83639 REL 10: Rev 1: WE F: Work Element Summary

Work Element Summary PDF

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Basics

Contract Number:

83639 REL 10

Contract Title:

1989-096-00 EXP GENETIC M&E PROG FOR SALMON/STEELHEAD

Contract Start Date:

4/1/2020

Contract End Date:

3/31/2021

WE ID:

162. Analyze/Interpret Data

Work Element Usage Report

Title:

F: 162 - Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, conventional monitoring (Tier 2)

Description:

Data analysis includes descriptive population genetic characterization for Tier 2 sites (gene-frequency monitoring), especially levels of variability, relative relationships among hatchery and wild populations, and changes in those parameters over time. Coordination among genetics labs has become an essential element of effective comanagement. Our interaction includes exchange and sharing of tissue samples, exchange of reference samples for standardization of genotyping and sharing of new data and new genetic markers.

WE Agreement Type:

Contracted

Deliverable Specification:

-Calculate population genetic metrics and parameter estimates (e.g., inbreeding coefficients, average heterozygosity, genetic distance, average relatedness, effective number of breeders), if applicable.

-Describe geographic structure of population genetic variation by using multivariate statistical analyses such as agglomerative clustering and ordination, if applicable.

-Contribute to basin-wide SNP baseline, if applicable.

-Coordinate research with other labs (phone, email, and data sharing), standardize data, and develop/implement new genetic markers.

WSE Effective Budget:

$8,000

% of Total WSE Effective Budget:

2.34%

WSE Start:

04/01/2020

WSE End:

03/31/2021

WSE Completion:

WSE Progress:

Other

WSE ID Continued From:

n/a

WSE ID Continued To:

n/a

Finite or Recurring:

Recurring

Budget History

SOWRevision	Planned	Updated	Contractor Comments (optional)	BPA Comments (optional)
Work Element Budget (Current Performance Period)	$8,000	$8,000	Time not in the lab was spent analyzing existing datasets

Milestones

6 Milestones

Sort	Type	Title	Start	End	Status	Modified By	Modified Date
A	PUBPROTOCOL	Review, revise, and publish Study Design and Methods in monitoringmethods.org	4/1/2020	3/31/2021	Concluded	Martin Allen	1/6/2020 2:59:12 PM
		Description: The Study Design (including temporal and spatial design) and Methods for this work element are stored at monitoringresources.org and need to be finalized (i.e., "Published" through monitoringresources.org), preferably prior to data collection. Preparations for contract renewals must include reviewing any previously published Study Design/Methods to ensure that they are consistent with how work will be done in any subsequent contract.
B		Descriptive population genetic analysis completed	4/1/2020	3/31/2021	Concluded	Martin Allen	1/6/2020 2:59:12 PM
		Description: Data analysis includes descriptive population genetic characterization for tier 2 sites (gene-frequency monitoring), especially levels of variability, relative relationships among hatchery and wild populations, and changes in those parameters over time.
C		Coordination and standardization activities completed	4/1/2020	3/31/2021	Concluded	Martin Allen	1/6/2020 2:59:12 PM
		Description: Coordination among genetics labs has become an essential element of effective comanagement. Formerly, lack of coordination resulted in incomplete data sets, redundancy, and duplication of effort. As described in detail in our proposal, we work closely with other BPA-funded genetics labs, including the CRITFC lab at Hagerman, ID, the IDFG lab at Eagle, USFWS, Anchorage, and WDFW in Olympia.
D		Develop methods for use of eDNA to generate allele frequencies at sampling sites	4/1/2020	3/31/2021	Active	Martin Allen	1/31/2020 11:38:35 AM
		Description: The use of eDNA to generate allele frequencies has not yet been demonstrated. We anticipate the development of this new technique will entail significant technological challenges, but would be highly beneficial to genetic monitoring projects in allowing for greater sampling coverage of streams, ease of sampling, and the ability to sample in waters that are too warm to safely sample by electrofishing.
E		New genetic marker development goals complete	4/1/2020	3/31/2021	Concluded	Martin Allen	1/31/2020 11:38:35 AM
		Description: Genetic markers are continually being refined and improved. New microsatellite markers and analysis tools are routinely tested and have been implemented on an ongoing basis throughout the history of this project. New SNP markers will also be tested on representative individuals of Chinook and steelhead (relevant to our monitoring efforts) as they become available.
F	DELIV	Coordinate genotype data, analyze, and interpret results		3/31/2021	Active	Martin Allen	1/31/2020 11:38:35 AM
		Description: -Calculate population genetic metrics and parameter estimates (e.g., inbreeding coefficients, average heterozygosity, genetic distance, average relatedness, effective number of breeders), if applicable. -Describe geographic structure of population genetic variation by using multivariate statistical analyses such as agglomerative clustering and ordination, if applicable. -Contribute to basin-wide SNP baseline, if applicable. -Coordinate research with other labs (phone, email, and data sharing), standardize data, and develop/implement new genetic markers.

