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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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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

  • Abundance

    • How many of them are there?

  • Productivity

    • How well do they reproduce & survive?

  • Spatial structure

    • Where are they?

  • Diversity

    • What are they like?


  • 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)


    Challenges for Snake River Steelhead

    • Data collection during spawning is very difficult

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


    “A-run” versus “B-run”

    “A-run” steelhead

    Grand RondeRiver

    “B-run” steelhead

    S.F. Clearwater


    Genetic Stock Identification

    • Characterize allele frequencies from contributing stocks

    • Genotype mixed sample

    • Estimate stock proportions from genetic baseline


    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


    METHODS


    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


    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


    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


    RESULTS


    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)


    Genetic Stock Composition

    N = 20,078

    A

    B

    B

    A

    A

    B

    B

    A

    A


    By Sex

    Female

    Male


    By Length


    By Total Age (3 or less)


    By Total Age (4)


    By Total Age (5 or greater)


    By Total Age (5 or greater)


    By Run-Timing (Early)


    By Run-Timing (Middle)


    By Run-Timing (Late)


    By Run-Timing (Early)


    By Run-Timing (Middle)


    By Run-Timing (Late)


    MAJOR FINDINGS


    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


    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?


    “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


    • 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


    • 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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