Environmental DNA (eDNA) data from the 2019 and 2020 Gulf of Alaska International Year of the Salmon Expeditions

This dataset contains environmental DNA (eDNA) data collected in the Northeast Pacific Ocean. These data were collected as part of the International Year of the Salmon (IYS) Gulf of Alaska High Seas Expedition conducted in March and April 2020 and 2021, to further improve the understanding of factors impacting salmon early marine winter survival. eDNA analysis uses the free DNA shed from organisms and available in the environment to assess species diversity and composition. The eDNA database will provide overall composition of nekton, micronekton and zooplankton allowing estimation of salmon prey and potential predators. Water collected with Niskin bottle from 2-3m. 2L filtered onto Sterivex column for each replicate. Filters flash frozen. DNA extracted from filters using DNeasy kits (QUIAGEN). 16S and COI rRNA gens were amplified with PCR and sequenced on Illumina MiSeq platform using SE at 300 cycles. Reads were processed using obitools (https://pythonhosted.org/OBITools/welcome.html) and queired against nt using BLASTn. Reads were assigned to OTU using MEGAN (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/). Results were filtered using a cuttoff of >/=10 reads for positive detection. Detection of obvious contaminations belonging to human or food waste (sheep, pig, chicken, cow) as well as artificial positive controls were removed. For detailed information contact Dr. Christoph Deeg: chdeeg@mail.ubc.ca

Access and Use

Licence: Creative Commons Attribution 4.0

Data and Resources

Citation

Keywords

Dataset extent

Map data © OpenStreetMap contributors

Metadata Reference Date(s) February 01, 2022 (Publication)
June 17, 2022 (Revision)
Dataset Reference Date(s) February 18, 2019 (Creation)
June 17, 2022 (Publication)
Frequency of Update As Needed

Responsible Party 1
Affiliation
North Pacific Anadromous Fish Commission
Email
secretariat@npafc.org
Role
Publisher
Responsible Party 2
Name
Christoph Deeg
Affiliation
Fisheries and Oceans Canada
Email
Christoph.Deeg@dfo-mpo.gc.ca
Role
  • Author
  • Custodian
  • Owner
Responsible Party 3
Name
Kristi Miller-Saunders
Affiliation
Fisheries and Oceans Canada
Email
Kristi.Saunders@dfo-mpo.gc.ca
Role
Principal Investigator
Responsible Party 4
Affiliation
Hakai Institute
Email
data@hakai.org
Role
Distributor

Field Value
Title Environmental DNA (eDNA) data from the 2019 and 2020 Gulf of Alaska International Year of the Salmon Expeditions
Description

This dataset contains environmental DNA (eDNA) data collected in the Northeast Pacific Ocean. These data were collected as part of the International Year of the Salmon (IYS) Gulf of Alaska High Seas Expedition conducted in March and April 2020 and 2021, to further improve the understanding of factors impacting salmon early marine winter survival. eDNA analysis uses the free DNA shed from organisms and available in the environment to assess species diversity and composition. The eDNA database will provide overall composition of nekton, micronekton and zooplankton allowing estimation of salmon prey and potential predators. Water collected with Niskin bottle from 2-3m. 2L filtered onto Sterivex column for each replicate. Filters flash frozen. DNA extracted from filters using DNeasy kits (QUIAGEN). 16S and COI rRNA gens were amplified with PCR and sequenced on Illumina MiSeq platform using SE at 300 cycles. Reads were processed using obitools (https://pythonhosted.org/OBITools/welcome.html) and queired against nt using BLASTn. Reads were assigned to OTU using MEGAN (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/). Results were filtered using a cuttoff of >/=10 reads for positive detection. Detection of obvious contaminations belonging to human or food waste (sheep, pig, chicken, cow) as well as artificial positive controls were removed. For detailed information contact Dr. Christoph Deeg: chdeeg@mail.ubc.ca

Keywords
Ocean Variables
  • Zooplankton biomass and diversity
  • Fish abundance and distribution
Citation

