Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017

Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Pierson, B.J. (ORCID: 0000-0001-8233-874X)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Menning, D.M. (ORCID: 0000-0003-3547-3062)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 20180403
Title:
Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017
Geospatial_Data_Presentation_Form: tabular digital data
Publication_Information:
Publication_Place: Anchorage, AK
Publisher: U.S. Geological Survey, Alaska Science Center
Other_Citation_Details:
Suggested citation: Wilson, R.E., Pierson, B.J., Sage, G.K., Sonsthagen, S.A., Gravley, M.C., Menning, D.M., and Talbot, S.L., 2018, Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017: U.S. Geological Survey data release, https://doi.org/10.5066/F7CF9P23
Online_Linkage: https://doi.org/10.5066/F7CF9P23
Larger_Work_Citation:
Citation_Information:
Originator: U.S. Geological Survey, Alaska Science Center
Publication_Date: 2000
Title:
Developing and Applying Molecular Tools to Natural Resource Problems in Alaska
Geospatial_Data_Presentation_Form: website
Series_Information:
Series_Name: Alaska Science Portal
Issue_Identification: 378
Publication_Information:
Publication_Place: Anchorage, Alaska
Publisher: U.S. Geological Survey, Alaska Science Center
Other_Citation_Details:
This is a link to the broader USGS Alaska Science Center research project supported by these data. Users will find a description of the research project and links to associated reports, publications, and data products.
Online_Linkage: https://alaska.usgs.gov/portal/project.php?project_id=378
Description:
Abstract:
Fragment data from 11 nuclear microsatellite loci and sequence data from the mitochondrial cytochrome b gene were gathered from Arctic cod (Boreogadus saida) in the Beaufort and Chukchi seas. Mitogenomic analyses of Arctic cod and three other co-distributed gadoids (Polar cod [Arctogadus glacialis], Saffron cod [Eleginus gracilis], Walleye Pollock [Gadus chalcogrammus]) were also completed. Transcriptomic analyses of Arctic cod were used to identify genes associated with environmental perturbations. Genome-wide scans using RAD-Seq of Arctic cod and the co-distributed Polar Cod were collected.
Purpose:
Data were collected to provide genetic, genomic and transcriptomic products that will provide insight into the population genetics and evolutionary history of Arctic cod (Boreogadus saida) within the context of changing Arctic ecosystems.
Supplemental_Information:
Both Boreogadus saida and Arctogadus glacialis are often referred to as both Arctic cod and Polar cod in the scientific literature. Recently, the American Fisheries Society and American Society of Ichthyologists and Herpetologists have recommended using Polar cod for Boreogadus saida to follow European taxonomic nomenclature (Page et al 2013). In this study, we use the common name "Arctic cod" to refer to Boreogadus saida and "Polar cod" refers to Arctogadus glacialis to remain consistent with the majority of Alaskan literature. In addition, the usage of the common names the Saffron cod and Walleye Pollock throughout this dataset refer to Eleginus gracilis and Gadus chalcogrammus, respectively.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2006
Ending_Date: 2015
Currentness_Reference: observed
Status:
Progress: Complete
Maintenance_and_Update_Frequency: Unknown
Spatial_Domain:
Description_of_Geographic_Extent:
Gulf of Alaska, Aleutian Islands, Norton Sound, Bering Sea, Chukchi Sea, and Beaufort Sea, USA and Gulf of St. Lawrence, Nova Scotia and Beaufort Sea, Canada
Bounding_Coordinates:
West_Bounding_Coordinate: 173.6158
East_Bounding_Coordinate: -59.6615
North_Bounding_Coordinate: 71.9526
South_Bounding_Coordinate: 49.9224
Keywords:
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC175
Theme:
Theme_Keyword_Thesaurus: NASA GCMD Earth Science Keywords Thesaurus
Theme_Keyword: Earth science
Theme_Keyword: Oceans
Theme_Keyword: Aquatic sciences
Theme_Keyword: Fisheries
Theme_Keyword: Bioshpere
Theme_Keyword: Aquatic ecosystems
Theme_Keyword: Marine habitat
Theme_Keyword: Ecological dynamics
Theme_Keyword: Species/population interactions
Theme_Keyword: Evolutionary adaptation
Theme_Keyword: Natural selection
Theme_Keyword: Population dynamics
Theme_Keyword: Use/feeding habitats
Theme_Keyword: Biospheric indicators
Theme_Keyword: Indicator species
Theme:
Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Genetics
Theme_Keyword: Ecological genetics
Theme_Keyword: Genetic structure
Theme_Keyword: Genetic diversity
Theme_Keyword: Genotype-environment interactions
Theme_Keyword: Genetic structure
Theme_Keyword: Biodiversity
Theme_Keyword: Gene distribution
Theme_Keyword: Population genetics
Theme_Keyword: Genetic variance
Theme_Keyword: Genetic markers
Theme_Keyword: Gene expression
Theme_Keyword: Genomes
Theme_Keyword: Hybrids
Theme_Keyword: Gene flow
Theme_Keyword: Genetic isolation
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota
Theme_Keyword: environment
Theme:
Theme_Keyword_Thesaurus: MeSH-National Library of Medicine
Theme_Keyword: Arctic Regions
Theme_Keyword: North America
Theme_Keyword: Alaska
Theme_Keyword: Canada
Theme_Keyword: Ecosystem
Theme_Keyword: Fisheries
Theme_Keyword: Gadiformes
Theme_Keyword: Sentinel Species
Theme_Keyword: DNA
Theme_Keyword: DNA, Mitochondrial
Theme_Keyword: Microsatellite Repeats
Theme_Keyword: Transcriptome
Theme_Keyword: Genomics
Theme_Keyword: Genetics, Population
Theme:
Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Sciences
Theme_Keyword: Life Sciences
Theme_Keyword: Genetics
Theme_Keyword: DNA sequencing
Theme_Keyword: Polymerase chain reaction
Theme_Keyword: Systematics and taxonomy
Theme_Keyword: Marine biology
Theme_Keyword: Fishery resources
Theme_Keyword: Marine fishery resources
Theme_Keyword: Ichthyology
Theme_Keyword: Fish
Place:
Place_Keyword_Thesaurus: USGS Geographic Names Information System
Place_Keyword: Gulf of Alaska
Place_Keyword: Aleutian Islands
Place_Keyword: Norton Sound
Place_Keyword: Bering Sea
Place_Keyword: Chukchi Sea
Place_Keyword: Beaufort Sea
Place_Keyword: Camden Bay
Place_Keyword: State of Alaska
Place_Keyword: United States of America
Place:
Place_Keyword_Thesaurus: NGA GEOnet Names Server
Place_Keyword: Canada
Place_Keyword: Beaufort Sea
Place_Keyword: Yukon Territory
Place_Keyword: Nova Scotia
Place_Keyword: Gulf of Saint Lawrence
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: collection
Taxonomic_Keywords: animals
Taxonomic_Keywords: vertebrates
Taxonomic_Keywords: multiple species
Taxonomic_Keywords: single species
Taxonomic_System:
Classification_System/Authority:
Classification_System_Citation:
Citation_Information:
Originator: Integrated Taxonomic Information System
Publication_Date: Unknown
Title: Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Publication_Information:
Publication_Place: online
Publisher: ITIS-North America
Other_Citation_Details:
Retrieved November 20, 2017, from the Integrated Taxonomic Information System on-line database http://www.itis.gov
Online_Linkage: http://www.itis.gov/
Classification_System_Modifications:
Both Boreogadus saida and Arctogadus glacialis are often referred to as both Arctic cod and Polar cod in the scientific literature. Recently, the American Fisheries Society and American Society of Ichthyologists and Herpetologists have recommended using Polar cod for Boreogadus saida to follow European taxonomic nomenclature (Page et al 2013). In this study, we use the common name "Arctic cod" to refer to Boreogadus saida and "Polar cod" refers to Arctogadus glacialis to remain consistent with the majority of Alaskan literature. In addition, the usage of the common names the Saffron cod and Walleye Pollock throughout this dataset refer to Eleginus gracilis and Gadus chalcogrammus, respectively.
Taxonomic_Procedures:
Samples were provided to the USGS Alaska Science Center labelled as Boreogadus saida, Arctogadus glacialis, Eleginus gracilis, or Gadus chalcogrammus.
Taxonomic_Completeness:
Seven samples provided and labelled as Arctic cod (B. saida) have a Gmo8 genotype consistent with Polar cod (A. glacialis) and were eliminated from Arctic cod analyses by the authors based on Madsen et al 2009. Although a single locus genotype is not sufficient to conclude that these individuals are Polar cod, their generally larger (than other Arctic cod) allele size distribution at locus Bsa 14-1 provided additional data these particular samples may have been misidentified in the field and a decision was made to eliminate them from further analyses. One of these seven samples (BOSA 14-16973) was confirmed to be a Polar cod (A. glacialis) with unpublished mtDNA. Five Polar cod (A. glacialis; PC20011098, PC20011414, PC20015832, PC20012107, PC20011525) are suspected to be Arctic cod (B. saida) based on either mitogenome or ddRad-Seq data associated with Arctic cod (B. saida). One Polar cod (A. glacialis) sample (PC20015632) provided to the lab labelled as "Arctogadus glacialis," had a Polar cod-like mitogenome with an Arctic cod-like nuclear genome, suggesting this individual is of a hybrid origin. Results have been provided in the dataset and discrepancies noted in the logical consistency portion of the metadata.
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Taxonomic_Classification:
Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:
Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Deuterostomia
Taxonomic_Classification:
Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Taxonomic_Classification:
Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Taxonomic_Classification:
Taxon_Rank_Name: Infraphylum
Taxon_Rank_Value: Gnathostomata
Taxonomic_Classification:
Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Actinopterygii
Taxonomic_Classification:
Taxon_Rank_Name: Class
Taxon_Rank_Value: Teleostei
Taxonomic_Classification:
Taxon_Rank_Name: Superorder
Taxon_Rank_Value: Paracanthopterygii
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Gadiformes
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Gadidae
Taxonomic_Classification:
Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Gadinae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Arctogadus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Arctogadus glacialis
Applicable_Common_Name: polar cod
Applicable_Common_Name: Arctic cod
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Boreogadus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Boreogadus saida
Applicable_Common_Name: Arctic cod
Applicable_Common_Name: polar cod
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Eleginus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Eleginus gracilis
Applicable_Common_Name: saffron cod
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Gadus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Gadus chalcogrammus
Applicable_Common_Name: Walleye Pollock
Access_Constraints: None
Use_Constraints:
If you use these data in a publication, presentation, or other product, it is requested that you credit USGS and the authors of this data for their contribution to your work.
