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Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
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Contract Number:
73153
Contract Title:
2010-026-00 EXP GSI FOR CHINOOK AND STEELHEAD SNAKE RIVER
Contract Start Date:
7/1/2016
Contract End Date:
6/30/2017
WE ID:
162. Analyze/Interpret Data
Work Element Usage Report
Title:
N: 162 - OBJ 3. Stock composition estimates
Description:
Individual assignment (IA) tests are used to assign individual fish back to their estimated population (and genetic stock) of origin (Pella and Milner 1987, Shaklee et al. 1999). In IA, the probability that each individual (i.e. smolt) originates from a baseline population is calculated based on the likelihood that the individual’s genotype belongs to that population, given baseline allele frequency estimates. Individual population estimates were first calculated and then summed into genetic stock estimates (allocate-sum procedure; Wood et al. 1987). Genetic stocks (aka reporting groups) are assemblages of reference (baseline) populations grouped primarily by genetic and geographic similarities and secondarily by political boundaries and/or management units.
WE Agreement Type:
Contracted
Deliverable Specification:
GSI methods will be utilized to estimate stock composition of mixture samples, by sex, by length, by age, and by run-timing
WSE Effective Budget:
$6,056
% of Total WSE Effective Budget:
0.90%
WSE Start:
07/01/2016
WSE End:
06/30/2017
WSE Completion:
06/30/2017
WSE Progress:
Concluded
WSE ID Continued From:
n/a
WSE ID Continued To:
n/a
Finite or Recurring:
Recurring

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Budget History

SOWRevision Planned Updated Contractor Comments (optional) BPA Comments (optional)
Work Element Budget (Current Performance Period) $6,056 $6,056

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Milestones

3 Milestones
Sort Type Title Start End Status Modified By Modified Date
A PUBPROTOCOL Review, revise, and Publish protocol, study design, and methods in monitoringmethods.org 7/1/2016 12/30/2016 Concluded Matthew Campbell 3/25/2016 10:37:55 AM
Description: The Protocol (including temporal and spatial design) and Methods for this work element are stored at monitoringmethods.org and need to be finalized (i.e., "Published" through monitoringmethods.org), preferably prior to data collection. Preparations for contract renewals must include reviewing any previously published Protocols/Methods to ensure that they are consistent with how work will be done in any subsequent contract.
B Analyze Data 1/2/2017 6/30/2017 Concluded Sharon Grant (Inactive) 5/23/2016 11:35:41 AM
Description: GSI methods will be utilized to estimate stock composition of mixture samples by sex, age, length (for steelhead), and run-timing.
C DELIV Estimate Stock Compositions 6/30/2017 Concluded Sharon Grant (Inactive) 5/23/2016 11:35:41 AM
Description: GSI methods will be utilized to estimate stock composition of mixture samples, by sex, by length, by age, and by run-timing

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Metrics

Implementation Metrics
Metric Planned Actual Contractor Comments Measures HLIs
1464. Primary R, M, and E Focal Strategy [Population Status, Hydrosystem, Tributary Habitat, Estuary/Ocean, Harvest, Hatchery, Predation, Multiple Strategies] Population Status Population Status
1472. Primary R, M, and E Type [Status and Trend Monitoring, Action Effectiveness Research, Uncertainties Research, Project Implementation/ Compliance Monitoring] Status and Trend Monitoring Status and Trend Monitoring
1478. Secondary R, M, and E Type [Status and Trend Monitoring, Action Effectiveness Research, Uncertainties Research, Project Implementation/ Compliance Monitoring] Uncertainty Research Uncertainty Research
1495. Secondary R, M, and E Focal Strategy [Population Status, Hydrosystem, Tributary Habitat, Estuary/Ocean, Harvest, Hatchery, Predation, Multiple Strategies] Population Status Population Status

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Location

<a target='blank' href='https://www.monitoringresources.org/Designer/Design/Detail/5863'>Location data for Area of Inference (AOI) should be entered into MonitoringResources.org. Click here to go to that site.</a>
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Focal Species

Primary Focal Species:
Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened); Chinook (O. tshawytscha) - Snake River Spring/Summer (not listed); Steelhead (O. mykiss) - Snake River DPS (Threatened)
Secondary Focal Species:
None

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Environmental Compliance

This work element does not require Environmental Compliance
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RM&E Metadata

