Enteroctopus Sampling Effects on Genetic Data, Prince William Sound, Alaska, 2012-2015

Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 201711
Title:
Enteroctopus Sampling Effects on Genetic Data, Prince William Sound, Alaska, 2012-2015
Geospatial_Data_Presentation_Form: spreadsheet
Publication_Information:
Publication_Place: Anchorage, AK
Publisher: U.S. Geological Survey, Alaska Science Center
Other_Citation_Details:
Talbot, S. L., 2017, Enteroctopus Sampling Effects on Genetic Data, Prince William Sound, Alaska, 2012-2015: U.S. Geological Survey data release, https://doi.org/10.5066/F7VM49HJ.
Online_Linkage: https://doi.org/10.5066/F7VM49HJ
Larger_Work_Citation:
Citation_Information:
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2000
Title:
Developing and Applying Molecular Tools to Natural Resource Problems in Alaska
Geospatial_Data_Presentation_Form: web site
Publication_Information:
Publication_Place: Anchorage, AK
Publisher: U.S. Geological Survey, Alaska Science Center
Online_Linkage: https://alaska.usgs.gov/portal/project.php?project_id=378
Description:
Abstract:
These are genetic data collected from replicated samples of 21 Enteroctopus (E. dofleini or a cryptic lineage) in Prince William Sound Alaska to evaluate tissue type, DNA extraction method, and time until analyses are completed on data reliability. Data collected from all samples include two microsatellites identified as possible lineage indicators, and nine microsatellite loci previously identified as polymorphic in both lineages. DNA sequence data from 528 bp of the octopine dehydrogenase (OCDE) gene were also collected.
Purpose:
Sample source (e.g. blood vs. tissue), storage buffers/techniques, and extraction methods for DNA samples in various species all have been shown to affect DNA quality and quantity. This study of Enteroctopus was undertaken to assess the practicality and reliability of non-invasive sampling techniques (epitehlial swabs) and the use of two microsatellite DNA markers as a lineage indicator to facilitate release of non-target lineages not identifiable by morphology alone.
Supplemental_Information:
Voucher specimens associated with this study and held at the California Academy of Science Invertebrate Zoology Collection include one Giant Pacific Octopus (CAS-IZ 190942) and 4 specimens of the "cryptic" lineage (CAS-IZ 190941, 192393, 193483, 193484).
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2012
Ending_Date: 2015
Currentness_Reference: observed
Status:
Progress: Complete
Maintenance_and_Update_Frequency: Unknown
Spatial_Domain:
Description_of_Geographic_Extent: Prince William Sound, Alaska, USA
Bounding_Coordinates:
West_Bounding_Coordinate: -148.6529421
East_Bounding_Coordinate: -145.8567922
North_Bounding_Coordinate: 61.2601045
South_Bounding_Coordinate: 59.9762196
Keywords:
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC145
Theme:
Theme_Keyword_Thesaurus: NASA GCMD Earth Science Keywords Thesaurus
Theme_Keyword: Biological Classification
Theme_Keyword: Animals/Invertebrates
Theme_Keyword: Mollusks
Theme_Keyword: Cephalopods
Theme:
Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Genetic Diversity
Theme_Keyword: Biodiversity
Theme_Keyword: Species Diversity
Theme_Keyword: Species Composition
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: Alaska
Theme_Keyword: Amino Acid Oxidoreductases
Theme_Keyword: Animals
Theme_Keyword: Cephalopoda
Theme_Keyword: DNA
Theme_Keyword: Genetic Markers
Theme_Keyword: Microsatellite Repeats
Theme_Keyword: Reproducibility of Results
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: Electrophoresis
Theme_Keyword: Biodiversity
Theme_Keyword: Systematics and taxonomy
Place:
Place_Keyword_Thesaurus: USGS Geographic Names Information System
Place_Keyword: Prince William Sound
Place_Keyword: Bald Head Chris Island
Place_Keyword: Port Wells
Place_Keyword: Long Bay
Place_Keyword: Chenega
Place_Keyword: Herring Bay
Place_Keyword: Prince of Wales Passage
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: Golden Bay, Port Wells
Place_Keyword: Western Prince William Sound
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: animals
Taxonomic_Keywords: collection
Taxonomic_Keywords: multiple species
Taxonomic_Keywords: single species
Taxonomic_Keywords: invertebrates
Taxonomic_Keywords: Enteroctopus
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
Series_Information:
Series_Name: Integrated Taxonomic Classification System
Issue_Identification: Taxonomic Serial No.: 557227
Publication_Information:
Publication_Place: on line
Publisher: ITIS-North America
Other_Citation_Details:
Retrieved June 14, 2017, from the Integrated Taxonomic Information System on-line database http://www.itis.gov. Taxonomic Serial Number: 557227.