Microsatellite data from this dataset cannot be combined with data generated outside the USGS Alaska Science Center without molecular size calibration between laboratories.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, Alaska Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99508
Country: USA
Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov
Data_Set_Credit:
This study was funded, in part, by the US Department of the Interior, Bureau of Ocean Energy Management (BOEM), Environmental Studies Program, Washington, DC, through Agreement Number M14PG00008 with the U.S. Geological Survey (USGS).
Cross_Reference:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Wedemeyer, K.
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Menning, D.M. (ORCID: 0000-0003-3547-3062)
Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Sexson, M.G. (ORCID: 0000-0002-1078-0835)
Originator: Nelson, R.J.
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2019
Title:
Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: ICES Journal of Marine Science
Issue_Identification: 76(6):1713-1721
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Wilson, R.E., Sage, G.K., Wedemeyer, K., Sonsthagen, S.A., Menning, D.M., Gravley, M.C., Sexson, M.G., Nelson, R.J., Talbot, S.L. 2019. Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska. ICES Journal of Marine Science 76(6):1713-1721 doi:10.1093/icesjms/fsz041
Online_Linkage: https://doi.org/10.1093/icesjms/fsz041
Cross_Reference:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Menning, D.M. (ORCID: 0000-0003-3547-3062)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2017
Title: Genomics of Arctic Cod
Geospatial_Data_Presentation_Form: document
Series_Information:
Series_Name: OCS Study BOEM
Issue_Identification: 2017-066
Publication_Information:
Publication_Place: online
Publisher: US DOI BOEM Alaska OCS Region
Other_Citation_Details:
Wilson, R.E, Sage G.K., Sonsthagen, S.A., Gravley, M.C., Menning, D.M., Talbot, S.L.. 2017. Genomics of Arctic Cod. Anchorage, AK: US Dept. of the Interior, Bureau of Ocean Energy Management, Alaska OCS Region. OCS Study BOEM 2017-066. 92pp.
To download a PDF file of this report, go to the U.S. Department of the Interior, Bureau of Ocean Energy Management Data and Information Systems webpage ( https://marinecadastre.gov/espis/# ) and search on 2017-066.
Online_Linkage: https://marinecadastre.gov/espis/#
Cross_Reference:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Menning, D.M. (ORCID: 0000-0003-3547-3062)
Originator: Wedemeyer, K.
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2018
Title: A transcriptome resource for the Arctic Cod (Boreogadus saida)
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Marine Genomics
Issue_Identification: 41:57-61
Publication_Information:
Publication_Place: online
Publisher: Elsevier
Other_Citation_Details:
Wilson, R.E., Menning, D.M., Wedemeyer, K., Talbot, S.L. 2018. A transcriptome resource for the Arctic Cod (Boreogadus saida). Marine Genomics 41:57-61 doi:10.1016/j.margen.2018.03.003
Online_Linkage: https://doi.org/10.1016/j.margen.2018.03.003
Cross_Reference:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Sme, N.
Originator: Gharett, A.J.
Originator: Majewski, A.
Originator: Wedemeyer, K.
Originator: Nelson, R.J.
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2020
Title:
Mitochondrial genome diversity and population mitogenomics of Polar Cod (Boreogadus saida) and Arctic dwelling gadoids
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Polar Biology
Issue_Identification: .
Publication_Information:
Publication_Place: online
Publisher: Springer Nature
Other_Citation_Details:
Wilson, R.E., Sonsthagen, S.A., Sme, N., Gharett, A.J., Majewski, A., Wedemeyer, K., Nelson, R.J., Talbot, S.L. 2020. Mitochondrial genome diversity and population mitogenomics of Polar Cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biology doi:10.1007/s00300-020-02703-5
Online_Linkage: https://doi.org/10.1007/s00300-020-02703-5
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
Individual sample ID's, collection dates, and sampling locations of samples provided by collectors were cross-checked and verified to match the accompanying worksheet and with curation records for those samples noted originating from the Burke Museum.
Sampling locations were cross-referenced to the Geographic Names Information Service (GNIS) and NGA GEOnet Names Server when possible.
Genotype numbers were determined by scoring based on allele size relative to an M13 DNA sequence ladder and to samples established as size standards that were run on each gel or were determined by calibration using the most common allele observed at each locus in the dataset and DNA samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada. Review individual microsatellite attribute information for specific locus information. Seven samples eliminated from further analyses due to results inconsistent with Arctic Cod (Boreogadus saida) at locus Gmo8 and Bsa14-1 (BOSA 14-16797, BOSA 14-16514, BOSA 14-16724, BOSA 14-16725, BOSA 14-16850, BOSA 14-16973, and BOSA 13-16340), have estimated allele sizes for loci Bsa14-1 and Gmo_8.
GenBank accession numbers were cross-referenced to the appropriate individual samples as recorded.
For quality control purposes, DNA from two to five individuals representing each designated population were extracted, amplified, and sequenced in duplicate. We observed sterile techniques in the handling of all DNA, and all procedures were performed with positive and negative controls to provide evidence of replication without contamination. Per laboratory standard operating procedures, if discrepancies occurred, analyses were repeated until the laboratory manager was satisfied results were accurate.
Mitogenome raw paired-end reads were assembled and mapped to their respective species reference mitogenome in Geneious 8.1.8 (BioMatters Limited, Auckland, New Zealand) using high sensitivity setting and minimum mapping quality was set to greater than 99.9% (minimum confidence that read is correctly mapped).
Logical_Consistency_Report:
For microsatellite data, reported allele sizes were reviewed to confirm they conform to expected distributions (e.g. dinucleotide repeats with 1 base pair differences were reviewed on gel images with laboratory personnel, gaps in allele sizes were reviewed, and single occurrences of an allele size were scrutinized). Seven samples provided and labelled as Arctic cod (B. saida) have a Gmo8 genotype consistent with Polar cod (A. glacialis) and were eliminated from Arctic cod analyses by the authors based on Madsen et al 2009. Although a single locus genotype is not sufficient to conclude that these individuals are Polar cod, their generally larger (than other Arctic cod) allele size distribution at locus Bsa 14-1 provided additional data these particular samples may have been misidentified in the field and a decision was made to eliminate them from further analyses. One of these seven samples (BOSA 14-16973) was confirmed to be a Polar cod (A. glacialis) with unpublished mtDNA cytochrome-b data. Four Polar cod (A. glacialis; PC20011098, PC20015832, PC20012107, PC20011525) are suspected to be Arctic cod (B. saida) based on either mitogenome or ddRad-Seq data associated with Arctic cod (B. saida). One Polar cod (A. glacialis) sample (PC20011414) provided to the lab labelled as "Arctogadus glacialis," had an Arctic cod-like mitogenome along with an Arctic cod-like nuclear genome suggesting this sample was misidentified in the field. One Polar cod (A. glacialis) sample (PC20015632) provided to the lab labelled as "Arctogadus glacialis," had a Polar cod-like mitogenome with an Arctic cod-like nuclear genome, suggesting this individual is of a hybrid origin. Results have been provided in the dataset. Furthermore, levels of error due to allelic dropout, null alleles, or scoring error was assessed for microsatellite loci using MICROCHECKER (Van Oosterhout et al 2004).
Completeness_Report:
Data omissions for particular entities are explained in the Entity and Attribute definitions. Blank data indicates no data were collected or not provided with the sample for a particular attribute. Collection years and sampling location coordinates are provided when available, but were not available for all samples provided to the laboratory.
Positional_Accuracy:
Horizontal_Positional_Accuracy:
Horizontal_Positional_Accuracy_Report:
Geospatial data were acquired from the contributing data sources. These methods were not documented in the source data.
Lineage:
Methodology:
Methodology_Type: Lab
Methodology_Description:
DNA extractions prior to 2015 were completed using a "salting out" procedure described by Medrano et al 1990 with modifications described in Sonsthagen et al 2004 and, as needed for low quality samples, Talbot et al 2011.
Methodology:
Methodology_Type: Lab
Methodology_Description:
DNA extractions of Chukchi Sea samples from 2015 were extracted using QIAGEN DNeasy Tissue Kit (QIAGEN, Valencia, CA) following the manufacturer’s recommendations.
Methodology:
Methodology_Type: Lab
Methodology_Description:
DNA extractions of RAD-Seq samples were extracted using QIAGEN DNeasy Blood and Tissue Kit (QIAGEN, Valencia, CA) following the manufacturer’s recommendations from 123 morphologically identified as Boreogadus saida and 14 Arctogadus glacialis using individuals with mitogenome information available when possible.
Methodology:
Methodology_Type: Lab
Methodology_Description:
Quantification of extracted DNA via fluorometry followed Handel et al 2006 or was completed using a Quant-iT dsDNA Broad-Range Kit (Invitrogen, Carlsbad, CA USA) and Turner Biosystems Modulus™ Plate Reader (Turner BioSystems, Sunnyvale, CA USA).