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

Location

<a target='blank' href='https://www.monitoringresources.org/Designer/Design/Detail/6864'>Location data for Area of Inference (AOI) should be entered into MonitoringResources.org. Click here to go to that site.</a>

Focal Species

Primary Focal Species:

Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened); Steelhead (O. mykiss) - Snake River DPS (Threatened)

Secondary Focal Species:

Chinook (O. tshawytscha) - Snake River Spring/Summer (not listed); Trout, Rainbow (Oncorhynchus mykiss)

Environmental Compliance

This work element does not require Environmental Compliance

RM&E Metadata

Data Repositories:

Title	Link
NOAA Public Access to Research Results (PARR)	https://www.ngdc.noaa.gov/parr.html
StreamNet Data Store	https://app.streamnet.org/datastore_search_classic.cfm

Study Plan:

Study Plan Name	Study Plan Owner	Protocol State	Sample Design Name
Conventional population monitoring of supplemented salmon &steelhead in the Snake River Basin v1.0	Ewann Berntson	Finalized	Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, Tier 2 - National Oceanic and Atmospheric Administration v1.0

Methods:

ID	Name	Type	Optional	Customized Based On	Status
1352	Assessing genetic population structure using fixation indices v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1354	Constructing a bootstrapped, neighbor-joining tree based on genetic distance 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
1353	DNeasy® 96 Fin tissue DNA Extraction Kit Protocol v1.0	Data Collection	No	N/A	Finalized
1345	Estimating Genetic Diversity v1.0	Data Analysis/Interpretation	No	N/A	Finalized
700	Fin tissue sampling for genetic analysis v1.0	Data Collection	No	N/A	Finalized
1431	Genetic Microsatellite Analysis using Chinook GAPS markers 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
4002	Microsatellite genotyping of Oncorhynchus mykiss using standardized SPAN loci v1.0	Data Collection	No	N/A	Finalized
117	Modified Electrofishing - Fish Processing and Recovery v1.0	Data Collection	No	Electrofishing - Fish Processing and Recovery v1.0	Finalized
1332	SNP genotyping on Fluidigm platform v1.0	Data Collection	No	N/A	Finalized
5446	SNP genotyping using Genotyping in Thousands (GT-seq) on Illumina Sequencer platform v1.0	Data Collection	No	N/A	Finalized
1357	Testing for Hardy-Weinberg equilibrium v1.0	Data Analysis/Interpretation	No	N/A	Finalized

Metrics:

Title	Category	Subcategory	Subcategory focus 1	Subcategory focus 2
Effective population size	Fish	Effective Population Size (ID: 65)	Fish Origin: Both	NA
Genetic diversity measured with microsatellite or SNP loci	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Both	NA
Genetic structure of populations	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Both	NA
Temporal estimates of genetic diversity	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Both	NA

Area of Inference:

Name	Value
HUC3 - Basin	Salmon
HUC4 - Sub Basin	IMNAHA
NPPC Subbasins	GRANDE RONDE

Please correct the errors noted below.

Implementation Metrics