Online_Linkage:
Classification_System_Modifications:
A "cryptic lineage" was added at the species level partially for which these data were collected. Differing morphology and supporting genetic data calls into question the taxonomic classification of these individuals.
Taxonomic_Procedures:
These data were collected to evaluate correlations of morphotypes and genetic haplotype with published morphotypes and haplotypes of Giant Pacific Octopus (GPO; Enteroctopus dofleini). Novel morphotypes and haplotypes preclude assignment of these "cryptic lineage" samples to currently recognized Enteroctopus dofleini. Voucher specimens of both E. dofleini and E. "cryptic" sp. have been deposited with the California Academy of Science Invertebrate Zoology (CASIZ) as noted in Hollenbeck et al. 2017.
Vouchers:
Specimen: individuals
Repository:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: California Academy of Science Invertebrate Zoology Collection
Contact_Address:
Address_Type: mailing
Address: Golden Gate Park
Address: 55 Music Concourse Drive
City: San Francisco
State_or_Province: CA
Postal_Code: 94118
Country: USA
Contact_Voice_Telephone: +1-415-379-5284
Contact_Electronic_Mail_Address: izg@calacademy.org
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Applicable_Common_Name: Animal
Applicable_Common_Name: animaux
Applicable_Common_Name: animals
Taxonomic_Classification:
Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:
Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Protostomia
Taxonomic_Classification:
Taxon_Rank_Name: Superphylum
Taxon_Rank_Value: Lophozoa
Taxonomic_Classification:
Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Mollusca
Applicable_Common_Name: mollusques
Applicable_Common_Name: molusco
Applicable_Common_Name: molluscs
Applicable_Common_Name: mollusks
Taxonomic_Classification:
Taxon_Rank_Name: Class
Taxon_Rank_Value: Cephalopoda
Applicable_Common_Name: octopuses
Applicable_Common_Name: squids
Applicable_Common_Name: calmars
Applicable_Common_Name: encornets
Applicable_Common_Name: pieuvres
Applicable_Common_Name: poulpes
Applicable_Common_Name: nautilo
Applicable_Common_Name: polvo
Applicable_Common_Name: cefalopode
Applicable_Common_Name: lula
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Coleoidea
Taxonomic_Classification:
Taxon_Rank_Name: Superorder
Taxon_Rank_Value: Octobrachia
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Octopoda
Taxonomic_Classification:
Taxon_Rank_Name: Suborder
Taxon_Rank_Value: Incirrina
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Octopodidae
Taxonomic_Classification:
Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Octopodinae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Enteroctopus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: dofleini
Applicable_Common_Name: Giant Pacific Octopus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: "cryptic lineage"
Access_Constraints: None
Use_Constraints:
If you use these data in a publication, presentation, or other product please use the citation below to credit the authors for their contribution to your work: Hollenbeck, N. et al. 2017. Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus. Am. Malacol. Bull.
Microsatellite data from this dataset cannot be combined with data generated outside the Alaska Science Center without molecular size calibration between laboratories. It is the sole responsibility of the user to use the data in an appropriate manner consistent with the limitations of the data, in general, and these data, in particular.
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:
Alaska Pacific University, Anchorage, AK Alaska Resources Education, Anchorage, AK
Cross_Reference:
Citation_Information:
Originator: Hollenbeck, N.
Originator: Scheel, D.