Methodology:
Methodology_Type: Lab
Methodology_Description:
Polymerase chain reaction (PCR) amplification followed Sonsthagen et al 2004 using primer pairs as published [Bsa101 (Nelson et al 2013), Gmo8 and Gmo34 (Miller et al 2000), PGmo32 (Jakobsdóttir et al 2006), Tch14 (O'Reilly et al 2000)], one primer redesigned in this study to produce a shorter fragment [Bsa14-Forward (Nelson et al 2013)/Bsa14-1-Reverse (GGAAGTCGACTTTTCATGGAC)], or both primers redesigned in this study to produce a shorter fragment [Bsa6 (Nelson et al 2013): Bsa6-1-Forward (GCACTAAAGCATGATGAAAGC)/Bsa6-1-Reverse (GACACTGCTTTTATACAGC); Bsa7 (Nelson et al 2013): Bsa7-1-Forward (AGGTTCGGTGTTTACCTGC)/Bsa7-1-Reverse (ACTGAACAGGTGTTCAGGC); Bsa15 (Nelson et al 2013): Bsa15-1-Forward (ACGCAGTTGGTCCAAAGC)/Bsa15-1-Reverse (ACTCAGAGCTCCTGTTGC); Bsa60 (Nelson et al 2013): Bsa60-1-Forward (AATTGAGATTCCCTGGGC)/Bsa60-1-Reverse (ATTTCTGACGTTTCTTGC); PGmo127 (Skirnisdottir et al 2008): PGmo127-1-Forward (CCCTCAAAATTCAACCTGG)/PGmo127-1-Reverse (TCTCCTCCCCTTGTGTGC)]. Additionally, once initial optimizations were completed, the 11 microsatellites were multiplexed in four reactions for simultaneous collection utilizing two different fluorescent labels and considering locus size differences (Multiplex 1:Bsa6-1/Bsa14-1; Multiplex 2: Bsa7-1/Bsa60-1/Tch14; Multiplex 3: Gmo8/Bsa15-1/Bsa101; Multiplex 4: Gmo34/PGmo32/PGmo127-1).
Methodology:
Methodology_Type: Lab
Methodology_Description:
Polymerase chain reaction (PCR) amplification and sequencing of mtDNA cytochrome b (cytb) gene were completed using primers designed from a Boreogadus saida reference mitogenome available on GenBank (Accession no. AM919428; https://www.ncbi.nlm.nih.gov/nuccore/AM919428 The resulting primer pairs amplified either a 818 bp (base pairs) portion of cytb (CB115-F:5'TTTGGCTCTCTTCTAGGC3'/CB993-R:5'GAATGTTAAACCTCGCTGC3') or a 1,266 bp fragment encompassing the entire gene and portion of the adjacent tRNA-Glu and tRNA-Thr (BOSA_cyb-F:5'ATGCCATAATTCCTGCCCAGA3'/BOSA_cyb-R:5'CGGTAATAATTGGATGYAGCAC3'). PCR amplifications were carried out in a 20-μL volume with 2–100 ng genomic DNA, 0.5 μM each primer, 1.0 μM dNTPs, 10× PCR Perkin Elmer Cetus #1 buffer, and 0.2 units Taq polymerase. PCR reactions began with 94 ºC for 10 min followed by 40 cycles of 94°C for 30 sec, 50°C for 30 sec, and 72°C for 90 sec with a 30 min final extension at 72°C. For the shorter fragment, the final 30 min extension was excluded. ExoSAP-IT® (USB Corporation, Cleveland, OH) was used to remove excess primers and dNTPs in PCR products. All samples were cycle-sequenced using the shorter fragment primer pair which yielded a 707 bp of sequence product consistent across all individuals on either a LI-COR 4200LR or ABI 3730xl. (Wilson et al 2017)
Methodology:
Methodology_Type: Lab
Methodology_Description:
Primers for polymerase chain reaction (PCR) amplification and sequencing of complete mitogenomes were designed by aligning mitogenomes (available in GenBank; https://www.ncbi.nlm.nih.gov/GenBank/ ) of Boreogadus saida (AM919428), Arctogadus glacialis (AM919429), Gadus ogac (DQ356941), Gadus chalcogrammus (AB182307) and Gadus morhua (NC002081). Long-Range PCR (LR-PCR) was used to amplify the mitogenome of each individual in 5-7 fragments with at least 500bp of overlap between amplicons. Each 20µLPCR reaction for each primer pair contained 2.0µL 10x LA PCR Buffer II (25 mM Mg2+), 3.20 µl 2.5 mM dNTP mixture, 0.1µL TaKaRa LA Taq (Takara Bio Company, Mountain View, CA, USA), 0.8-1.50 µL 10 µM of each primer, 1 µL of template DNA, and 10.60-12.00 µL of RNA-free water. For samples that failed to amplify, 0.80 µl of PCR additive 5M Betaine was added to the PCR reaction. The PCR conditions were 94°C for 5 minutes followed by 30 cycles of 98°C for 15 seconds, 50°C for 15 secs and 68°C for 11 minutes, ending with 72°C for 10 minutes. The resulting amplicons for each individual were purified using ExoSAP-IT (Affymetrix, Cleveland, OH USA), quantified with Quant-iT dsDNA High Sensitivity Kit (Invitrogen, Carlsbad, CA USA), and then pooled by individual in equimolar concentrations. Pooled amplicons for each individual sample were used to construct libraries using a Nextera XT 96 sample DNA kit using standard Illumina barcodes (Illumina, San Diego, CA USA). Next-generation sequencing was performed on a MiSeq Desktop Sequencer (2 × 250 bp read-length configuration) at the U.S. Geological Survey Alaska Science Center, U.S. Geological Survey following manufacturer’s protocol. (Wilson et al 2017)
Methodology:
Methodology_Type: Lab
Methodology_Description:
Six whole individuals for the transcriptome portion of the dataset were preserved in RNAlater® (Sigma-Aldrich, St.Aldrich, St. Louis, MO, USA) for a maximum of 12 hours, then stored at minus 80°C until processing to obtain the field-acclimatized transcriptome profile (Wilson et al 2019).
Methodology:
Methodology_Type: Lab
Methodology_Description:
Total RNA was extracted from individuals using a MasterPure™ RNA Purification Kit (Epicentre, Madison, WI, USA) following manufacturer’s protocol and quantified using a Quant-iT RNA Assay Kit (Invitrogen, Carlsbad, CA USA). Of the 6 individuals, 3 measuring between 21 and 37 mm were classified as juveniles/age 0/hatchlings and a cross-section encompassing multiple organs was taken from behind the pectoral fin for RNA extraction. The remaining 3 individuals were >73 mm long and of sufficient size to allow RNA extraction on 3 tissue types (gill, muscle with skin, and abdomen/intestine). (Wilson et al 2017)
Methodology:
Methodology_Type: Lab
Methodology_Description:
Libraries were generated from high-quality RNA using the TruSeq® stranded mRNA library preparation kit following the low sample protocol (Illumina, San Diego, CA USA). Concentrations of the final library were quantified using Quant-iT RNA Assay Kit and sequenced on the Illumina MiSeq Desktop Sequencer [2 × 150 bp (base pair) read-length configuration] within a pooled library consisting of 12 total libraries. (Wilson et al 2019)
Methodology:
Methodology_Type: Lab
Methodology_Description:
RAD-seq followed DaCosta and Sorenson 2014 with the exceptions of using high fidelity versions of SbfI and MspI as restriction enzymes (New England Biolabs, Ipswich, MA, USA), increasing number of cycles to 24 in the post-selection step, and the sequencing run having a size of 150 bp. Sequencing of the multi-plexed library and assignment of reads to individual samples based on barcode/index sequences using bcl2fastq-1.8.4 software (Illumina Inc.) was on an Illumina HiSeq 2500 at the Tufts University Core Genomics Facility. This resulted in a total of 138,598,600 raw sequencing reads with a maximum 150 bp length using single-end sequencing (Wilson et al 2019).
Source_Information:
Source_Citation:
Citation_Information:
Originator: (1) Burke Museum, University of Washington
Originator: (2) Bureau of Ocean Energy Management (BOEM)
Originator:
(3) Vanessa von Biela, U.S, Geological Survey, Alaska Science Center
Originator: (4) R. John Nelson, Seastar Biotech
Originator: (5) Noel Sme, University of Alaska Fairbanks
Originator: (5) Anthony Gharrett, University of Alaska Fairbanks
Originator: (6) Andrew Majewski, Fisheries and Oceans Canada
Publication_Date: Unpublished material
Title: Individual Contributors of Samples
Geospatial_Data_Presentation_Form: samples and sampling location information
Type_of_Source_Media: tissue/DNA for genetic analyses
Source_Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2006
Ending_Date: 2015
Source_Currentness_Reference: observed
Source_Citation_Abbreviation: samples_samplingInformation
Source_Contribution:
(1) All Sample_ID's containing "UW" were obtained from the Burke Museum, University of Washington.
(2) All other Boreogadus saida from 2011, 2013, and 2014 were provided by the Bureau of Ocean Energy Management (BOEM)
(3) Boreogadus saida from 2015 were provided by Vanessa von Biela, U.S. Geological Survey.
(4) Boreogadus saida from 2008 and Boreogadus saida containing an "SL" in Sample_ID were provided by R. John Nelson, Seastar Biotech.
(5) Eleginus gracilis were provided by Noel Sme and Anthony Gharrett, University of Alaska-Fairbanks.
(6) Arctogadus glacialis were provided by Andrew Majewski, Fisheries and Ocean Canada.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Chevreux, B.
Originator: Wetter, T.
Originator: Suhai, S.
Publication_Date: 1999
Title:
Genome sequence assembly using trace signals and additional sequence information
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Proceedings of the German Conference on Bioinformatics
Issue_Identification: 1999:45–56
Publication_Information:
Publication_Place: Hannover, Germany
Publisher: German Conference on Bioinformatics
Other_Citation_Details:
Chevreux, B., Wetter, T., Suhai, S. 1999. Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics 1999:45–56
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 1999
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Chevreux et al 1999
Source_Contribution: Procedure for reconstructing mitogenomes.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Conesa, A.
Originator: Gotz, S.
Originator: García-Gómez, J.M.
Originator: Terol, J.
Originator: Talón, M.
Originator: Robles, M.
Publication_Date: 2005
Title:
Blast2Go: a universal tool for annotation, visualization and analysis for functional genomics research
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Bioinformatics
Issue_Identification: 21(18):3674–3676
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Conesa, A., Gotz, S., García-Gómez, J.M., Terol, J., Talón, M., Robles, M. 2005. Blast2Go: a universal tool for annotation, visualization and analysis for functional genomics research. Bioinformatics 21(18):3674–3676 doi:10.1093/bioinformatics/bti610
Online_Linkage: https://doi.org/10.1093/bioinformatics/bti610
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2005
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Conesa et al 2005
Source_Contribution: Used to map transcripts to existing gene categories.
