46273 REL 131: Rev 1: WE G: Work Element Summary

Work Element Summary PDF

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Basics

Contract Number:

46273 REL 131

Contract Title:

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

Contract Start Date:

4/15/2017

Contract End Date:

3/31/2018

WE ID:

162. Analyze/Interpret Data

Work Element Usage Report

Title:

G: 162 - Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, tier 3

Description:

Data analysis includes descriptive population genetic characterization for tier 3 sites involves parentage analysis to document differences in reproductive success among hatchery fish, wild fish, and progeny of captive parents. 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 genetic markers developed in our lab.

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).

-Document relative reproductive success among multiple treatment groups of Chinook salmon in Catherine Creek and Lostine River, and steelhead in Little Sheep Creek.

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

WSE Effective Budget:

$61,300

% of Total WSE Effective Budget:

16.38%

WSE Start:

04/15/2017

WSE End:

03/31/2018

WSE Completion:

03/20/2018

WSE Progress:

Concluded

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)	$61,300	$61,300

Milestones

5 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	4/15/2017	3/31/2018	Concluded	Martin Allen	3/8/2017 10:56:05 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		Reproductive success analyses from tier 3 sites completed	4/15/2017	3/31/2018	Concluded	Martin Allen	3/8/2017 10:56:05 AM
		Description: Experimental design at tier 3 sites involves parentage analysis to document differences in reproductive success among hatchery fish, wild fish, resident fish, and progeny of captive parents as related to phenotypic traits such as rearing history (hatchery, captive progeny, wild) time of return, and adult body size.
C		Coordination and standardization activities completed	4/15/2017	3/31/2018	Concluded	Martin Allen	3/8/2017 10:56:05 AM
		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		New genetic marker development goals complete	4/15/2017	3/31/2018	Concluded	Martin Allen	3/8/2017 10:56:05 AM
		Description: Genetic markers are continually being refined and improved. New microsatellite markers 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.
E	DELIV	Coordinate, analyze, and interpret research		3/31/2018	Concluded	Martin Allen	2/5/2017 5:11:35 PM
		Description: -Calculate population genetic metrics and parameter estimates (e.g., inbreeding coefficients, average heterozygosity, genetic distance, average relatedness, effective number of breeders). -Document relative reproductive success among multiple treatment groups of Chinook salmon in Catherine Creek and Lostine River, and steelhead in Little Sheep Creek. -Coordinate research with other labs (phone, email, and data sharing), standardize data, and develop/implement new genetic markers.

Metrics

Implementation Metrics

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

Location

<a target='blank' href='https://www.monitoringresources.org/Designer/Design/Detail/6866'>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
Relative reproductive success of Chinook and steelhead in the Snake River basin v1.0	Ewann Berntson	Finalized	Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, tier 3 - National Oceanic and Atmospheric Administration v1.0

Methods:

ID	Name	Type	Optional	Customized Based On	Status
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
5404	Modified Backpack Electrofishing Method Template v1.0	Data Collection	No	Backpack Electrofishing Method Template v1.0	Finalized
5446	Modified SNP genotyping using Genotyping in Thousands (GT-seq) on Illumina Sequencer platform v1.0	Data Collection	No	SNP genotyping using Genotyping in Thousands (GT-seq) on Illumina Sequencer platform v1.0	Finalized
1430	Parentage Analysis using Cervus v1.0	Data Analysis/Interpretation	No	N/A	Finalized
729	Relative reproductive success (RRS) of hatchery and wild adults v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1332	SNP genotyping on Fluidigm 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)	NA	NA
Genetic diversity of populations	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Both	NA
Hardy-Weinberg estimation	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Both	NA
Number of offspring per spawner	Fish	Relative Reproductive Success (RRS) (ID: 88)	Fish Origin: Both	NA
Relative reproductive success of hatchery and natural adults	Fish	Relative Reproductive Success (RRS) (ID: 88)	Fish Origin: Both	NA
Variance of reproductive success	Fish	Reproductive Success (Nb/N) (ID: 89)	Fish Origin: Both	NA

Area of Inference:

Name	Value
HUC4 - Sub Basin	IMNAHA
NPPC Subbasins	GRANDE RONDE

Please correct the errors noted below.

Implementation Metrics