Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales
Data Set (DS) | Northwest Fisheries Science Center (NWFSC)GUID: gov.noaa.nmfs.inport:18597 | Updated: August 9, 2022 | Published / External
Item Identification
Title: | Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales |
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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 |
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UNCONTROLLED | |
None | genetics |
None | killer whale |
None | Puget Sound |
Spatial Keywords
Thesaurus | Keyword |
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UNCONTROLLED | |
None | NWFSC Montlake |
Instrument Keywords
Thesaurus | Keyword |
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UNCONTROLLED | |
None | DNA Sequencer |
Physical Location
Organization: | Northwest Fisheries Science Center |
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City: | Seattle |
State/Province: | WA |
Country: | USA |
Data Set Information
Data Set Scope Code: | Data Set |
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Data Set Type: | Spreadsheet |
Data Presentation Form: | Table (digital) |
Support Roles
Data Steward
Date Effective From: | 2015-10-01 |
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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
Date Effective From: | 2015-10-01 |
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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
Date Effective From: | 2015-10-01 |
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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
Date Effective From: | 2015-10-01 |
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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
Date Effective From: | 2015-10-01 |
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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
W° Bound: | -122.3062 | |
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E° Bound: | -122.3062 | |
N° Bound: | 47.6449 | |
S° Bound: | 47.6449 | |
Description |
NWFSC Montlake: NWFSC Montlake lab |
Extent Group 1 / Time Frame 1
Time Frame Type: | Continuing |
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Start: | 2011-01-01 |
Access Information
Security Class: | Unclassified |
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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
Start Date: | 2018-02-05 |
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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
Start Date: | 2018-02-05 |
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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
URL: | https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/3030 |
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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 |
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Data Quality
Accuracy: |
High |
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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 |
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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. |
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Child Items
Rubric scores updated every 15m
Type | Title |
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Entity | Combined Snp And Usat Genotypes Feb 10 2017 |
Catalog Details
Catalog Item ID: | 18597 |
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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 |