Originator: Gravley, M. (ORCID: 0000-0002-4947-0236)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Toussaint, R. (ORCID: 0000-0001-7993-2051)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 201711
Title:
Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: American Malacological Bulletin
Issue_Identification: Vol. 35. Issue 2, Pgs. 145-157
Publication_Information:
Publication_Place: Washington, DC, USA
Publisher: BioOne
Other_Citation_Details:
Hollenbeck, N., D. Scheel, M.C. Gravley, G.K. Sage, R. Toussaint, and S.L. Talbot. 2017. Use of Swabs for Sampling Epithelial Cells for Molecular Genetics Analyses in Enteroctopus. American Malacological Bulletin 35(2):145-157 · November 2017 DOI: 10.4003/006.035.0207
Online_Linkage: https://doi.org/10.4003/006.035.0207
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
Sequence data were collected to independently verify correct lineage assignment via the genotyping method. Individual sample ID's, collection dates, and sampling locations of individual samples provided by collectors were cross-checked and verified to match the accompanying worksheet. Sampling locations were verified with collectors and formally labelled and cross-referenced to the Geographic Names Information Service (GNIS) when possible. Genbank accession numbers were cross-referenced to the appropriate individual samples as recorded. For quality control purposes, a minimum of 10% of the samples were extracted, amplified, and genotyped for all loci. We observed sterile technique in the handling of all DNA, and all procedures were performed with positive and negative controls to provide evidence of replication without contamination.
Logical_Consistency_Report:
For microsatellite data, reported allele sizes were reviewed to confirm they conform to expected distributions (e.g. genotypes for all replicates of the same individual matched at all loci and loci distinguishing the GPO from the cryptic species indeed differentiated the samples as labelled as GPO vs. cryptic).
Completeness_Report:
Data omissions for particular entities are explained in the Entity and Attribute definitions. Blank data indicates no data were collected for a particular attribute. For GenBank OCDE, blank cells indicate that an individual sample matched a previously known allele (see "ALLELE1 and ALLELE2"). Attribute data equaling “NP” in a cell of the data set refers to a sample that did not amplify or show any product (“no product”).
Lineage:
Methodology:
Methodology_Type: Lab
Methodology_Description:
Two methods of DNA extraction were used in this study. One identified as "CTAB" in the attributes refers to a published DNA extraction method (Stewart and Via 1993) with modifications by the author of eliminating ascorbic acid and DIECA (diethyldithiocarbamic acid)to avoid analysis complications caused by mucopolysaccarides in DNA samples. The other identified as "MVZ salt" in the attributes refers to a published DNA extraction method following Medrano et al. (1990) with modifications reported in Sonsthagen et al. (2004).
Methodology_Citation:
Citation_Information:
Originator: Stewart, Jr., C.N.
Originator: Via, L.E.
Publication_Date: 1993
Title:
A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications.
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: BioTechniques
Issue_Identification: 14 (5)
Publication_Information:
Publication_Place: on line
Publisher: The International Journal of Life Science Methods
Online_Linkage: http://www.biotechniques.com/
Methodology_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)
Publication_Information:
Publication_Place: on line
Publisher: The International Journal of Life Science Methods
Online_Linkage: http://www.biotechniques.com/
Methodology_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: Condor
Issue_Identification: 106 (4)
Publication_Information:
Publication_Place: on line
Publisher: American Ornithological Society
Online_Linkage: https://www.bioone.org/loi/cond
Methodology:
Methodology_Type: Lab
Methodology_Description:
Quantification of extracted DNA via fluorometry followed Handel et al. (2006).
Methodology_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: 200611
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: 34:1094-1100
Publication_Information:
Publication_Place: online
Publisher: The Wildlife Society
Other_Citation_Details: DOI: 10.2193/0091-7648(2006)34[1094:UOBSFS]2.0.CO;2
Online_Linkage:
Methodology:
Methodology_Type: Lab
Methodology_Description:
Polymerase chain reaction (PCR) amplification, scoring of microsatellites, and amplification and bi-directional sequencing of OCDE followed Toussaint, Sheel, et al. (2012) and Toussaint, Sage, et al. (2012).
Methodology_Citation:
Citation_Information:
Originator: Toussaint, R.K. (ORCID: 0000-0001-7993-2051)
Originator: Scheel, D.