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Scope Dataset
Status Completed
Metadata Dates
Metadata Date 1
Date
2022-02-01
Type
Publication
Metadata Date 2
Date
2022-06-17
Type
Revision
Resource Dates
Resource Date 1
Date
2019-02-18
Type
Creation
Resource Date 2
Date
2022-06-17
Type
Publication
Maintenance and update frequency As Needed
Maintenance Note Generated from https://cioos-siooc.github.io/metadata-entry-form
Point of Contact
Point of Contact 1
Name
Christoph Deeg
Affiliation
Fisheries and Oceans Canada
Email
Christoph.Deeg@dfo-mpo.gc.ca
Role
Custodian
Responsible Party
Responsible Party 1
Affiliation
North Pacific Anadromous Fish Commission
Email
secretariat@npafc.org
Role
Publisher
Responsible Party 2
Name
Christoph Deeg
Affiliation
Fisheries and Oceans Canada
Email
Christoph.Deeg@dfo-mpo.gc.ca
Role
  • Author
  • Owner
Responsible Party 3
Name
Kristi Miller-Saunders
Affiliation
Fisheries and Oceans Canada
Email
Kristi.Saunders@dfo-mpo.gc.ca
Role
Principal Investigator
Distributor
Distributor 1
Affiliation
Hakai Institute
Email
data@hakai.org
Role
Distributor
Spatial Extent { "coordinates": [ [ [ -154.1, 47.67 ], [ -124.5, 47.67 ], [ -124.5, 58.94 ], [ -154.1, 58.94 ], [ -154.1, 47.67 ] ] ], "type": "Polygon" }
North Bounding Latitude 58.94
South Bounding Latitude 47.67
East Bounding Longitude -124.5
West Bounding Longitude -154.1
Temporal Extent
Begin
2019-02-18
End
2020-04-05
Vertical Extent
Min
2.0
Max
3.0
Default Locale English
Citation identifier
Code
10.21966/2cpk-8922
XML Metadata File Location https://pac-dev1.cioos.org/dev/metadata/iys/environmental_dna__edna__data__223a4.xml
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<gco:CharacterString>info@dfo-mpo.gc.ca</gco:CharacterString> </cit:electronicMailAddress> </cit:CI_Address> </cit:address> <cit:onlineResource> <cit:CI_OnlineResource> <cit:linkage> <gco:CharacterString>https://www.dfo-mpo.gc.ca/index-eng.html</gco:CharacterString> </cit:linkage> <cit:protocol> <gco:CharacterString>WWW:LINK</gco:CharacterString> </cit:protocol> <cit:function> <cit:CI_OnLineFunctionCode codeList="https://standards.iso.org/iso/19115/resources/Codelists/cat/codelists.xml#CI_OnLineFunctionCode" codeListValue="information"></cit:CI_OnLineFunctionCode> </cit:function> </cit:CI_OnlineResource> </cit:onlineResource> </cit:CI_Contact> </cit:contactInfo> <cit:individual> <cit:CI_Individual> <cit:name> <gco:CharacterString>Kristi Miller-Saunders</gco:CharacterString> </cit:name> <cit:contactInfo> <cit:CI_Contact> <cit:address> <cit:CI_Address> <cit:deliveryPoint> <gco:CharacterString></gco:CharacterString> </cit:deliveryPoint> <cit:city> <gco:CharacterString></gco:CharacterString> </cit:city> <cit:country> <gco:CharacterString></gco:CharacterString> </cit:country> <cit:electronicMailAddress> <gco:CharacterString>Kristi.Saunders@dfo-mpo.gc.ca</gco:CharacterString> </cit:electronicMailAddress> </cit:CI_Address> </cit:address> </cit:CI_Contact> </cit:contactInfo> <cit:positionName> <gco:CharacterString></gco:CharacterString> </cit:positionName> </cit:CI_Individual> </cit:individual> </cit:CI_Organisation> </cit:party> </cit:CI_Responsibility> </cit:citedResponsibleParty> </cit:CI_Citation> </mri:citation> <mri:abstract xsi:type="lan:PT_FreeText_PropertyType"> <gco:CharacterString>This dataset contains environmental DNA (eDNA) data collected in the Northeast Pacific Ocean. These data were collected as part of the International Year of the Salmon (IYS) Gulf of Alaska High Seas Expedition conducted in March and April 2020 and 2021, to further improve the understanding of factors impacting salmon early marine winter survival. eDNA analysis uses the free DNA shed from organisms and available in the environment to assess species diversity and composition. The eDNA database will provide overall composition of nekton, micronekton and zooplankton allowing estimation of salmon prey and potential predators. Water collected with Niskin bottle from 2-3m. 2L filtered onto Sterivex column for each replicate. Filters flash frozen. DNA extracted from filters using DNeasy kits (QUIAGEN). 16S and COI rRNA gens were amplified with PCR and sequenced on Illumina MiSeq platform using SE at 300 cycles. Reads were processed using obitools (https://pythonhosted.org/OBITools/welcome.html) and queired against nt using BLASTn. Reads were assigned to OTU using MEGAN (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/). Results were filtered using a cuttoff of &gt;/=10 reads for positive detection. Detection of obvious contaminations belonging to human or food waste (sheep, pig, chicken, cow) as well as artificial positive controls were removed. For detailed information contact Dr. Christoph Deeg: chdeeg@mail.ubc.ca</gco:CharacterString> <lan:PT_FreeText> <lan:textGroup> <lan:LocalisedCharacterString locale="#fr">Ce jeu de données contient des données d&#39;ADN environnemental (ADNe) collectées dans le nord-est de l&#39;océan Pacifique. Ces données ont été collectées dans le cadre de l&#39;expédition en haute mer dans le golfe d&#39;Alaska de l&#39;Année internationale du saumon (AIJ) menée en mars et avril 2020 et 2021, afin d&#39;améliorer encore la compréhension des facteurs ayant une incidence sur la survie hivernale précoce du saumon en mer. disponibles dans l&#39;environnement pour évaluer la diversité et la composition des espèces. La base de données EDNA fournira la composition globale du nekton, du micronekton et du zooplancton, ce qui permettra d&#39;estimer les proies du saumon et les prédateurs potentiels. Eau recueillie avec une bouteille Niskin de 2 à 3 m. 2 litres filtrés sur colonne Sterivex pour chaque réplique. Les filtres sont gelés. ADN extrait des filtres à l&#39;aide de kits DNEasy (QUIAGEN). Les gènes d&#39;ARNr 16S et COI ont été amplifiés par PCR et séquencés sur la plateforme Illumina MiSeq en utilisant l&#39;ES à 300 cycles. Les lectures ont été traitées à l&#39;aide d&#39;obitools (https://pythonhosted.org/OBITools/welcome.html) et ont été interrogées pour ne pas utiliser BlastN. Les lectures ont été attribuées à l&#39;OTU à l&#39;aide de MEGAN (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/). Les résultats ont été filtrés en utilisant un seuil de &gt;/=10 lectures pour une détection positive. La détection de contaminations évidentes appartenant à des déchets humains ou alimentaires (mouton, porc, poulet, vache) ainsi que les témoins positifs artificiels ont été supprimés. 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