Source_Information:
Source_Citation:
Citation_Information:
Originator: DaCosta, J.M.
Originator: Sorenson, M.D.
Publication_Date: 2014
Title:
Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: PLoS ONE
Issue_Identification: 9(9):e106713
Publication_Information:
Publication_Place: online
Publisher: PLoS, San Francisco, CA
Other_Citation_Details:
DaCosta, J.M., Sorenson, M.D. 2014. Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLoS ONE 9(9):e106713 doi:10.1371/journal.pone.0106713
Online_Linkage: https://doi.org/10.1371/journal.pone.0106713
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2014
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: DaCosta and Sorenson 2014
Source_Contribution: Laboratory methods for RAD-seq
Source_Information:
Source_Citation:
Citation_Information:
Originator: Edgar, R.C.
Publication_Date: 2010
Title: Search and clustering orders of magnitude faster than BLAST
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Bioinformatics
Issue_Identification: 26(19):2460–2461
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461 doi:10.1093/bioinformatics/btq461
Online_Linkage: https://doi.org/10.1093/bioinformatics/btq461
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2010
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Edgar 2010
Source_Contribution: Used to filtering DNA sequence data.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Edgar, R.C.
Publication_Date: 2004
Title:
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Nucleic Acids Research
Issue_Identification: 32(5):1792–1797
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5):1792–1797 doi:10.1093/nar/gkh340
Online_Linkage: https://doi.org/10.1093/nar/gkh340
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2004
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Edgar 2004
Source_Contribution: Used to construct and align mitogenomes.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Hahn, C.
Originator: Bachmann, L.
Originator: Chevreux, B.
Publication_Date: 2013
Title:
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads –- a baiting and iterative approach
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Nucleic Acids Research
Issue_Identification: 41(13):e129
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Hahn, C., Bachmann, L., Chevreux, B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads –- a baiting and iterative approach. Nucleic Acids Research 41(13):e129 doi:10.1093/nar/gkt371
Online_Linkage: https://doi.org/10.1093/nar/gkt371
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2013
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Hahn et al 2013
Source_Contribution: Procedure for reconstructing mitogenomes.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Handel, C.M. (ORCID: 0000-0002-0267-7408)
Originator: Pajot, L.M. (ORCID: 0000-0001-5704-2381)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Publication_Date: 2006
Title:
Use of buccal swabs for sampling DNA from nestling and adult birds
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Wildlife Society Bulletin
Issue_Identification: 34(4):1094-1100
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
Handel, C.M., Pajot, L.M., Talbot, S.L. , Sage, G.K. 2006. Use of buccal swabs for sampling DNA from nestling and adult birds. Wildlife Society Bulletin 34(4):1094-1100 doi:10.2193/0091-7648(2006)34[1094:UOBSFS]2.0.CO;2
Online_Linkage: https://doi.org/10.2193/0091-7648(2006)34[1094:UOBSFS]2.0.CO;2
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2006
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: >Handel et al 2006
Source_Contribution: DNA quantification via fluorometry
Source_Information:
Source_Citation:
Citation_Information:
Originator: Iwasaki, W.
Originator: Fukunaga, T.
Originator: Isagozawawa, R.
Originator: Yamada, K.
Originator: Maeda, Y.
Originator: Satoh, T.P.
Originator: Sado, T.
Originator: Mabuchi, K.
Originator: Takeshima, H.
Originator: Miya, M.
Originator: Nishida, M.
Publication_Date: 2013
Title:
MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Molecular Biology and Evolution
Issue_Identification: 30(11):2531–2540
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Iwasaki, W., Fukunaga, T., Isagozawawa, R., Yamada, K., Maeda, Y., Satoh, T.P., Sado, T., Mabuchi, K., Takeshima, H., Miya, M., Nishida, M. 2013. MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular Biology and Evolution 30(11):2531–2540 doi:10.1093/molbev/mst141
Online_Linkage: https://doi.org/10.1093/molbev/mst141
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2013
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Iwasaki et al 2013
Source_Contribution: Used to annotate mitogenomes.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Jakobsdóttir, K.B.
Originator: Jörundsdóttir, Þ.D.
Originator: Skírnisdóttir, S.
Originator: Hjörleifsdóttir, S.
Originator: Hreggviðsson, G.Ó.
Originator: Daníelsdóttir, A.K.
Originator: Pampoulie, C.
Publication_Date: 2006
Title:
Nine new polymorphic microsatellite loci for the amplification of archived otolith DNA of Atlantic cod, Gadus morhua L.
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Molecular Ecology Notes
Issue_Identification: 6(2):337-339
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
Jakobsdóttir, K.B., Jörundsdóttir, Þ.D., Skírnisdóttir, S., Hjörleifsdóttir, S., Hreggviðsson, G.Ó., Daníelsdóttir, A.K., Pampoulie, C. 2006. Nine new polymorphic microsatellite loci for the amplification of archived otolith DNA of Atlantic cod, Gadus morhua L. Molecular Ecology Notes 6(2):337-339 doi:/10.1111/j.1471-8286.2005.01223.x
Online_Linkage: https://doi.org/10.1111/j.1471-8286.2005.01223.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2006
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Jakobsdóttir et al 2006
Source_Contribution: Primer sequence PGmo32
Source_Information:
Source_Citation:
Citation_Information:
Originator: Jones, P.
Originator: Binns, D.
Originator: Chang, H-Y.
Originator: Fraser, M.
Originator: Li, W.
Originator: McAnulla, C.
Originator: McWilliam, H.
Originator: Maslen, J.
Originator: Mitchell, A.
Originator: Nuka, G.
Originator: Pesseat, S.
Originator: Quinn, A.F.
Originator: Sangrador-Vegas, A.
Originator: Scheremetjew, M.
Originator: Yong, S-Y.
Originator: Lopez, R.
Originator: Hunter, S.
Publication_Date: 2014
Title: InterProScan 5: genome-scale protein function classification
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Bioinformatics
Issue_Identification: 30(9):1236-1240
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Jones, P., Binns, D., Chang, H-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A.F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S-Y., Lopez, R., Hunter, S. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236-1240 doi:10.1093/bioinformatics/btu031
Online_Linkage: https://doi.org/10.1093/bioinformatics/btu031
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2014
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Jones et al 2014
Source_Contribution: Used to annotate transcripts.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Madsen, M.L.
Originator: Fevolden, S-E.
Originator: Christiansen, J.S.
Publication_Date: 2009
Title:
A simple molecular approach to distinguish between two Arctic gadoid fishes Arctogadus glacialis (Peters, 1874) and Boreogadus saida (Lepechin, 1774)
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Polar Biology
Issue_Identification: 32(6):937-939
Publication_Information:
Publication_Place: online
Publisher: Springer Nature
Other_Citation_Details:
Madsen, M.L., Fevolden, S-E., Christiansen, J.S. 2009. A simple molecular approach to distinguish between two Arctic gadoid fishes Arctogadus glacialis (Peters, 1874) and Boreogadus saida (Lepechin, 1774). Polar Biology 32(6):937-939 doi:10.1007/s00300-009-0616-3
Online_Linkage: https://doi.org/10.1007/s00300-009-0616-3
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2009
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Madsen et al 2009
Source_Contribution: Used to genotypically distinguish between cod species.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Medrano, C.F.
Originator: Aasen, E.
Originator: Sharrow, J.
Publication_Date: 1990
Title: DNA extraction from nucleated red blood cells.
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: BioTechniques
Issue_Identification: 8(1):43
Publication_Information:
Publication_Place: online
Publisher: Future Science, Ltd.
Other_Citation_Details:
Medrano, J.F., Aasen, E., Sharrow, L. 1990. DNA extraction from nucleated red blood cells. BioTechniques 8(1):43
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 1990
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Medrano et al 1990
Source_Contribution: DNA extraction technique.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Miller, K.M.
Originator: Le, K.D.
Originator: Beacham, T.D.
Publication_Date: 2000
Title:
Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua)
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Molecular Ecology
Issue_Identification: 9(2):238-239
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
Miller, K.M., Le, K.D., Beacham, T.D. 2000. Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua). Molecular Ecology 9(2):238-239 doi:10.1046/j.1365-294x.2000.00804-2.x
Online_Linkage: https://doi.org/10.1046/j.1365-294x.2000.00804-2.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2000
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Miller et al 2000
Source_Contribution: Primer sequences Gmo8 and Gmo34
Source_Information:
Source_Citation:
Citation_Information:
Originator: Nelson, R.J.
Originator: Bouchard, C.
Originator: Madsen, M.
Originator: Praebel, K.
Originator: Rondeau, E.
Originator: von Schalburg, K.
Originator: Leong, J.S.
Originator: Jantzen, S.
Originator: Sandwith, Z.
Originator: Puckett, S.
Originator: Messmer, A.
Originator: Fevolden, S-E.
Originator: Koop, B.F.
Publication_Date: 2013
Title:
Microsatellite loci for genetic analysis of the Arctic gadids Boreogadus saida and Arctogadus glacialis
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Conservation Genetics Resources
Issue_Identification: 5(2):445-448
Publication_Information:
Publication_Place: online
Publisher: Springer Nature
Other_Citation_Details:
Nelson, R.J., Bouchard, C., Madsen, M., Praebel, K., Rondeau, E., von Schalburg, K., Leong, J.S., Jantzen, S., Sandwith, Z., Puckett, S., Messmer, A., Fevolden, S-E., Koop, B.F. 2013. Microsatellite loci for genetic analysis of the Arctic gadids Boreogadus saida and Arctogadus glacialis. Conservation Genetics Resources 5(2):445-448 doi:10.1007/s12686-012-9824-1
Online_Linkage: https://doi.org/10.1007/s12686-012-9824-1
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2013
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Nelson et al 2013
Source_Contribution:
Primer sequence Bsa101;
One primer redesigned in this study to produce a shorter fragment: [Bsa14-Forward/Bsa14-1-Reverse (GGAAGTCGACTTTTCATGGAC)];
Both primers redesigned in this study to produce a shorter fragment: [Bsa6: Bsa6-1-Forward (GCACTAAAGCATGATGAAAGC)/Bsa6-1-Reverse (GACACTGCTTTTATACAGC), Bsa7: Bsa7-1-Forward (AGGTTCGGTGTTTACCTGC)/Bsa7-1-Reverse (ACTGAACAGGTGTTCAGGC), Bsa15: Bsa15-1-Forward (ACGCAGTTGGTCCAAAGC)/Bsa15-1-Reverse (ACTCAGAGCTCCTGTTGC), Bsa60: Bsa60-1-Forward (AATTGAGATTCCCTGGGC)/Bsa60-1-Reverse (ATTTCTGACGTTTCTTGC)
Source_Information:
Source_Citation:
Citation_Information:
Originator: O'Reilly, P.T.
Originator: Canino, M.F.
Originator: Bailey, K.M.
Originator: Bentzen, P.
Publication_Date: 2000
Title:
Isolation of twenty low stutter di- and tetranucleotide microsatellites for population analyses of walleye pollock and other gadoids
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Journal of Fish Biology
Issue_Identification: 56(5):1074–1086
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
O'Reilly, P.T., Canino, M.F., Bailey, K.M., Bentzen, P. 2000. Isolation of twenty low stutter di- and tetranucleotide microsatellites for population analyses of walleye pollock and other gadoids. 56(5):1074–1086 doi:10.1111/j.1095-8649.2000.tb02124.x
Online_Linkage: https://doi.org/10.1111/j.1095-8649.2000.tb02124.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2000
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: O'Reilly et al 2000
Source_Contribution: Primer sequences Tch14
Source_Information:
Source_Citation:
Citation_Information:
Originator: Page, L.M.
Originator: Espinosa-Pérez, H.
Originator: Findley, L.T.
Originator: Gilbert, C.R.
Originator: Lea, R.N.
Originator: Mandrak, N.E.
Originator: Mayden, R.L.
Originator: Nelson, J.S.
Publication_Date: 2013
Title:
Common and scientific names of fishes from the United States, Canada, and Mexico, 7th edition
Geospatial_Data_Presentation_Form: book
Series_Information:
Series_Name:
Common and scientific names of fishes from the United States, Canada, and Mexico
Issue_Identification: 7th edition
Publication_Information:
Publication_Place: Bethesda, Maryland
Publisher: American Fisheries Society
Other_Citation_Details:
Page, L.M., Espinosa-Pérez, H., Findley, L.T., Gilbert, C.R., Lea, R.N., Mandrak, N.E., Mayden, R.L., Nelson, J.S. 2013. Common and scientific names of fishes from the United States, Canada, and Mexico, 7th edition. American Fisheries Society, Special Publication 34, Bethesda, Maryland ISBN-13:978-1-934874-31-8
Type_of_Source_Media: book
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2013
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Page et al 2013
Source_Contribution: Used to determine taxonomy.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Skirnisdottir, S.
Originator: Pampoulie, C.
Originator: Hauksdottir, S.
Originator: Schulte, I.
Originator: Olafsson, K.
Originator: Hreggvidsson, G.O.
Originator: Hjorleifdottir, S.
Publication_Date: 2008
Title:
Characterization of 18 new microsatellite loci in Atlantic cod (Gadus morhua L.)
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Molecular Ecology Resources
Issue_Identification: 8(6):1503-1505
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
Skirnisdottir, S., Pampoulie, C., Hauksdottir, S., Schulte, I., Olafsson, K., Hreggvidsson, G.O., Hjorleifdottir, S. 2008. Characterization of 18 new microsatellite loci in Atlantic cod (Gadus morhua L.). Molecular Ecology Resources 8(6):1503-1505 doi:10.1111/j.1755-0998.2008.02327.x
Online_Linkage: https://doi.org/10.1111/j.1755-0998.2008.02327.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2008
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Skirnisdottir et al 2008
Source_Contribution:
Primer sequences PGmo127: PGmo127-1-Forward (CCCTCAAAATTCAACCTGG)/PGmo127-1-Reverse (TCTCCTCCCCTTGTGTGC)
Source_Information:
Source_Citation:
Citation_Information:
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: White, C.M.
Publication_Date: 2004
Title:
Gene flow and genetic characterization of Northern Goshawks breeding in Utah
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: The Condor
Issue_Identification: 106(4):826-836
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Sonsthagen, S.A., Talbot, S.L., White, C.M. 2004. Gene flow and genetic characterization of Northern Goshawks breeding in Utah. Condor 106(4):826-836 doi:10.1650/7448
Online_Linkage: https://doi.org/10.1650/7448
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2004
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Sonsthagen et al 2004
Source_Contribution: Modifications to DNA extraction technique.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Talbot, S.L. (ORCID 0000-0002-3312-7214)
Originator: Palmer, A.G.
Originator: Sage, G.K. (ORCID 0000-0003-1431-2286)
Originator: Sonsthagen, S.A. (ORCID 0000-0001-6215-5874)
Originator: Swem, T.
Originator: Brimm, D.J.
Originator: White, C.M.
Publication_Date: 2011
Title: Lack of genetic polymorphism among peregrine falcons of Fiji
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Journal of Avian Biology
Issue_Identification: 42(5):415-428
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
Talbot, S.L., Palmer, A.G., Sage, G.K., Sonsthagen, S.A., Swem, T., Brimm, D.J., White, C.M. 2011. Lack of genetic polymorphism among peregrine falcons of Fiji. Journal of Avian Biology 42(5):415-428 doi:10.1111/j.1600-048X.2011.05280.x
Online_Linkage: https://doi.org/10.1111/j.1600-048X.2011.05280.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2011
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Talbot et al 2011
Source_Contribution: Modifications to DNA extraction technique.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Van Oosterhout, C.
Originator: Hutchinson, W.F.
Originator: Wills, D.P.M.
Originator: Shipley, P.
Publication_Date: 2004
Title:
MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Molecular Ecology Notes
Issue_Identification: 4(3):535-538
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
Van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M., Shipley, P. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4(3):535-538. doi:10.1111/j.1471-8286.2004.00684.x
Online_Linkage: https://doi.org/10.1111/j.1471-8286.2004.00684.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2004
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Van Oosterhout et al 2004
Source_Contribution:
Used to identify potential scoring errors and null alleles of microsatellites.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Wedemeyer, K.
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Menning, D.M. (ORCID: 0000-0003-3547-3062)
Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Sexson, M.G. (ORCID: 0000-0002-1078-0835)
Originator: Nelson, R.J.
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2019
Title:
Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: ICES Journal of Marine Science
Issue_Identification: 76
Publication_Information:
Publication_Place: online
Publisher: Oxford University Press
Other_Citation_Details:
Wilson, R.E., Sage, G.K., Wedemeyer, K., Sonsthagen, S.A., Menning, D.M., Gravley, M.C., Sexson, M.G., Nelson, R.J., Talbot, S.L. 2019. Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska. ICES Journal of Marine Science 76: doi:10.1093/icesjms/fsz041
Online_Linkage: https://doi.org/10.1093/icesjms/fsz041
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2019
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Wilson et al 2019
Source_Contribution:
Publication supported by these data. Provides methods used for laboratory and data processing.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Menning, D.M. (ORCID: 0000-0003-3547-3062)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2017
Title: Genomics of Arctic Cod
Geospatial_Data_Presentation_Form: document
Series_Information:
Series_Name: OCS Study BOEM
Issue_Identification: 2017-066
Publication_Information:
Publication_Place: online
Publisher: US DOI BOEM Alaska OCS Region
Other_Citation_Details:
Wilson, R.E, Sage G.K., Sonsthagen, S.A., Gravley, M.C., Menning, D.M., Talbot, S.L.. 2017. Genomics of Arctic Cod. Anchorage, AK: US Dept. of the Interior, Bureau of Ocean Energy Management, Alaska OCS Region. OCS Study BOEM 2017-066. 92pp.
To download a PDF file of this report, search for: 2017-066 in the US Department of the Interior, Bureau of Ocean Energy Management, Data and Information Systems website https://www.boem.gov/espis/
Online_Linkage: https://www.boem.gov/
Type_of_Source_Media: document
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2017
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Wilson et al 2017
Source_Contribution:
Report supported by these data. Provides methods used for laboratory and data processing.
Process_Step:
Process_Description:
Genotype numbers for all loci but Tch14 were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. Initial microsatellite allele sizes for Tch14 were determined by scoring based on PCR product size relative to an M13 DNA sequence ladder using Gene Profiler 4.05 (Scanalytics, Inc.). Subsequent gels included these known size individuals from which relative sizes of unknown individuals were assigned using Gene Profiler 4.05 (Scanalytics, Inc.).
Process_Date: Unknown
Process_Step:
Process_Description:
MICRO-CHECKER, v. 2.2.3 (Van Oosterhout et al 2004) was used to identify potential scoring errors and null alleles of microsatellites.
Process_Date: Unknown
Process_Step:
Process_Description:
Cyt-B sequences from opposite strands were reconciled using LI-COR eSeq imaging software with visual proofing and aligned using AlignIR 2.0 or Sequencher 4.1.2 (Gene Codes Corporation, Ann Arbor, MI).
Process_Date: Unknown
Process_Step:
Process_Description:
For individual mitogenome assembly and verification, each sample was recovered from the Mi-Seq run by identifying individual barcodes and adaptor trimming was performed with MiSeq Reporter software (Illumina, San Diego, CA USA). The raw paired-end reads were assembled and mapped to their respective species reference mitogenome in Geneious 8.1.8 (BioMatters Limited, Auckland, New Zealand) using high sensitivity setting and minimum mapping quality set to greater than 99.9% (minimum confidence that read is correctly mapped). Since an Eleginus gracilis reference mitogenome was not publicly available, mitogenomes from four samples were reconstructed with a subset of reads (~7,000) using the bait and iterative mapping approach in the programs MIRA 3.4.1 (Chevreux et al 1999) and MITOBIM v 1.8 (Hahn et al 2013) to serve as a reference.
Process_Date: Unknown
Process_Step:
Process_Description:
To detect the presence of pseudogenes or gene rearrangements in the consensus mitogenomes, each mitogenome was annotated using MITOannotator: http://mitofish.aori.u-tokyo.ac.jp/ Iwasaki et al 2013. New Sanger sequences from an 818 bp fragment of cytb for 16 Boreogadus saida samples and sequences previously published and publicly available in GenBank for Walleye Pollock and Saffron cod, were used to verify we did not have a nuclear pseudogene in the consensus mitogenomes.