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2012
Title:
Nuclear and mitochondrial markers reveal evidence for genetically segregated cryptic speciation in giant Pacific octopuses from Prince William Sound, Alaska
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Conservation Genetics
Issue_Identification: 13:1483
Publication_Information:
Publication_Place: on line
Publisher: Springer Netherlands
Other_Citation_Details: DOI: 10.1007/s10592-012-0392-4
Online_Linkage: https://link.springer.com/article/10.1007%2Fs10592-012-0392-4
Methodology_Citation:
Citation_Information:
Originator: Toussaint, R.K. (ORCID: 0000-0001-7993-2051)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: Scheel, D.
Publication_Date: 2012
Title:
Microsatellite marker isolation and development for the giant Pacific octopus (Enteroctopus dofleini)
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Conservation Genetics Resources
Issue_Identification: 4:545
Publication_Information:
Publication_Place: on line
Publisher: Springer Netherlands
Other_Citation_Details: DOI: 10.1007/s12686-011-9588-z
Online_Linkage: https://link.springer.com/article/10.1007%2Fs12686-011-9588-z
Methodology:
Methodology_Type: Lab
Methodology_Description:
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. The code “NP” in a cell of the data set refers to a sample that did not amplify or show any product (“no product”). Given the original purpose for generating this data set (developing a non-invasive DNA sampling method and the application of non-traditional markers for rapid lineage determination), paired sampling and multiple data collections on the same individuals were rigorously scrutinized to confirm sample quality effects that might provide incorrect or partial data.
Methodology_Citation:
Citation_Information:
Originator: Hollenbeck, N.
Originator: Scheel, D.
Originator: Gravley, M. (ORCID: 0000-0002-4947-0236)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Toussaint, R. (ORCID: 0000-0001-7993-2051)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2017
Title:
Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: American Malacological Bulletin
Issue_Identification: TBD
Publication_Information:
Publication_Place: on line
Publisher: BioOne on behalf of The American Malacological Society
Online_Linkage: https://www.bioone.org/loi/malb
Process_Step:
Process_Description:
For microsatellites, a small subset of individuals were run on a gel for each locus alongside an M13 sequence ladder of known size and allele sizes assigned using Gene Profiler 4.05 (Scanalytics, Inc.). Subsequent gels included these known size individuals on every gel from which relative sizes of unknown individuals were assigned, using Gene Profiler 4.05 (Scanalytics).
Process_Date: Unknown
Process_Step:
Process_Description:
Simultaneous bi-directional sequencing reads were analyzed using LI-COR e-Seq imaging software and aligned using LI-COR AlignIR 2.0 (LI-COR, Lincoln, NE).
Process_Date: Unknown
Process_Step:
Process_Description:
Quality of DNA sequences obtained was assessed comparing results of paired samples from swab vs. whole tissue extracts by comparing phred quality (Q) scores and base calling error rate provided by the sequencing alignment package LI-COR AlignIR 2.0 (LI-COR, Lincoln, NE) and the number of base pair reads and manual edits required.
Process_Date: Unknown
Spatial_Data_Organization_Information:
Indirect_Spatial_Reference:
Place names provided are general in nature and linked to an official USGS GNIS entry or a nearby landmark when possible.
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label:
Enteroctopus Sampling Effects on Genetic Data, Prince William Sound Alaska, 2012-2015
Entity_Type_Definition: Data set
Entity_Type_Definition_Source: Author defined
Attribute:
Attribute_Label: Sample ID
Attribute_Definition:
This is the original label assigned in the field to each individual sample received in the laboratory.
Attribute_Definition_Source: Field assigned
Attribute_Domain_Values:
Unrepresentable_Domain:
These are field assigned sample labels as received by the laboratory. The extension with "replicate 1, 2, 3 or 4" has been added to differentiate treatment groups for this laboratory method validation study.
Attribute:
Attribute_Label: Lab ID
Attribute_Definition:
Unique sample ID including genus, individual, sample type, replicate (if appropriate), and designation of type of delayed extraction (if appropriate).
