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Short Citation:
Northwest Fisheries Science Center, 2022: Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales, https://www.fisheries.noaa.gov/inport/item/18597.

Item Identification

Title: Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales
Short Name: Killer Whale Genetic Data (Genetic marker development and applications for southern resident killer whales)
Status: In Work
Creation Date: 2005-01-01
Publication Date: 2018-02-05
Abstract:

The southern residents face several well-documented external threats. However, the population might also be subject to internal factors that limit population growth, including a reduction in fitness due to inbreeding. Understanding how inbreeding affects individual fitness and thus the health status of the population is critical for evaluating the relative influence of other factors on southern resident recovery. Assessing the risk of inbreeding depression – specifically called for in the NMFS recovery plan – is important for conducting accurate Population Viability Analyses and correctly understanding the urgency of recovery efforts. Here, we propose using genomic methods to evaluate inbreeding and inbreeding depression in the southern resident population and a comparable but healthier Alaskan resident population. Measures of inbreeding will serve as an important health marker, supporting the integration of individual metrics aimed at understanding population performance.

Measures of inbreeding can be obtained directly by estimating variation at millions of DNA markers in an individual’s genome. Complete genomic sequences for 100 southern and 50 Alaska residents will be collected in collaboration with the genomics company BGI. Inbreeding values for each individual will be obtained using genome wide measures of homozygosity and relatedness. We will then combine measured of inbreeding with data on individual fitness, to evaluate whether inbreeding leads to inbreeding depression. Generalized additive models will be used to determine whether survivorship, fecundity and size-at-age is influenced by different levels of inbreeding. Using this data, we will measure the degree of current and predicted future of inbreeding in the southern residents and compare this risk with the Alaska residents that have experienced consistent population growth. We will then evaluate whether inbreeding depression explains individual variance in fitness, and estimate its influence on the status of southern residents, using Population Viability Analyses.

Microsatellite, SNP, and mtDNA sequence data from southern resident killer whales.

Purpose:

Addresses Legal Mandate

Raw/field data, Laboratory data

Notes:

Loaded by batch 4488, 02-28-2013 15:16

Supplemental Information:

Subject to Public Access to Research Results (PARR): Yes

Database: Inbreeding and heterozygosity data are provided the southern resident killer whale health database.

Peer Reviewed Publication: Publication submitted March 2017. Additional publication expected in 2018.

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
None genetics
None killer whale
None Puget Sound

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
None NWFSC Montlake

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
None DNA Sequencer

Physical Location

Organization: Northwest Fisheries Science Center
City: Seattle
State/Province: WA
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Spreadsheet
Data Presentation Form: Table (digital)

Support Roles

Data Steward

CC ID: 848163
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Ford, Mike J
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
Email Address: Mike.Ford@noaa.gov
Phone: 206-860-5612

Distributor

CC ID: 848164
Date Effective From: 2015-10-01
Date Effective To:
Contact (Organization): Northwest Fisheries Science Center (NWFSC)
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
USA
Email Address: nmfs.nwfsc.metadata@noaa.gov
Phone: 206-860-3200
URL: NWFSC Home

Metadata Contact

CC ID: 848162
Date Effective From: 2015-10-01
Date Effective To:
Contact (Organization): Northwest Fisheries Science Center (NWFSC)
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
USA
Email Address: nmfs.nwfsc.metadata@noaa.gov
Phone: 206-860-3200
URL: NWFSC Home

Originator

CC ID: 848166
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Park, Linda
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
Email Address: Linda.Park@noaa.gov
Phone: 206-860-3241

Point of Contact

CC ID: 848165
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Ford, Mike J
Address: 2725 Montlake Boulevard East
Seattle, WA 98112
Email Address: Mike.Ford@noaa.gov
Phone: 206-860-5612

Extents

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 848172
W° Bound: -122.3062
E° Bound: -122.3062
N° Bound: 47.6449
S° Bound: 47.6449
Description

NWFSC Montlake: NWFSC Montlake lab

Extent Group 1 / Time Frame 1

CC ID: 848171
Time Frame Type: Continuing
Start: 2011-01-01

Access Information

Security Class: Unclassified
Data Access Procedure:

At this time, contact the Data Manager for information on obtaining access to this data set. In the near future, the NWFSC will strive to provide all non-sensitive data resources as a web service in order to meet the NOAA Data Access Policy Directive (https://nosc.noaa.gov/EDMC/PD.DA.php).

Data Access Constraints:

NA

Distribution Information

Distribution 1

CC ID: 848168
Start Date: 2018-02-05
End Date: Present
Download URL: https://www.webapps.nwfsc.noaa.gov/apex/parr/combined_snp_and_usat_genotypes_feb_10_2017/data/page/
Distributor: Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present)
File Name: Combined Snp And Usat Genotypes Feb 10 2017 (RESTf
Description:

Table of multi-locus microsatellite and single nucleotide polymorphism (SNP) genotypes collected from southern resident killer whales.

Distribution 2

CC ID: 848167
Start Date: 2018-02-05
End Date: Present
Download URL: https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/tables/table/combined_snp_and_usat_genotypes_feb_10_2017
Distributor: Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present)
File Name: Combined Snp And Usat Genotypes Feb 10 2017
Description:

Table of multi-locus microsatellite and single nucleotide polymorphism (SNP) genotypes collected from southern resident killer whales.

URLs

URL 1

CC ID: 848169
URL: https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/3030
Name: Killer Whale Genetic Data
URL Type:
Online Resource
File Resource Format: Web site
Description:

NWFSC Dataset Information page. Microsatellite, SNP, and mtDNA sequence data from southern resident killer whales

Technical Environment

Description:

Spreadsheet

Data Quality

Accuracy:

High

Quality Control Procedures Employed:

These data were collected and processed in accordance with established protocols and best practices under the direction of the project’s Principal Investigator. Contact the dataset Data Manager in section 3 for full QA/QC methodology.

Data Management

Have Resources for Management of these Data Been Identified?: No
Approximate Percentage of Budget for these Data Devoted to Data Management: 0
Do these Data Comply with the Data Access Directive?: No
Is Access to the Data Limited Based on an Approved Waiver?: No
If Distributor (Data Hosting Service) is Needed, Please Indicate: No
Approximate Delay Between Data Collection and Dissemination: 0 days
If Delay is Longer than Latency of Automated Processing, Indicate Under What Authority Data Access is Delayed:

No Delay

Actual or Planned Long-Term Data Archive Location: NCEI-MD
Approximate Delay Between Data Collection and Archiving: 365
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

The Northwest Fisheries Science Center facilitates backup and recovery of all data and IT components which are managed by IT Operations through the capture of static (point-in-time) backup data to physical media. Once data is captured to physical media (every 1-3 days), a duplicate is made and routinely (weekly) transported to an offsite archive facility where it is maintained throughout the data's applicable life-cycle.

Lineage

Lineage Statement:

DNA genotyping: These data were collected and processed in accordance with established protocols and best practices under the direction of the project’s Principal Investigator. Contact the dataset Data Manager for full QA/QC methodology.

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity Combined Snp And Usat Genotypes Feb 10 2017

Catalog Details

Catalog Item ID: 18597
GUID: gov.noaa.nmfs.inport:18597
Metadata Record Created By: SysAdmin InPortAdmin
Metadata Record Created: 2013-02-28 15:16+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-08-09 17:11+0000
Metadata Record Published: 2019-06-04
Owner Org: NWFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2019-06-04
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2020-06-04