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Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam. Tim Copeland Matthew Campbell, Christine Kozfkay, and Bill Schrader Idaho Department of Fish and Game.

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Tim Copeland Matthew Campbell, Christine Kozfkay, and Bill Schrader

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Tim copeland matthew campbell christine kozfkay and bill schrader

Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam

Tim Copeland

Matthew Campbell, Christine Kozfkay, and Bill Schrader

Idaho Department of Fish and Game


Viable salmonid population parameters

Viable Salmonid Population Parameters

  • Abundance

    • How many of them are there?

  • Productivity

    • How well do they reproduce & survive?

  • Spatial structure

    • Where are they?

  • Diversity

    • What are they like?


  • Tim copeland matthew campbell christine kozfkay and bill schrader

    Abundance & Productivity

    • Abundance is a primary status metric

      • Salmon/steelhead = number of spawning adults

    • Productivity = abundance x age comp. through time

    • Combination measures population resiliency

      • Necessary for sustainable harvest

      • Necessary for conservation of weak stocks & biodiversity

    Abundance (10 yr geomean)

    5% extinction risk

    A

    25% extinction risk

    B

    Productivity (geomean R/S)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    Challenges for Snake River Steelhead

    • Data collection during spawning is very difficult

    • Status assessments used aggregate data & habitat models from outside DPS


    Tim copeland matthew campbell christine kozfkay and bill schrader

    “A-run” versus “B-run”

    “A-run” steelhead

    Grand RondeRiver

    “B-run” steelhead

    S.F. Clearwater


    Tim copeland matthew campbell christine kozfkay and bill schrader

    Genetic Stock Identification

    • Characterize allele frequencies from contributing stocks

    • Genotype mixed sample

    • Estimate stock proportions from genetic baseline


    Strategy

    Strategy

    • Sample aggregate at Lower Granite Dam

      (numbers & age composition)

    • Use genetic stock identification

    • Develop data suitable for VSP assessments

      (abundance & productivity)

    • Address A vs B dichotomy


    Tim copeland matthew campbell christine kozfkay and bill schrader

    METHODS


    Tim copeland matthew campbell christine kozfkay and bill schrader

    GENETIC BASELINE

    • 66 sample collections

    • 9 geographic groups

    • 1) Elk Creek (Joseph)

    • 2) Snake/Lower Clearwater

    • 3) South FkClearwater

    • 4) Upper Clearwater

    • 5) Imnaha

    • 6) Lower Salmon

    • 7) South FkSalmon

    • 8) Middle FkSalmon

    • 9) Upper Salmon


    Tim copeland matthew campbell christine kozfkay and bill schrader

    2008 Adult Sampling at Lower Granite Dam

    • Wild steelhead only!

    • Aug 24 – Nov 25

    • Scales taken, length recorded

    • 13 microsatellite loci from standard set

    • Genetic sex marker


    Tim copeland matthew campbell christine kozfkay and bill schrader

    Mixture Analyses

    • Proportion by group estimated with ONCOR

      • For the entire wild run (all samples)

      • By sex (male and female)

      • By size (fork length <78 cm or >78 cm)

      • By run-timing (early, middle, late)

      • By total age (3, 4, and 5 year olds)

    • 95% bootstrap confidence interval


    Tim copeland matthew campbell christine kozfkay and bill schrader

    RESULTS


    Lower granite dam sampling

    Lower Granite Dam Sampling

    • Sample period missed first 13% of run

    • 46% unclipped fish were hatchery-origin

    • 20,078 wild fish

    • 992 aged, 1,076 genotyped

    • 65.7% genetically female


    Age composition n 992

    Age composition(n = 992)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    Genetic Stock Composition

    N = 20,078

    A

    B

    B

    A

    A

    B

    B

    A

    A


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Sex

    Female

    Male


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Length


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Total Age (3 or less)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Total Age (4)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Total Age (5 or greater)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Total Age (5 or greater)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Run-Timing (Early)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Run-Timing (Middle)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Run-Timing (Late)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Run-Timing (Early)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Run-Timing (Middle)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    By Run-Timing (Late)


    Tim copeland matthew campbell christine kozfkay and bill schrader

    MAJOR FINDINGS


    Tim copeland matthew campbell christine kozfkay and bill schrader

    Stock Contribution

    • Genetic groups did not conform with TRT population structure

    • Majority from 3 stocks (65%):

      • Snake/Lower Clearwater, Upper Clearwater, Lower Salmon

      • Grand Ronde likely lumped with Snake/Lower Clearwater

    • Two large areas of good habitat have poor representation

      • Middle Fk Salmon & South Fk Salmon


    Tim copeland matthew campbell christine kozfkay and bill schrader

    Sex Composition

    • Females comprise 2/3 of adult steelhead

    • Female-biased sex ratios may result from:

      • Males residualize more than females

      • Females may be more iteroparous

    • Dams & long migration reduces successful iteroparity

    • No population effects = widespread male residualization?


    Tim copeland matthew campbell christine kozfkay and bill schrader

    “A-run” versus “B-run”

    • Length conformed with A/B expectations

    • Salmon River B stocks return over Lower Granite earlier

    • Lower Salmon stock has older age comp than other A-runs

    • All stocks produce smaller/younger & larger/older adults

    • A/B dichotomy masks important diversity for conservation


    Tim copeland matthew campbell christine kozfkay and bill schrader

    • Summary

    • First time Snake River steelhead abundance estimated at the stock/population level

    • This approach provides information relevant to VSP criteria

      • Abundance

      • Age composition

      • Sex ratio

      • Genetic diversity

      • Life history diversity


    Tim copeland matthew campbell christine kozfkay and bill schrader

    • Future

      • Improve baseline

        • Better resolution within some groups (e.g., Lemhi R)

        • Coverage needed in some areas (e.g., Grand Ronde)

        • Resolve differences with TRT population structure?

        • Annual maintenance sampling

  • Sample entire adult run

  • Transition to SNPs

  • Include smolt sampling at Lower Granite Dam


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