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Unrepresentable_Domain:
This is a 10-20 character (including spaces) label generated for laboratory identification of samples which includes a 4 letter taxonomic code (ENDO), 3-8 alphabetical or alphanumerical code corresponding to original field labelled Sample ID and 1-6 character code indicating sample type ("T" or "S" for tissue or swab, respectively), whether the swab was the first or second in the sample ("1" or "2"), the time to extraction after receipt in the lab (blank for immediate and "A" or "C" for 8-31 months post-receipt; "A" if via salt or "C" if via CTAB protocols, and if the sample was extracted in duplicate ["(1)"] for quality control of the extraction as assessed by DNA yield.
Attribute:
Attribute_Label: Collection Date
Attribute_Definition:
This is the season (either Autumn or Spring) and year (2012 or 2013) the sample was collected from the field.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Autumn 2012
Enumerated_Domain_Value_Definition: This denotes an octopus captured in autumn 2012.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Spring 2013
Enumerated_Domain_Value_Definition: This denotes an octopus captured in spring 2013.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Autumn 2013
Enumerated_Domain_Value_Definition: This denotes an octopus captured in autumn 2013.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Lineage
Attribute_Definition:
Lineage assignment to either Giant Pacific Octopus (GPO) or Cryptic based on morphology in the field and confirmed by rapid screen of 2 diagnostic microsatellite markers in this data set.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: GPO
Enumerated_Domain_Value_Definition:
Species designation of Giant Pacific Octopus (Enteroctopus dofleini; GPO) as determined by morphology in the field and confirmed by laboratory DNA analyses in this data set.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Cryptic
Enumerated_Domain_Value_Definition:
Novel morphotypes from field measurements and DNA haplotypes from this data set preclude assignment of these "cryptic lineage" samples to currently recognized Giant Pacific Octopus (Enteroctopus dofleini).
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Field Sex
Attribute_Definition:
This is the sex of the individual as determined by morphology in the field and provided on data sheets with the samples upon arrival in the laboratory.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: F
Enumerated_Domain_Value_Definition:
Individual identified as a female based on morphology in the field.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: M
Enumerated_Domain_Value_Definition:
Individual identified as a male based on morphology in the field.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: Depth (m)
Attribute_Definition:
This is the ocean depth at or range of depth in which a sample was collected according to information provided to the laboratory by biologists.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 54.9
Range_Domain_Maximum: 185
Attribute_Units_of_Measure: Meters
Attribute:
Attribute_Label: Sampling Location
Attribute_Definition:
This is the specific geographic area in which the sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Bald Head Chris
Enumerated_Domain_Value_Definition: Bald Head Chris Island, Alaska
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Golden Bay, Port Wells
Enumerated_Domain_Value_Definition:
Golden Bay in Port Wells, Alaska (presumed to be the bay at the mouth of the Golden River (60.96697 N, 147.99572 W; 60.96606 N, 147.98176 W) coming from Davis Lake north of Esther Island)
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Long Bay
Enumerated_Domain_Value_Definition: Long Bay, Alaska
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Western Prince William Sound
Enumerated_Domain_Value_Definition:
A general area presumed to be some smaller "western" area than the overall geographic bounding of "Prince William Sound" as a whole.
Enumerated_Domain_Value_Definition_Source: Field assigned
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Prince of Wales Passage
Enumerated_Domain_Value_Definition: Prince of Wales Passage, Alaska
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Chenega
Enumerated_Domain_Value_Definition:
Chenega, Alaska (presumed to be from the waters surrounding Chenega Island, Prince William Sound Alaska (60.3147222 N, 148.0716667 W; 60.3102778 N, 148.1305556 W)
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Herring Bay
Enumerated_Domain_Value_Definition: Herring Bay, Alaska
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System
Attribute:
Attribute_Label: Locale
Attribute_Definition:
This is the general geographic area in which the sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Prince William Sound
Enumerated_Domain_Value_Definition: Prince William Sound, Alaska
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System
Attribute:
Attribute_Label: Extraction
Attribute_Definition:
This indicates the method by which DNA was extracted from the sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: CTAB
Enumerated_Domain_Value_Definition:
This refers to a published DNA extraction method with modifications by the author to avoid analysis complications caused by mucopolysaccarides in DNA samples (Hollenbeck, N. et al. 2017. Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus. Am. Malacol. Bull.).
