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Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales
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.
Resources
4 resources available
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Combined Snp And Usat Genotypes Feb 10 2017
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Combined Snp And Usat Genotypes Feb 10 2017 (RESTf
TEXT/HTML -
GCMD Keyword Forum Page
TEXT/HTML -
Full Metadata Record
TEXT/HTML
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | non-public |
| contactPoint |
{ "fn": "Ford, Mike J", "@type": "vcard:Contact", "hasEmail": "mailto:mike.ford@noaa.gov" } |
| describedByType | application/octet-steam |
| description | 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. |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Combined Snp And Usat Genotypes Feb 10 2017", "accessURL": "https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/tables/table/combined_snp_and_usat_genotypes_feb_10_2017", "mediaType": "text/html", "description": "Table of multi-locus microsatellite and single nucleotide polymorphism (SNP) genotypes collected from southern resident killer whales.", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "Combined Snp And Usat Genotypes Feb 10 2017 (RESTf", "accessURL": "https://www.webapps.nwfsc.noaa.gov/apex/parr/combined_snp_and_usat_genotypes_feb_10_2017/data/page/", "mediaType": "text/html", "description": "Table of multi-locus microsatellite and single nucleotide polymorphism (SNP) genotypes collected from southern resident killer whales.", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "GCMD Keyword Forum Page", "accessURL": "https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords", "mediaType": "text/html", "description": "Global Change Master Directory (GCMD). 2026. GCMD Keywords, Version 24. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "Full Metadata Record", "accessURL": "https://www.fisheries.noaa.gov/inport/item/18597", "mediaType": "text/html", "description": "View the complete metadata record on InPort for more information about this dataset.", "describedByType": "application/octet-stream" } ] |
| identifier | https://data.noaa.gov/waf/NOAA/nmfs/nwfsc/iso/xml/18597.xml |
| issued | 2005-01-01T00:00:00.000+00:00 |
| keyword |
[ "Puget Sound", "genetics", "killer whale", "NWFSC Montlake", "DNA Sequencer", "DOC/NOAA/NMFS/NWFSC > Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA. U.S. Department of Commerce", "CB (Conservation Biology) Division" ] |
| landingPage | https://www.fisheries.noaa.gov/inport/item/18597 |
| language |
[]
|
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2018-02-05T00:00:00.000+00:00 |
| publisher |
{ "name": "Northwest Fisheries Science Center", "@type": "org:Organization" } |
| rights | otherRestrictions, unclassified |
| spatial | -122.2962,47.6449,-122.3062,47.6549 |
| temporal | 2011-01-01T00:00:00+00:00/2011-01-01T00:00:00+00:00 |
| theme |
[ "geospatial" ] |
| title | Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales |
