Short Citation:
Pacific Islands Fisheries Science Center, 2021: HMSRP Hawaiian Monk Seal Microsatellite Genotypes, https://www.fisheries.noaa.gov/inport/item/11545.

Item Identification

Title: HMSRP Hawaiian Monk Seal Microsatellite Genotypes
Status: In Work
Publication Date: 2018-02-28
Abstract:

Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual, identified by the Seal ID number. An additional dataset is being generated that will expand these genotypes by another 30 loci.

Purpose:

The National Marine Fisheries Service (NMFS) is the lead agency responsible for the recovery of the Hawaiian monk seal. Each year the NMFS Pacific Islands Fisheries Science Center, Protected Species Division, Hawaiian Monk Seal Research Program conducts studies at the main breeding sites to provide information necessary to evaluate (1) the status and trends of the monk seal subpopulations, (2) natural history traits such as survival, reproduction, growth, behavior, and feeding habits, and (3) the success of various activities designed to facilitate population growth. Microsatellite data may be used to identify individuals, assign parentage, and assess population dynamics and fitness.

Supplemental Information:

Division: Protected Species

Division Chief: Charles Littnan

Program: Monk Seal Research Program

Authorities: Endangered Species Act

Ownership: PIFSC

Temporal Resolution: Year

Type of Data Collected: Genetic

Collection Method: DNA extraction, PCR, fragment analysis, allele calling

Recording Media: Access Database

Quality Control Validation and QC procedures: Available

Storage Location: Work computer 1845 Wasp Blvd., Bldg 176, Honolulu, HI 96818, Conservation Genetics/Genomics Laboratory (American Museum of Natural History, New York)

Storage Media: Hard drive and back-up drive, PIFSC network drive

Storage Format :Access database

Backups: Available, includes offsite storage

Data Distribution Method: Electronic

Keywords

Theme Keywords

Thesaurus Keyword
None DNA
None Hawaiian monk seal
None health and disease program
None microsatellite
None MSRP
None PIFSC
None protected species
None PSD
None seal ID
None specimen number

Spatial Keywords

Thesaurus Keyword
None Hawaiian Islands

Physical Location

Organization: Pacific Islands Fisheries Science Center
City: Honolulu
State/Province: HI
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Database
Maintenance Frequency: Annually
Data Presentation Form: Table (digital)
Entity Attribute Overview:

The entity is a table containing microsatellite genotypes for Hawaiian monk seals. Individual seals are in rows, columns contain alleles for each locus.

Entity Attribute Detail Citation:

ENT Table: GENETICS

Data Set Credit: Genetic analysis completed through collaboration with the Sackler Institute for Comparative Genomics at the American Museum of Natural History

Support Roles

Data Steward

CC ID: 44874
Date Effective From: 2011-10-20
Date Effective To:
Contact (Person): Robinson, Stacie
Address: 1845 Wasp Blvd.
Honolulu, HI 96839
USA
Email Address: stacie.robinson@noaa.gov
Phone: (808)725-5740

Data Steward

CC ID: 44875
Date Effective From: 2011-10-20
Date Effective To:
Contact (Person): Kaufman, Angela C
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: angie.kaufman@noaa.gov
Phone: (808)725-5708

Distributor

CC ID: 841975
Date Effective From: 2019-05-24
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Phone: 808-725-5300
URL: http://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Distributor

CC ID: 247175
Date Effective From: 2015-11-05
Date Effective To:
Contact (Person): Robinson, Stacie
Address: 1845 Wasp Blvd.
Honolulu, HI 96839
USA
Email Address: stacie.robinson@noaa.gov
Phone: (808)725-5740

Metadata Contact

CC ID: 247178
Date Effective From: 2015-11-05
Date Effective To:
Contact (Person): Robinson, Stacie
Address: 1845 Wasp Blvd.
Honolulu, HI 96839
USA
Email Address: stacie.robinson@noaa.gov
Phone: (808)725-5740

Originator

CC ID: 103309
Date Effective From: 2011-10-20
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Phone: 808-725-5300
URL: http://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 44876
Date Effective From: 2011-10-20
Date Effective To:
Contact (Person): Littnan, Charles L
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: charles.littnan@noaa.gov
Phone: (808)725-5711

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 44877
W° Bound: 180
E° Bound: -150
N° Bound: 30
S° Bound: 10
Description

Hawaiian Archipelago, Pacific Region

Extent Group 1 / Time Frame 1

CC ID: 44878
Time Frame Type: Continuing
Start: 1984

Access Information

Security Class: Unclassified
Data Access Policy:

NMFS/PIFSC, Protected Species Division, Hawaiian Monk Seal Research Program Data Access, Sharing, and Dissemination Guidelines

Data Access Procedure:

Requestor will be asked to submit a request to Charles Littnan (charles.littnan@noaa.gov)

Data Access Constraints:

NMFS/PIFSC, Protected Species Division, Hawaiian Monk Seal Research Program Data Access, Sharing, and Dissemination Guidelines

Data Use Constraints:

Use of the data set will ideally be cleared with NMFS/PIFSC, Protected Species Division. These data are PRELIMINARY and have not be completely screened for accuracy. NOAA can not be held liable for use of these data in a manner other than for perusal of preliminary data. The developers of these data are concerned with assuring its proper use. Before data are used to draw specific scientific conclusions, potential users are requested to contact NMFS/PIFSC, Protected Species Division for background on the data. Acknowledgement of the data should be cited. Different versions of the dataset may exist. The user must be sure to use the appropriate data set for the time period of interest. While efforts have been made to ensure that these data are accurate and reliable, NOAA cannot assume liablility for any damages or misrepresentation caused by any inaccuracies in the data or as a result of changes to the data caused by system transfers.

