AFSC/RACE/EcoFOCI: NPRB_1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically important fish species and selected i...
Data Set (DS) | Alaska Fisheries Science Center (AFSC)GUID: gov.noaa.nmfs.inport:21948 | Updated: January 15, 2024 | Published / External
Summary
Short Citation
Alaska Fisheries Science Center, 2024: AFSC/RACE/EcoFOCI: NPRB_1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically important fish species and selected invertebrates in the northeast Pacif, https://www.fisheries.noaa.gov/inport/item/21948.
Full Citation Examples
Accurate identification of various life history stages and prey items of marine fishes and invertebrates is central for understanding distribution,abundance, trophic ecology, and biodiversity of these species. Taxonomic approaches have been successfully applied to ichthyoplankton identification and diet analysis efforts for many years. Identification to the species level requires varying degrees of taxonomic expertise. and diagnostic characters for eggs or larvae in some species have not been elucidated.
In the current dataset we assembled a mitochondrial DNA (mtDNA) database for which
used standard laboratory protocols (restriction fragment length polymorphism
and Sanger DNA sequencing) to accurately identify any life history stages of selected fish and
shrimp species, with special emphasis on those species that have been difficult or impossible
to identify by conventional taxonomic means. Fish and shrimp specimens were collected between 2010 - 2013.
We developed a restriction fragment length polymorphism (RFLP)protocol, based upon mitochondrial DNA sequences
to distinguish between Pacific halibut and Greenland halibut, but were unable to develop one to discriminate
between Bering flounder and flathead sole. We used direct Sanger sequencing of mitochondrial DNA for species
identification of 32 species of sculpin and four species of caridean shrimp. PCR products from fish and shrimp
samples were sequenced using an ABI 3730 automated sequencer (Applied Biosystems, Inc). DNA sequences from museum
voucher specimens were compared with entries in the public databases for those species. Sequences from voucher
specimens have greater taxonomic authority for use in species identification than those without vouchers,
adding greater confidence to species identifications based upon our data.
Distribution Information
There are no legal restrictions on access to the data. They reside in public
domain and can be freely distributed.
User must read and fully comprehend the metadata prior to use. Applications or
inferences derived from the data should be carefully considered for accuracy.
Acknowledgementof NOAA/NMFS/AFSC, as the source from which these data were obtained in
any publications and/or other representations of these, data is suggested.
Controlled Theme Keywords
biota
Child Items
No Child Items for this record.
Contact Information
Point of Contact
Michael F Canino
mike.canino@noaa.gov
206 526 4108
Metadata Contact
Metadata Coordinators MC
AFSC.metadata@noaa.gov
Extents
-178.46° W,
-120.1° E,
71.5° N,
42.42° S
Chukchi Sea, Bering Sea, Gulf of Alaska, northeastern Pacific Ocean, Washington State, Puget Sound, Oregon State
2000 - 2013
Item Identification
| Title: | AFSC/RACE/EcoFOCI: NPRB_1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically important fish species and selected invertebrates in the northeast Pacif |
|---|---|
| Short Name: | AFSC/RACE/EcoFOCI: NPRB 1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically im |
| Status: | Completed |
| Abstract: |
Accurate identification of various life history stages and prey items of marine fishes and invertebrates is central for understanding distribution,abundance, trophic ecology, and biodiversity of these species. Taxonomic approaches have been successfully applied to ichthyoplankton identification and diet analysis efforts for many years. Identification to the species level requires varying degrees of taxonomic expertise. and diagnostic characters for eggs or larvae in some species have not been elucidated. In the current dataset we assembled a mitochondrial DNA (mtDNA) database for which used standard laboratory protocols (restriction fragment length polymorphism and Sanger DNA sequencing) to accurately identify any life history stages of selected fish and shrimp species, with special emphasis on those species that have been difficult or impossible to identify by conventional taxonomic means. Fish and shrimp specimens were collected between 2010 - 2013. We developed a restriction fragment length polymorphism (RFLP)protocol, based upon mitochondrial DNA sequences to distinguish between Pacific halibut and Greenland halibut, but were unable to develop one to discriminate between Bering flounder and flathead sole. We used direct Sanger sequencing of mitochondrial DNA for species identification of 32 species of sculpin and four species of caridean shrimp. PCR products from fish and shrimp samples were sequenced using an ABI 3730 automated sequencer (Applied Biosystems, Inc). DNA sequences from museum voucher specimens were compared with entries in the public databases for those species. Sequences from voucher specimens have greater taxonomic authority for use in species identification than those without vouchers, adding greater confidence to species identifications based upon our data. |
| Purpose: |
To develop cost effective molecular protocols for accurate identification of flatfish eggs, larvae and digested prey remains of sculpins and caridean marine shrimps. |
| Notes: |