Process_Date: Unknown
Process_Step:
Process_Description:
Strict mitogenome consensus sequence for each sample was constructed and aligned using Muscle (Edgar 2004) within Geneious 8.1.8 (BioMatters Limited, Auckland, New Zealand) using default settings with the final alignment visually inspected.
Process_Date: Unknown
Process_Step:
Process_Description:
Transcriptome sequencing of the 12 libraries yielded 13,880,362 150-bp paired end reads with an average of 1.16 (± 0.43) million for each library. Prior to de novo assembly, adaptor trimming and reads with low quality Phred scores were filtered using MiSeq Reporter software (Illumina, San Diego, CA USA). We pooled all reads before using the de novo assembler in CLC Genomics Workbench v.9.5.1 (CLC Bio, Aarhus Denmark) using default settings in order to recover as complete a transcriptome as possible. A total of 64,457 contigs were obtained with an average length of 295 bp (range: 59 – 5,024 bp) and 47.7% GC content.
Process_Date: Unknown
Process_Step:
Process_Description:
Transcripts were annotated using BLAST-X (NCBI) and InterProScan (Jones et al 2014), implemented in Blast2Go (Conesa et al 2005). A BLAST-X homology search, using 1e-3 E-value cutoff against the NCBI non-redundant (nr) protein database for bony fish (taxa ID: 7898), resulted in a total of 23,714 transcript annotations of which 14,912 were mapped to existing gene categories in Blast2Go (Supplemental Material). The InterProScan analysis was merged with the mapped gene ontologies resulting in 15,474 annotated contigs (SRA accession: SRP116959: see https://www.ncbi.nlm.nih.gov/sra/?term=SRP116959
Process_Date: Unknown
Process_Step:
Process_Description:
Post-data collection processing steps of RAD-Seq portions of the dataset followed DaCosta and Sorenson 2014 using the computational pipeline found at https://github.com/BU-RAD-seq/ddRAD-seq-Pipeline. Pre-processing of reads was done using a custom python script (developed by Jeff DaCosta, Boston College University) that removed chimera sequences (SbfI-SbfI or MspI-MspI) or reads containing 2 or more mismatches in SbfI recognition site and trimmed reads to either MspI concatemer or P2 adapter. Reads per sample then were collapsed into identical clusters using the CondenseSequences.py script with low-quality reads (i.e. sequences that failed to cluster with any other reads (identity threshold setting of 0.90) and an average per-base Phred score less than 20) filtered out with the FilterSequences.py script and the UCLUST function in USEARCH v.5 (Edgar 2010). Condensed and filtered reads from all samples were then concatenated and clustered with an identity threshold setting of 0.85 in UCLUST. MUSCLE v.3 (Edgar 2004) was used to align and cluster reads, and samples within each aligned cluster were genotyped using the RADGenotypes.py script. Homozygotes and heterozygotes were identified based on thresholds outlined in DaCosta and Sorenson 2014, with individual genotypes falling into three categories: 'missing' (no data), 'good' (unambiguously genotyped) and 'flagged' (recovered heterozygous genotype, but with haplotype counts outside of acceptable thresholds or with >2 alleles detected). We retained polymorphic loci with a median depth of 10, less than 10% missing genotypes, and less than 10% flagged genotypes were retained for downstream analyses based on the Polar cod sample size. Loci flagged for manual editing were skipped for preliminary analysis but will be included in the final dataset.
Process_Date: Unknown
Spatial_Data_Organization_Information:
Indirect_Spatial_Reference:
General sampling locations have been described by corresponding entries in the USGS Geographic Names Information System (GNIS) when possible.
Direct_Spatial_Reference_Method: Point
Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Geographic:
Latitude_Resolution: 0.0001
Longitude_Resolution: 0.0001
Geographic_Coordinate_Units: Decimal degrees
Geodetic_Model:
Horizontal_Datum_Name: World Geodetic System of 1984
Ellipsoid_Name: World Geodetic System of 1984
Semi-major_Axis: 6378137
Denominator_of_Flattening_Ratio: 298.257223563
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label:
cod_samplingNcbiAccessionsMicrosat_arcticNAmerica_wilson_2006_2015
Entity_Type_Definition:
Sampling information, mtDNA and microsatellite results. Presented in a Comma Separated Value (CSV) formatted table.
Entity_Type_Definition_Source: Author defined
Attribute:
Attribute_Label: Sample_ID
Attribute_Definition:
This is a U.S. Geological Survey, Alaska Science Center, Molecular Ecology Laboratory alphanumeric label that uniquely identifies each sample.
Attribute_Definition_Source: Field assigned
Attribute_Domain_Values:
Unrepresentable_Domain:
Unique Identifier. This is an alphanumeric combination representing a single individual in this dataset. Two to four leading letters are species indicators assigned by collectors (BOSA [Boreogadus saida], SL [Boreogadus saida], SACD [Eleginus gracilis], ALPO [Gadus chalcogrammus], PC [Arctogadus glacialis]). Careful attention should be given regarding species labels indicated within this attribute and special notations and discrepancies in the "Species" attribute based on genetic data. Nineteen BOSA and 33 ALPO samples include "UW" followed by the 6 digit University of Washington (UW) Burke Museum catalog number and a portion of these with "underscore number" indicating an individual of a multi-individual catalog entry. Hyphenated numbers indicate sampling year followed by 2-5 digit unique identifiers. All other samples are identified with species codes followed by 3-8 digit unique identifiers. The presence of "RNA" in Sample_ID indicates sample was one of 6 used in the transcriptome portion of the study.
Attribute:
Attribute_Label: Species
Attribute_Definition:
This indicates the species of a sample based upon information provided with the sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Boreogadus saida
Enumerated_Domain_Value_Definition: This indicates the sample is presumed to be Boreogadus saida.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Arctogadus glacialis
Enumerated_Domain_Value_Definition:
This indicates the sample is presumed to be Arctogadus glacialis.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Eleginus gracilis
Enumerated_Domain_Value_Definition: This indicates the sample is presumed to be Eleginus gracilis.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Gadus chalcogrammus
Enumerated_Domain_Value_Definition:
This indicates the sample is presumed to be Gadus chalcogrammus.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Arctogadus glacialis x Boreogadus saida
Enumerated_Domain_Value_Definition:
This sample was provided to the lab labelled as "Arctogadus glacialis," had a Polar cod-like mitogenome with an Arctic cod-like nuclear genome, suggesting this individual is of a hybrid origin.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: rev. Arctogadus glacialis
Enumerated_Domain_Value_Definition:
This indicates the sample was provided to the lab labelled as "Boreogadus saida," but genetic results at locus "Gmo8" and "Bsa14-1" indicate the sample is likely "Arctogadus glacialis" though species identification cannot be verified using these markers. In absence of additional mtDNA or sequence data it is not possible to say authoritatively whether these are not Boreogadus saida or some hybrid thereof. These samples were eliminated from further analyses.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: rev. Boreogadus saida
Enumerated_Domain_Value_Definition:
This indicates the sample was provided to the lab labelled as "Arctogadus glacialis," but genetic results exhibit closer affinity to Boreogadus saida. In absence of additional mtDNA or sequence data it is not possible to say authoritatively whether these are not Arctogadus glacialis or some hybrid thereof.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Collection_Day
Attribute_Definition:
This indicates the day (month/day/year) the DNA source was sampled from the field. Blank cells indicate information is not available or date is only known to the year of sampling (see Collection_Year).
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 6/23/2006
Range_Domain_Maximum: 8/17/2013
Attribute_Units_of_Measure: date (MM/DD/YYYY)
Attribute:
Attribute_Label: Collection_Year
Attribute_Definition:
This indicates the year the DNA source was sampled from the field. Blank cells indicate information is not available.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 2006
Range_Domain_Maximum: 2015
Attribute_Units_of_Measure: date (YYYY)
Attribute:
Attribute_Label: Latitude
Attribute_Definition:
This indicates the latitude at which the DNA source was sampled from the field. Blank cells indicate information is not available.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 51.8609
Range_Domain_Maximum: 71.9526
Attribute_Units_of_Measure: Decimal degrees (WGS 84)
Attribute:
Attribute_Label: Longitude
Attribute_Definition:
This indicates the longitude at which the DNA source was sampled from the field. Blank cells indicate information is not available.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: -174.7540
Range_Domain_Maximum: 177.4162
Attribute_Units_of_Measure: Decimal degrees (WGS 84)
Attribute:
Attribute_Label: Station
Attribute_Definition:
For all sampling years but 2015, this indicates the sampling location designated as part of on-going Bureau of Ocean Energy Management (BOEM) Environmental Studies Program. Final station names, sampling dates, and latitudes and longitudes were provided by personal communication, Kate Wedemeyer, BOEM, November 23, 2016. For 2015 station data, values reflect a sequential trawling transect number followed by approximate depth in meters of the trawl. Location information for 2015 samples were provided by V. von Biela, U.S. Geological Survey, Alaska Science Center, personal communication. Blank cells indicate information is not available.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
Unique Identifier. These alphanumeric designations each represent a sampling location. All but 2015, have been used in a multi-year Bureau of Ocean Energy Management (BOEM) Environmental Studies Program, and have been included to facilitate integration of data with other studies using the same station names, if desired.
Attribute:
Attribute_Label: State/Territory/Province
Attribute_Definition:
This indicates the state, territory or province of the sampling location. Blank cells indicate information is not available.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Alaska
Enumerated_Domain_Value_Definition:
This indicates a location in the State of Alaska, United States of America.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Nova Scotia
Enumerated_Domain_Value_Definition:
This indicates a location in the province of Nova Scotia, Canada.
Enumerated_Domain_Value_Definition_Source: NGA GEOnet Names Server (GNS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Yukon Territory
Enumerated_Domain_Value_Definition:
This indicates a location in the territory of Yukon Territory, Canada.