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: MVZ salt
Enumerated_Domain_Value_Definition:
This refers to a published DNA extraction method with modifications by the author which reduces cost and time required compared to many commercial DNA extraction kits (Sonsthagen, S.A., et al. 2004. Gene flow and genetic characterization of Northern Goshawks breeding in Utah. Condor 106: 826–836.).
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: DNA Yield
Attribute_Definition:
This is the concentration of extracted DNA of each sample as determined with fluorometry in relation to a known standard (100 nanograms/microliter) of calf thymus DNA. All DNA's used in subsequent PCR amplifications were diluted to working stocks of 50 nanograms/microliter.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 2
Range_Domain_Maximum: 765
Attribute_Units_of_Measure: nanograms of DNA per microliter (ng/ul)
Attribute:
Attribute_Label: GenBank OCDE
Attribute_Definition:
This is the GenBank (https://www.ncbi.nlm.nih.gov/genbank/) accession number for associated nuclear octopine dehydrogenase gene nucleotide sequence data associated with a particular sample, where applicable. Blank cells indicate replicate samples for which sequences were not generated or samples for which sequence matching previously identified alleles were collected (see attributes "ALLELE1" and "ALLELE2" to differentiate between no sequence generated and non-novel sequence generated).
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: KT225573
Range_Domain_Maximum: KT225574
Attribute_Units_of_Measure: GenBank accession number
Attribute:
Attribute_Label: Manually Edited BP
Attribute_Definition:
Average number of base pairs of forward and reverse nuclear octopine dehydrogenase(OCDE) sequence manually edited after auto-sequencing of the sample using Licor's eSeq v. 3.1 and AlignIR 2.0. An asterisk (*) indicates the sequence required greater than 20% manual editing, is considered an outlier for the sequencing reaction results and was not used in manuscript pairwise comparisons of tissue versus swab results.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 21
Range_Domain_Maximum: 140.5
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: Auto-called BP
Attribute_Definition:
Average number of base pairs of forward and reverse nuclear octopine dehydrogenase(OCDE) sequence auto-sequenced and accepted as called using Licor's eSeq v. 3.1 and AlignIR 2.0(trademark), LI-COR Inc., Lincoln, NE.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 360.5
Range_Domain_Maximum: 550
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: Quality (SD)
Attribute_Definition:
These are the phred quality (Q) scores and base calling error rate (in standard deviation or SD) provided by the sequencing alignment package AlignIR 2.0 (trademark), LI-COR Inc., Lincoln, NE).
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 25.72 (9.78)
Range_Domain_Maximum: 37.38 (7.38)
Attribute_Units_of_Measure: phred quality (Q) scores (standard deviation)
Attribute:
Attribute_Label: OCDE_1
Attribute_Definition:
This is the first of two allele assignments for the nuclear octopine dehydrogenase (OCDE) gene based on up to 6 site substitutions from 528 base pairs of nucleotide sequence data. A blank cell indicates data were not generated at this locus for that sample. As a diploid locus, data from OCDE_1 must only be considered in relation to data for OCDE_2 for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Codeset_Domain:
Codeset_Name: OCDE Alleles
Codeset_Source:
Assignment of OCDE1, OCDE2, or OCDE3 corresponds with sequence data matching alleles described in Genbank under accession numbers KT213460 (OCDE1), KT213461 (OCDE2), and KT225573 (OCDE3).
Attribute:
Attribute_Label: OCDE_2
Attribute_Definition:
This is the second of two allele assignments for the nuclear octopine dehydrogenase (OCDE) gene based on up to 6 site substitutions from 528 base pairs of nucleotide sequence data. A blank cell indicates data were not generated at this locus for that sample. As a diploid locus, data from OCDE_2 must only be considered in relation to data for OCDE_1 for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Codeset_Domain:
Codeset_Name: OCDE Alleles
Codeset_Source:
Assignment of OCDE1, OCDE2, OCDE3, or OCDE4 corresponds with sequence data matching alleles described in Genbank under accession numbers KT213460 (OCDE1), KT213461 (OCDE2), KT225573 (OCDE3), and KT225574 (OCDE4);
Attribute:
Attribute_Label: EdoµA6_1
Attribute_Definition:
Microsatellite allele one of the EdoµA6 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. NP indicates resulting PCR product was absent or of insufficient quality to enable analysis. A blank cell indicates data were not generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 168
Range_Domain_Maximum: 202
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NP
Enumerated_Domain_Value_Definition:
Designation as "NP" indicates no product was visible precluding size determination at this locus.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: EdoµA6_2
Attribute_Definition:
Microsatellite allele two from the EdoµA6 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. NP indicates resulting PCR product was absent or of insufficient quality to enable analysis. A blank cell indicates data were not generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 190
Range_Domain_Maximum: 228
Attribute_Units_of_Measure: base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NP
Enumerated_Domain_Value_Definition:
Designation as "NP" indicates no product was visible precluding size determination at this locus.