Data Repositories:
Title Link
IDFG Fisheries Technical Reports https://collaboration.idfg.idaho.gov/FisheriesTechnicalReports/Forms/AllItems.aspx
Study Plan:
Study Plan Name Study Plan Owner Protocol State Sample Design Name
Snake River steelhead and Chinook salmon stock composition estimates (2010-026-00) v1.0 Matthew Campbell Finalized OBJ 3. Stock composition estimates - Idaho Department of Fish and Game (IDFG) v1.0

ID Name Type Optional Customized Based On Status
1334 Assigning individual samples using Individual Assignment (IA) genetic methods v1.0 Data Analysis/Interpretation No N/A Finalized
1347 Contemporary effective population size estimated using the software program LDNe v1.0 Data Analysis/Interpretation No N/A Finalized
1345 Estimating Genetic Diversity v1.0 Data Analysis/Interpretation No N/A Finalized
1340 Genetic Sex Marker for O. mykiss and O. tshawytscha v1.0 Data Collection No N/A Finalized
1342 Inbreeding effective population size estimated using the software program Colony v1.0 Data Analysis/Interpretation No N/A Finalized
1333 Mixture modeling to estimate stock proportions v1.0 Data Analysis/Interpretation No N/A Finalized
1339 Nexttec 96-Well Tray DNA Extraction Kit Protocol v1.0 Data Collection No N/A Finalized
1356 O. mykiss and O. tshawytscha SNP marker sets for PBT and GSI use in the Columbia River basin v1.0 Data Collection No N/A Finalized
1362 Obtaining genetic samples from juvenile steelhead and Chinook salmon v1.0 Data Collection No N/A Finalized
1366 Obtaining scale samples from adult steelhead and salmon v1.0 Data Collection No N/A Finalized
1360 Obtaining scales from juvenile steelhead and Chinook salmon v1.0 Data Collection No N/A Finalized
1341 Parentage assignments using SNPPIT software v1.0 Data Analysis/Interpretation No N/A Finalized
1332 SNP genotyping on Fluidigm platform v1.0 Data Collection No N/A Finalized

Title Category Subcategory Subcategory focus 1 Subcategory focus 2
Stock proportions of juveniles Fish Abundance of Fish (ID: 46) Fish Life Stage: Juvenile - Migrant Fish Origin: Natural
Annual abundance of juvenile stocks migrating downstream of LGD Fish Abundance of Fish (ID: 46) Fish Life Stage: Juvenile Fish Fish Origin: Natural
Annual abundance of adult stocks returning over LGD Fish Abundance of Fish (ID: 46) Fish Life Stage: Adult - Returner Fish Origin: Natural
Stock proportions of adults Fish Abundance of Fish (ID: 46) Fish Life Stage: Adult - Returner Fish Origin: Natural
Ne of adults PIT-tagged at LGD, detected upstream Fish Effective Population Size (ID: 65) NA NA
Genetic diversity of adults PIT tagged at LGD, detected upstream Fish Genetics: Fish Diversity, Fitness or Variation (ID: 72) Fish Origin: Natural NA
Genetic diversity of Snake River stocks passing LGD Fish Genetics: Fish Diversity, Fitness or Variation (ID: 72) Fish Origin: Natural NA
Temporal estimates of genetic diversity of Snake River stocks Fish Genetics: Fish Diversity, Fitness or Variation (ID: 72) Fish Origin: Natural NA
Sex ratio of juvenile stocks migrating downstream at LGD Fish Sex Ratio: Fish (ID: 92) Fish Life Stage: Juvenile - Migrant Fish Origin: Natural
Sex ratio of adult stocks returning above LGD Fish Sex Ratio: Fish (ID: 92) Fish Life Stage: Adult - Returner Fish Origin: Natural
Sex ratio of adults PIT tagged at LGD, detected upstream Fish Sex Ratio: Fish (ID: 92) Fish Life Stage: Adult Fish Fish Origin: Natural
Stock origin of individual juveniles migrating downstream at LGD Fish Stock Identity (ID: 95) Fish Life Stage: Juvenile - Migrant NA
Stock origin of individual adults migrating upstream of LGD Fish Stock Identity (ID: 95) Fish Life Stage: Adult - Returner NA
Stock origin of adults PIT tagged at LGD, detected upstream Fish Stock Identity (ID: 95) Fish Life Stage: Adult Fish NA
Adult to adult productivity of Snake River stocks Fish Productivity: Fish (ID: 163) Fish Life Stage: RANGE: Adult to Adult Fish Origin: Natural
Adult to juvenile productivity of Snake River stocks Fish Productivity: Fish (ID: 163) Fish Life Stage: RANGE: Adult to Juvenile Fish Origin: Natural
Area of Inference:
Name Value
NPPC Provinces MOUNTAIN SNAKE

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