Enumerated_Domain_Value_Definition_Source: NGA GEOnet Names Server (GNS)
Attribute:
Attribute_Label: Country
Attribute_Definition: This indicates the country of the sampling location.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: United States
Enumerated_Domain_Value_Definition: This refers to the country of the United States of America.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Canada
Enumerated_Domain_Value_Definition: This refers to the country of Canada.
Enumerated_Domain_Value_Definition_Source: NGA GEOnet Names Server (GNS)
Attribute:
Attribute_Label: Waterbody
Attribute_Definition:
This is the geographic label for the waterbody from which the sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Beaufort Sea
Enumerated_Domain_Value_Definition: This refers to the Beaufort Sea.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Chukchi Sea
Enumerated_Domain_Value_Definition: This refers to the Chukchi Sea.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Norton Sound
Enumerated_Domain_Value_Definition: This refers to the Norton Sound.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Gulf of Alaska
Enumerated_Domain_Value_Definition: This refers to the Gulf of Alaska.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Bering Sea
Enumerated_Domain_Value_Definition: This refers to the Bering Sea.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Aleutian Islands
Enumerated_Domain_Value_Definition: This refers to the waters surrounding the Aleutian Islands.
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Gulf of St. Lawrence
Enumerated_Domain_Value_Definition:
This refers to the Gulf of St. Lawrence off the coast of Nova Scotia, Canada.
Enumerated_Domain_Value_Definition_Source: NGA GEOnet Names Server (GNS)
Attribute:
Attribute_Label: Locality_Code
Attribute_Definition:
This is a 2-5 letter abbreviation indicating the geographic locale of a sample. Blank cells indicate samples were not assigned a locality.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: BSC
Enumerated_Domain_Value_Definition: Samples collected in the central Beaufort Sea.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: BSCam
Enumerated_Domain_Value_Definition: Samples collected in Camden Bay.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: BSS
Enumerated_Domain_Value_Definition: Samples collected in the Beaufort Sea southern shelf.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: BSU
Enumerated_Domain_Value_Definition:
Samples lacking lat/longs, but known to be collected in the Beaufort Sea unassigned to a more specific sub-region.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: BSW
Enumerated_Domain_Value_Definition: Samples collected in the western Beaufort Sea.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: CSE
Enumerated_Domain_Value_Definition:
Samples collected in the eastern Chukchi Sea (approx.72°N 164°W).
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: CSS
Enumerated_Domain_Value_Definition:
Samples collected in the southern Chukchi Sea (approx. 67°N 169°W).
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: CSU
Enumerated_Domain_Value_Definition:
Samples lacking lat/longs, but known to be collected in the Chukchi Sea unassigned to a more specific sub-region.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: SL
Enumerated_Domain_Value_Definition: Samples collected in the Gulf of St. Lawrence.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: BioProject_Accession
Attribute_Definition:
This is the NCBI Transcriptome BioProject Accession Number. This number may be used to retrieve detailed sample and experiment information from https://www.ncbi.nlm.nih.gov/
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
This is an alphanumeric accession number searchable from https://www.ncbi.nlm.nih.gov/
Attribute:
Attribute_Label: Mitogenome_Accession
Attribute_Definition:
GenBank accession number associated with sequence obtained from the complete mtDNA. Sequences available online at https://www.ncbi.nlm.nih.gov/GenBank/
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
GenBank accession numbers are assigned by GenBank and may be used to review complete sequences at https://www.ncbi.nlm.nih.gov/GenBank/
Attribute:
Attribute_Label: Partial_CytB_Accession
Attribute_Definition:
GenBank accession number associated with sequence obtained from a 707 base pair portion of the mtDNA Cytochrome B. Complete sequences available online at https://www.ncbi.nlm.nih.gov/GenBank/
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
These GenBank accession numbers (MG100209-MG100615) are assigned by GenBank and may be used to review complete sequences at https://www.ncbi.nlm.nih.gov/GenBank/
Attribute:
Attribute_Label: mtDNA_CytB_Haplotype
Attribute_Definition:
mtDNA CytB haplotype assigned based on 64 variable sites across 707 base pairs sequenced for each individual as referenced in Wilson et al 2017. Individual sequences have been submitted to GenBank.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 82
Attribute_Units_of_Measure: GenBank Accession Number
Attribute:
Attribute_Label: Bsa6_1_Allele_1
Attribute_Definition:
Microsatellite allele one from the Bsa6-1 locus. Both primers were redesigned in this study to produce a shorter fragment (ca. 61 base pairs less) than those reported in Nelson et al 2013: Bsa6-1-Forward (GCACTAAAGCATGATGAAAGC)/Bsa6-1-Reverse (GACACTGCTTTTATACAGC). Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 170
Range_Domain_Maximum: 210
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa6_1_Allele_2
Attribute_Definition:
Microsatellite allele two from the Bsa6-1 locus. Both primers were redesigned in this study to produce a shorter (ca. 61 base pairs less) fragment than those reported in Nelson et al 2013: Bsa6-1-Forward (GCACTAAAGCATGATGAAAGC)/Bsa6-1-Reverse (GACACTGCTTTTATACAGC). Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 190
Range_Domain_Maximum: 220
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa7_1_Allele_1
Attribute_Definition:
Microsatellite allele one from the Bsa7-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 86 base pairs less) than those reported in Nelson et al 2013: Bsa7-1-Forward (AGGTTCGGTGTTTACCTGC)/Bsa7-1-Reverse (ACTGAACAGGTGTTCAGGC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 174
Range_Domain_Maximum: 192
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa7_1_Allele_2
Attribute_Definition:
Microsatellite allele two from the Bsa7-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 86 base pairs less) than those reported in Nelson et al 2013: Bsa7-1-Forward (AGGTTCGGTGTTTACCTGC)/Bsa7-1-Reverse (ACTGAACAGGTGTTCAGGC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 186
Range_Domain_Maximum: 198
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa14_1_Allele_1
Attribute_Definition:
Microsatellite allele one of the Bsa14-1 locus. One primer was redesigned in this study to produce a shorter fragment (ca. 41 base pairs less) than those reported in Nelson et al 2013: Bsa14-Forward (as published)/Bsa14-1-Reverse (GGAAGTCGACTTTTCATGGAC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. Seven samples eliminated from further analyses due to results inconsistent with Arctic Cod (Boreogadus saida) at locus Gmo8 and Bsa14-1 (BOSA 14-16797, BOSA 14-16514, BOSA 14-16724, BOSA 14-16725, BOSA 14-16850, BOSA 14-16973, and BOSA 13-16340), have estimated allele sizes for locus Bsa14-1. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 180
Range_Domain_Maximum: 222
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa14_1_Allele_2
Attribute_Definition:
Microsatellite allele two from the Bsa14-1 locus. One primer was redesigned in this study to produce a shorter fragment (ca. 41 base pairs less) than those reported in Nelson et al 2013: Bsa14-Forward (as published)/Bsa14-1-Reverse (GGAAGTCGACTTTTCATGGAC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. Seven samples eliminated from further analyses due to results inconsistent with Arctic Cod (Boreogadus saida) at locus Gmo8 and Bsa14-1 (BOSA 14-16797, BOSA 14-16514, BOSA 14-16724, BOSA 14-16725, BOSA 14-16850, BOSA 14-16973, and BOSA 13-16340), have estimated allele sizes for locus Bsa14-1. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 185
Range_Domain_Maximum: 227
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa15_1_Allele_1
Attribute_Definition:
Microsatellite allele one of the Bsa15-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 91 base pairs less) than those reported in Nelson et al 2013: Bsa15-1-Forward (ACGCAGTTGGTCCAAAGC)/Bsa15-1-Reverse (ACTCAGAGCTCCTGTTGC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 179
Range_Domain_Maximum: 199
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa15_1_Allele_2
Attribute_Definition:
Microsatellite allele two from the Bsa15-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 91 base pairs less) than those reported in Nelson et al 2013: Bsa15-1-Forward (ACGCAGTTGGTCCAAAGC)/Bsa15-1-Reverse (ACTCAGAGCTCCTGTTGC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 195
Range_Domain_Maximum: 207
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa60_1_Allele_1
Attribute_Definition:
Microsatellite allele one of the Bsa60-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 61 base pairs less) than those reported in Nelson et al (2013): Bsa60-1-Forward (AATTGAGATTCCCTGGGC)/Bsa60-1-Reverse (ATTTCTGACGTTTCTTGC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 165
Range_Domain_Maximum: 217
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa60_1_Allele_2
Attribute_Definition:
Microsatellite allele two from the Bsa60-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 61 base pairs less) than those reported in Nelson et al 2013: Bsa60-1-Forward (AATTGAGATTCCCTGGGC)/Bsa60-1-Reverse (ATTTCTGACGTTTCTTGC)]. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 173
Range_Domain_Maximum: 229
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa101_Allele_1
Attribute_Definition:
Microsatellite allele one of the Bsa101 Nelson et al 2013 locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 128
Range_Domain_Maximum: 154
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Bsa101_Allele_2
Attribute_Definition:
Microsatellite allele two of the Bsa101 Nelson et al 2013 locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 128
Range_Domain_Maximum: 158
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Gmo8_Allele_1
Attribute_Definition:
Microsatellite allele one of the Gmo8 (Miller et al 2000) locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. Seven samples eliminated from further analyses due to results inconsistent with Arctic Cod (Boreogadus saida) at locus Gmo8 and Bsa14-1 (BOSA 14-16797, BOSA 14-16514, BOSA 14-16724, BOSA 14-16725, BOSA 14-16850, BOSA 14-16973, and BOSA 13-16340), have estimated allele sizes for locus Gmo_8. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 115
Range_Domain_Maximum: 231
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ns
Enumerated_Domain_Value_Definition:
Samples with value of ns indicates sample "not sized" for this locus due to results outside the normal range of Arctic cod in this study and eliminated from further analyses.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Gmo8_Allele_2
Attribute_Definition:
Microsatellite allele two of the Gmo8 (Miller et al 2000) locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. Seven samples eliminated from further analyses due to results inconsistent with Arctic Cod (Boreogadus saida) at locus Gmo8 and Bsa14-1 (BOSA 14-16797, BOSA 14-16514, BOSA 14-16724, BOSA 14-16725, BOSA 14-16850, BOSA 14-16973, and BOSA 13-16340), have estimated allele sizes for locus Gmo_8. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 117
Range_Domain_Maximum: 247
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ns
Enumerated_Domain_Value_Definition:
Samples with value of ns indicates sample "not sized" for this locus due to results outside the normal range of Arctic cod in this study and eliminated from further analyses.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Gmo34_Allele_1
Attribute_Definition:
Microsatellite allele one of the Gmo34 (Miller et al 2000) locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 63
Range_Domain_Maximum: 95
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Gmo34_Allele_2
Attribute_Definition:
Microsatellite allele two of the Gmo34 (Miller et al 2000) locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 71
Range_Domain_Maximum: 99
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: PGmo32_Allele_1
Attribute_Definition:
Microsatellite allele one of the PGmo32 (Jakobsdóttir et al 2006) locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 103
Range_Domain_Maximum: 108
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: PGmo32_Allele_2
Attribute_Definition:
Microsatellite allele two of the PGmo32 (Jakobsdóttir et al 2006) locus. Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 103
Range_Domain_Maximum: 115
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: Pgmo127_1_Allele_1
Attribute_Definition:
Microsatellite allele one of the PGmo127-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 140 base pairs less) than those reported in Skirnisdottir et al 2008: PGmo127-1-Forward (CCCTCAAAATTCAACCTGG)/PGmo127-1-Reverse (TCTCCTCCCCTTGTGTGC). Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 276
Range_Domain_Maximum: 296
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Pgmo127_1_Allele_2
Attribute_Definition:
Microsatellite allele one of the PGmo127-1 locus. Both primers redesigned in this study to produce a shorter fragment (ca. 140 base pairs less) than those reported in Skirnisdottir et al 2008: PGmo127-1-Forward (CCCTCAAAATTCAACCTGG)/PGmo127-1-Reverse (TCTCCTCCCCTTGTGTGC). Genotype numbers were determined by scoring based on allele size relative to DNA reference samples provided by Dr. R. John Nelson, Seastar Biotech, Victoria, British Columbia, Canada for inter-laboratory calibration. Samples associated with the current study were established as size standards from the initial inter-laboratory calibration and were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 284
Range_Domain_Maximum: 316
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Tch14_Allele_1
Attribute_Definition:
Microsatellite allele one of the Tch14 (O'Reilly et al 2000) locus. Genotype numbers were determined by scoring based on allele size relative to an M13 DNA sequence ladder and to samples established as size standards that were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 112
Range_Domain_Maximum: 216
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Tch14_Allele_2
Attribute_Definition:
Microsatellite allele two of the Tch14 (O'Reilly et al 2000) locus. Genotype numbers were determined by scoring based on allele size relative to an M13 DNA sequence ladder and to samples established as size standards that were run on each gel. A blank cell indicates data were not collected at this locus for that sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 140
Range_Domain_Maximum: 244
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: np
Enumerated_Domain_Value_Definition:
Samples with value of np indicates sample did not have product to assign allele size.
