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Summary
Item Identification
Keywords
Physical Location
Data Set Info
Support Roles
Extents
Access Info
Distribution Info
Tech Environment
Data Quality
Data Management
Lineage
Catalog Details

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

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.

Distribution Information

Access Constraints:

There are no legal restrictions on access to the data. They reside in public

domain and can be freely distributed.

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.

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

Geographic Area 1

-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

Time Frame 1
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

CC ID: 249770
Date Effective From: 2015
Date Effective To:
Contact (Person): Canino, Michael F
Email Address: mike.canino@noaa.gov
Phone: 206 526 4108
Contact Instructions:

email

Distributor

CC ID: 172726
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

CC ID: 172724
Date Effective From: 2014-07-18
Date Effective To:
Contact (Person): MC, Metadata Coordinators
Email Address: AFSC.metadata@noaa.gov

Originator

CC ID: 172728
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

CC ID: 172727
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

CC ID: 172725
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

CC ID: 172723
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

CC ID: 172722
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

CC ID: 249768
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