Distribution Information

Distribution 1

CC ID: 247177
Download URL: https://oceanwatch.pifsc.noaa.gov/xfer/PIFSC_PIRO_bulk_data_download_InPort_11545.tgz
Distributor: Pacific Islands Fisheries Science Center (PIFSC) (2019-05-24 - Present)
File Name: Genetics.csv
File Type: csv

Data Quality

Representativeness:

Data are collected both during dedicated efforts and opportunistically at Hawaiian monk seal haulout locations during variable-length field seasons over multiple years.

Bias:

Seal cohorts are not equally represented in the data set.

Completeness Measure:

Seal cohorts are not equally represented in the data set, and reproductive information obtained through field observations varies over time and by location

Completeness Report:

Data requires further checking prior to analysis

Quality Control Procedures Employed:

Steps were taken to avoid contamination of samples during DNA extraction and amplification steps.

A percentage of samples were run in duplicate to compare for consistency in amplification and allele classification.

Data Management

Have Resources for Management of these Data Been Identified?: Yes
Approximate Percentage of Budget for these Data Devoted to Data Management: Unknown
Do these Data Comply with the Data Access Directive?: Yes
Is Access to the Data Limited Based on an Approved Waiver?: No
Approximate Delay Between Data Collection and Dissemination: 12 months
Actual or Planned Long-Term Data Archive Location: To Be Determined
If To Be Determined, Unable to Archive, or No Archiving Intended, Explain:

we are figuring this out

Approximate Delay Between Data Collection and Archiving: 12 months
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

good question

Lineage

Lineage Statement:

1 - samples collected from monk seals in field locations

2 - DNA extracted

3 - PCR used to amplify target microsatellite loci

4 - Genetic analyzer used to generate electropherograms indicating allele size

5 - Electropherograms scored by eye to determine allele classifications

6 - Error checking protocol completed

7 - Samples re-analyzed as needed to fill gaps or verify suspect genotypes

Sources

Hawaiian monk seal biological samples

CC ID: 841976
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center

Process Steps

Process Step 1

CC ID: 841977
Description:

1 - samples collected from monk seals in field locations

Process Contact: Barbieri, Michelle M
Phone (Voice): 808-725-5734
Email Address: michelle.barbieri@noaa.gov
Source: Hawaiian monk seal biological samples

Process Step 2

CC ID: 841978
Description:

1 - samples collected from monk seals in field locations

2 - DNA extracted

Process Contact: Barbieri, Michelle M
Phone (Voice): 808-725-5734
Email Address: michelle.barbieri@noaa.gov
Source: Hawaiian monk seal biological samples

Process Step 3

CC ID: 841979
Description:

3 - PCR used to amplify target microsatellite loci

Process Contact: Robinson, Stacie
Phone (Voice): (808)725-5740
Email Address: stacie.robinson@noaa.gov
Source: Hawaiian monk seal biological samples

Process Step 4

CC ID: 841980
Description:

4 - Genetic analyzer used to generate electropherograms indicating allele size

Process Contact: Robinson, Stacie
Phone (Voice): (808)725-5740
Email Address: stacie.robinson@noaa.gov
Source: Hawaiian monk seal biological samples

Process Step 5

CC ID: 841981
Description:

5 - Electropherograms scored by eye to determine allele classifications

Process Contact: Robinson, Stacie
Phone (Voice): (808)725-5740
Email Address: stacie.robinson@noaa.gov
Source: Hawaiian monk seal biological samples

Process Step 6

CC ID: 841982
Description:

6 - Error checking protocol completed

Process Contact: Robinson, Stacie
Phone (Voice): (808)725-5740
Email Address: stacie.robinson@noaa.gov
Source: Hawaiian monk seal biological samples

Process Step 7

CC ID: 841983
Description:

7 - Samples re-analyzed as needed to fill gaps or verify suspect genotypes

Process Contact: Robinson, Stacie
Phone (Voice): (808)725-5740
Email Address: stacie.robinson@noaa.gov
Source: Hawaiian monk seal biological samples

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity (ENT) Table: GENETICS

Catalog Details

Catalog Item ID: 11545
Metadata Record Created By: Brent M Miyamoto
Metadata Record Created: 2011-12-27 22:09+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2021-03-18 17:49+0000
Metadata Record Published: 2015-12-08
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2016-12-08