Enumerated_Domain_Value_Definition_Source: Author defined
Detailed_Description:
Entity_Type:
Entity_Type_Label: cod_mitogenomePrimers_arcticNAmerica_wilson_2006_2015
Entity_Type_Definition:
Mitogenomes for this dataset were compiled from overlapping sequences of 7 different long range PCR products. Primers are described herein. Presented in a Comma Separated Value (CSV) formatted table.
Entity_Type_Definition_Source: Author defined
Attribute:
Attribute_Label: Primer_Name
Attribute_Definition: Name assigned to primer.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
Unique Identifier. Alphanumeric label with first four letters taken from the first two letters each of the genus and species (Boreogadus saida) upon which the primer was designed, followed by a number and either an "H" or "L" indicating the base position on either the "heavy" or "light" strand of mtDNA.
Attribute:
Attribute_Label: Direction
Attribute_Definition:
This is the directional designation of the given primer sequence.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Forward
Enumerated_Domain_Value_Definition:
Primers listed as "Forward" anneal to the template strand in the same direction as listed (5' to 3').
Enumerated_Domain_Value_Definition_Source: Author defined.
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Reverse
Enumerated_Domain_Value_Definition:
Primers listed as "Reverse" anneal to the template strand as a 3' to 5' reverse complement of the sequence listed 5' to 3'.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Primer_Sequence
Attribute_Definition: Primer sequence is given in the 5' to 3' direction.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
DNA sequence of primers for polymerase chain reaction (PCR) amplification and sequencing of complete mitogenomes designed by aligning mitogenomes available in GenBank https://www.ncbi.nlm.nih.gov/GenBank/ of Boreogadus saida (AM919428), Arctogadus glacialis (AM919429), Gadus ogac (DQ356941), Gadus chalcogrammus (AB182307) and Gadus morhua (NC002081).
Attribute:
Attribute_Label: Location
Attribute_Definition:
Location indicates the mitochondrial gene within which the primer sequence is located.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: 12S RNA
Enumerated_Domain_Value_Definition:
12S RNA is an abbreviation of the mictochondrially encoded 12S RNA gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: tRNA-Gln
Enumerated_Domain_Value_Definition:
tRNA-Gln is an abbreviation of the mitochondrially encoded glutaminyl-tRNA(Gln) gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ND1
Enumerated_Domain_Value_Definition:
ND1 is an abbreviation of the mitochondrially encoded NADH dehydrogenase, subunit 1 gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: tRNA-Trp
Enumerated_Domain_Value_Definition:
tRNA-Trp is an abbreviation of the mitochondrially encoded tryptophan-tRNA gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: tRNA-Cys
Enumerated_Domain_Value_Definition:
tRNA-Cys is an abbreviation of the mitochondrially encoded cysteinyl-tRNA gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: COI
Enumerated_Domain_Value_Definition:
COI is an abbreviation of the mitochondrially encoded cytochrome oxidase subunit I gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: COII
Enumerated_Domain_Value_Definition:
COII is an abbreviation of the mitochondrially encoded cytochrome oxidase subunit II gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ATPase6
Enumerated_Domain_Value_Definition:
ATPase6 is an abbreviation of the mitochondrially encoded subunit 6 of mictochondrial ATP synthase gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ND4L
Enumerated_Domain_Value_Definition:
ND4L is an abbreviation of the mitochondrially encoded NADH dehydrogenase subunit 4L gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ND4
Enumerated_Domain_Value_Definition:
ND4 is an abbreviation of the mitochondrially encoded NADH Dehydrogenase, Subunit 4 (Complex I) gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ND5
Enumerated_Domain_Value_Definition:
ND5 is an abbreviation of the mitochondrially encoded NADH dehydrogenase subunit 5 gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: tRNA-Glu
Enumerated_Domain_Value_Definition:
tRNA-Glu is an abbreviation of the mitochondrially encoded transfer RNA glutamic acid gene.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Alignment_Location
Attribute_Definition:
Base pair location of primers relative to the alignment of Gadid mitogenomes using Boreogadus saida as the reference.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
DNA sequence of primers for polymerase chain reaction (PCR) amplification and sequencing of complete mitogenomes were designed by locating conserved sequences in aligned mitogenomes. Available in GenBank; https://www.ncbi.nlm.nih.gov/GenBank/ Boreogadus saida (AM919428), Arctogadus glacialis (AM919429), Gadus ogac (DQ356941), Gadus chalcogrammus (AB182307) and Gadus morhua (NC002081) using Boreogadus saida as the reference.
Detailed_Description:
Entity_Type:
Entity_Type_Label: cod_geneOntology_arcticNAmerica_wilson_2006_2015
Entity_Type_Definition:
Gene ontology results of transcriptome sequencing. Presented in a Comma Separated Value (CSV) formatted table.
Entity_Type_Definition_Source: Author defined
Attribute:
Attribute_Label: Contig_Number
Attribute_Definition:
Number assigned by assembly software to contiguous sequence joined when multiple sequences overlap each other to infer a combined sequence longer than either individual sequence by itself.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 64454
Attribute_Units_of_Measure: Contig Sequence
Attribute:
Attribute_Label: GO_Terms
Attribute_Definition: Gene ontology terms returned by InterProScan (Jones et al 2014)
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Codeset_Domain:
Codeset_Name: InterProScan
Codeset_Source: Jones et al 2014
Detailed_Description:
Entity_Type:
Entity_Type_Label: cod_transcriptomeBlastResults_arcticNAmerica_wilson_2013
Entity_Type_Definition:
Top gene hits of each contig from transcriptome sequencing. Presented in a Comma Separated Value (CSV) formatted table.
Entity_Type_Definition_Source: Author defined
Attribute:
Attribute_Label: Contig_Number
Attribute_Definition:
Number assigned by assembly software to contiguous sequence joined when multiple sequences overlap each other to infer a combined sequence longer than either individual sequence by itself.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 64454
Attribute_Units_of_Measure: Contig Sequence
Attribute:
Attribute_Label: BlastX_Top_Hit
Attribute_Definition:
NCBI's Blast search using a filter of bony fish (Taxa: 7898) already within NCBI and sequences generated as a part of this study https://www.ncbi.nlm.nih.gov/sra/?term=SRP116959 returns a protein most likely coded for by the sequence.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
BLASTX Top-Hit gene description (filter bony fish Taxa: 7898) by contig sequence (from this study) number.
Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, Alaska Science Center
Contact_Address:
Address_Type: Mailing and Physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99508
Country: USA
Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov
Resource_Description:
The USGS Alaska Science Center is the authoritative source and distributor of these data.
Distribution_Liability:
Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data for other purposes or on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: CSV
Format_Information_Content:
Data are distributed in a Zip package containing data in CSV format and FGDC metadata in XML and HTML formats.
File_Decompression_Technique:
Compression applied by the 7-Zip utility using default compression (5). The Zip package can be decompressed and unpacked by open source or commercially available unzip tools.
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: https://doi.org/10.5066/F7CF9P23
Fees: None
Metadata_Reference_Information:
Metadata_Date: 20201125
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, Alaska Science Center
Contact_Address:
Address_Type: Mailing and Physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99508
Country: USA
Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov
Metadata_Standard_Name:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001.1-1999
Generated by mp version 2.9.50 on Thu Jul 2 17:02:53 2020