Loaded by FGDC Metadata Uploader, batch 5028, 07-18-2014 14:16 The following FGDC sections are not currently supported in InPort, but were preserved and will be included in the FGDC export: - Taxonomy (FGDC:taxonomy) - Entity Attribute Information (FGDC:eainfo) |
Keywords
Theme Keywords
| Thesaurus | Keyword |
|---|---|
| ISO 19115 Topic Category |
biota
|
| UNCONTROLLED | |
| PARR Exclusion | Non-Federal Funding |
| None | control region |
| None | cytochrome b |
| None | cytochrome oxidase |
| None | DNA barcoding |
| None | gut contents |
| None | mitochondrial DNA |
| None | ND1 |
| None | species identification |
Spatial Keywords
| Thesaurus | Keyword |
|---|---|
| UNCONTROLLED | |
| None | Alaska |
| None | Bering Sea |
| None | Chuckchi Sea |
| None | Oregon State |
| None | Puget Sound |
| None | Washington State |
Physical Location
| Organization: | Alaska Fisheries Science Center |
|---|---|
| City: | Seattle |
| State/Province: | WA |
| Country: | USA |
Data Set Information
| Data Set Scope Code: | Data Set |
|---|---|
| Data Set Type: | Database |
| Maintenance Frequency: | None Planned |
| Data Presentation Form: | Table (digital) |
Support Roles
Data Steward
| Date Effective From: | 2015 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Canino, Michael F |
| Email Address: | mike.canino@noaa.gov |
| Phone: | 206 526 4108 |
| Contact Instructions: |
|
Distributor
| Date Effective From: | 2014-07-18 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Canino, Michael F |
| Email Address: | mike.canino@noaa.gov |
| Phone: | 206 526 4108 |
Metadata Contact
| Date Effective From: | 2014-07-18 |
|---|---|
| Date Effective To: | |
| Contact (Person): | MC, Metadata Coordinators |
| Email Address: | AFSC.metadata@noaa.gov |
Originator
| Date Effective From: | 2014-07-18 |
|---|---|
| Date Effective To: | |
| Contact (Organization): | Alaska Fisheries Science Center (AFSC) |
| Address: |
7600 Sand Point Way N.E., Building 4 Seattle, WA 98115 USA |
| Email Address: | afsc.webmaster@noaa.gov |
| Phone: | (206) 526-4000 |
| Fax: | (206) 526-4004 |
| URL: | https://www.fisheries.noaa.gov/about/alaska-fisheries-science-center |
| Business Hours: | 0700-1700 Pacific Time |
Originator
| Date Effective From: | 2014-07-18 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Canino, Michael F |
| Email Address: | mike.canino@noaa.gov |
| Phone: | 206 526 4108 |
Point of Contact
| Date Effective From: | 2014-07-18 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Canino, Michael F |
| Email Address: | mike.canino@noaa.gov |
| Phone: | 206 526 4108 |
Extents
| Currentness Reference: | Ground Condition |
|---|
Extent Group 1
Extent Group 1 / Geographic Area 1
| W° Bound: | -178.46 | |
|---|---|---|
| E° Bound: | -120.1 | |
| N° Bound: | 71.5 | |
| S° Bound: | 42.42 | |
| Description |
Chukchi Sea, Bering Sea, Gulf of Alaska, northeastern Pacific Ocean, Washington State, Puget Sound, Oregon State |
|
Extent Group 1 / Time Frame 1
| Time Frame Type: | Range |
|---|---|
| Start: | 2000 |
| End: | 2013 |
Access Information
| Security Class: | Unclassified |
|---|---|
| Data Access Policy: |
Contact Distributor |
| Data Access Procedure: |
Contact Distributor |
| Data Access Constraints: |
There are no legal restrictions on access to the data. They reside in public domain and can be freely distributed. |
| Data Use Constraints: |
User must read and fully comprehend the metadata prior to use. Applications or inferences derived from the data should be carefully considered for accuracy. Acknowledgementof NOAA/NMFS/AFSC, as the source from which these data were obtained in any publications and/or other representations of these, data is suggested. |
| Metadata Access Constraints: |
none |
| Metadata Use Constraints: |
none |
Distribution Information
Distribution 1
| Download URL: | http://ncei.noaa.gov |
|---|---|
| Distributor: |
Technical Environment
| Description: |
FAS files can bge worked in any simple text editor such as notepad, MS Word 2012 |
|---|
Data Quality
| Accuracy: |
Molecular size standards and restriction maps |
|---|---|
| Completeness Report: |
Base calls with PHRED scores less than 19 were omitted from analysis. Novel mutations were verified by sequencing DNA segments in both directions. |
| Quality Control Procedures Employed: |
See Abstract. |
Data Management
| Have Resources for Management of these Data Been Identified?: | No |
|---|---|
| Approximate Percentage of Budget for these Data Devoted to Data Management: | Unknown |
| Do these Data Comply with the Data Access Directive?: | No |
| Is Access to the Data Limited Based on an Approved Waiver?: | No |
| Approximate Delay Between Data Collection and Dissemination: | unknown |
| Actual or Planned Long-Term Data Archive Location: | To Be Determined |
| If To Be Determined, Unable to Archive, or No Archiving Intended, Explain: |
no archive for this type of data |
| Approximate Delay Between Data Collection and Archiving: | unknown |
| How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?: |
unknown |
Lineage
| Lineage Statement: |
unknown |
|---|
Catalog Details
| Catalog Item ID: | 21948 |
|---|---|
| GUID: | gov.noaa.nmfs.inport:21948 |
| Metadata Record Created By: | Nancy Roberson |
| Metadata Record Created: | 2014-07-18 14:16+0000 |
| Metadata Record Last Modified By: | SysAdmin InPortAdmin |
| Metadata Record Last Modified: | 2024-01-15 12:08+0000 |
| Metadata Record Published: | 2016-05-18 |
| Owner Org: | AFSC |
| Metadata Publication Status: | Published Externally |
| Do Not Publish?: | N |
| Metadata Last Review Date: | 2016-05-18 |
| Metadata Review Frequency: | 1 Year |
| Metadata Next Review Date: | 2017-05-18 |