58
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Outplant Dates in 2007 Tota
l Lifetim
e F
itness
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Parental Fitness
GLM
Estimate z value Pr(>|z|) CI 95%
(Intercept) 2.468 2.03 0.04 1.055 - 5.812
Julian date 0.993 -3.364 7.6E-4 0.989 - 0.997
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Outplant Date Tota
l Lifetim
e F
itness
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GLM
Estimate z value Pr(>|z|) CI 95%
(Intercept) 2.068 1.230 0.220 0.906 -4.752
Julian date 0.994 -2.741 6.1E-3 0.990 - 0.997
Estimate z value Pr(>|z|) CI 95%
(Intercept) 2.468 2.030 0.040 1.055-5.812
Julian date 0.993 -3.364 7.6E-4 0.989-0.997
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GLMs continued
Females Estimate z value Pr(>|z|) CI 95%
(Intercept) 1.14 0.455 0.649 0.67 - 2.01
Hard Rock 0.54 -1.820 0.069 0.02 - 1.04
Bridge 1980 0.45 -1.908 0.056 0.02 – 1.02
Bridge 430 0.52 -2.014 0.044 0.27 – 0.97
Males Estimate z value Pr(>|z|) CI 95%
(Intercept) 3.53 1.956 0.051 1.00 - 12.67
Julian Date 0.99 -3.044 0.002 0.986 – 0.997
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Tota
l Lifetim
e F
itness
Bet Hedging
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Female Cohort Replacement Rate
113/269 = 0.38
111
269 Outplanted
in 2007
113 Adult Progeny
2010-2012
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Effective Population Size
•Ne : 112-146
•Pedigree
•99 Females
•115 Males
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Summary
• Spring Chinook that returned early assigned at
a higher rate than later returning fish
• Chinook outplanted later in the season
produced fewer adult returns
• More mates associated with higher fitness
•Females Cohort Replacement Rate <0.50
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Thanks to:
US Army
Corps of Engineers
OSU:
Carl Schreck
Jen Britt
Sana Banks
Miles Naughton
ODFW:
Mark Wade
Nik Zymonas
Lisa Borgerson
Kanani Bowden
Ben Clemens