Enumerated_Domain_Value_Definition_Source: Author defined
Attribute:
Attribute_Label: EdoµA8_1
Attribute_Definition:
Microsatellite allele one of the EdoµA8 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 181
Range_Domain_Maximum: 209
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA8_2
Attribute_Definition:
Microsatellite allele two from the EdoµA8 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 181
Range_Domain_Maximum: 237
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA105_1
Attribute_Definition:
Microsatellite allele one of the EdoµA105 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 187
Range_Domain_Maximum: 203
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA105_2
Attribute_Definition:
Microsatellite allele two from the EdoµA105 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 191
Range_Domain_Maximum: 217
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA106_1
Attribute_Definition:
Microsatellite allele one of the EdoµA106 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 110
Range_Domain_Maximum: 126
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA106_2
Attribute_Definition:
Microsatellite allele two from the EdoµA106 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 110
Range_Domain_Maximum: 126
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA110_1
Attribute_Definition:
Microsatellite allele one of the EdoµA110 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 124
Range_Domain_Maximum: 164
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA110_2
Attribute_Definition:
Microsatellite allele two from the EdoµA110 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 126
Range_Domain_Maximum: 164
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA118_1
Attribute_Definition:
Microsatellite allele one of the EdoµA118 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 225
Range_Domain_Maximum: 253
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA118_2
Attribute_Definition:
Microsatellite allele two from the EdoµA118 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 227
Range_Domain_Maximum: 303
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA122_1
Attribute_Definition:
Microsatellite allele one of the EdoµA122 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 178
Range_Domain_Maximum: 219
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA122_2
Attribute_Definition:
Microsatellite allele two from the EdoµA122 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 182
Range_Domain_Maximum: 241
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA125_1
Attribute_Definition:
Microsatellite allele one of the EdoµA125 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 162
Range_Domain_Maximum: 222
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA125_2
Attribute_Definition:
Microsatellite allele two from the EdoµA125 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 172
Range_Domain_Maximum: 268
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA129_1
Attribute_Definition:
Microsatellite allele one of the EdoµA129 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 127
Range_Domain_Maximum: 153
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµA129_2
Attribute_Definition:
Microsatellite allele two from the EdoµA129 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 127
Range_Domain_Maximum: 155
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµE11_1
Attribute_Definition:
Microsatellite allele one of the EdoµE11 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 generated at this locus for that sample. As a diploid locus, data from allele one must only be considered in relation to data for allele two for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 135
Range_Domain_Maximum: 211
Attribute_Units_of_Measure: base pairs
Attribute:
Attribute_Label: EdoµE11_2
Attribute_Definition:
Microsatellite allele two from the EdoµE11 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 generated at this locus for that sample. As a diploid locus, data from allele two must only be considered in relation to data for allele one for the same individual.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 139
Range_Domain_Maximum: 219
Attribute_Units_of_Measure: base pairs
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 Dr.
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: Authoritative source for access to 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 (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: Zip
Format_Version_Number: 19.0
Format_Information_Content:
Zip file containing the data in CSV file format and FGDC metadata in XML and HTML formats.
File_Decompression_Technique: Winzip legacy compression applied
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: https://doi.org/10.5066/F7VM49HJ
Fees: No fees.
Metadata_Reference_Information:
Metadata_Date: 20201125
Metadata_Review_Date: 20160630
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
Metadata_Security_Information:
Metadata_Security_Classification_System: None
Metadata_Security_Classification: Unclassified
Metadata_Security_Handling_Description: None

Generated by mp version 2.9.44 on Mon Nov 20 15:03:29 2017