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MCR LTER: Coral Reef: Population Dynamics: Symbiodinium population initial sampling conditions in corals of Moorea

General Information
Data Package:
Local Identifier:knb-lter-mcr.15.13
Title:MCR LTER: Coral Reef: Population Dynamics: Symbiodinium population initial sampling conditions in corals of Moorea
Alternate Identifier:knb-lter-mcr.15
Alternate Identifier:DOI PLACE HOLDER
Abstract:

These data consist of sample collection locations and conditions only, not the results of sequencing. These data were an initial collection of an expected time series which was not repeated. Clade data derived from the sample collection described here are archived on GeoSymbio.

Coral are symbiotic with photosynthetic dinoflagellates from the genus Symbiodinium. There are eight divergent clades (A-H) within the genus which each contain many genetic varieties. Different types of Symbiodinium have been shown to affect the growth rate and thermal tolerance of the coral. The diversity and population structure of Symbiodinium on a reef and how it changes over time is therefore critical to the stability and resilience of coral reefs. Our research conducted through the MCR LTER project aims at defining the population structure of Symbiodinium present in the corals of Moorea and documenting changes over time.

Short Name:Symbiodinium
Publication Date:2022-03-16
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2007-04-03
End:
2007-04-12

People and Organizations
Contact:Information Manager (Moorea Coral Reef LTER) [  email ]
Organization:Moorea Coral Reef LTER
Creator:Gates, Ruth (Moorea Coral Reef LTER, Investigator)
Associate:Stat, Michael (Moorea Coral Reef LTER, Assistant Researcher)
Associate:Wheeler II, Benjamin (Moorea Coral Reef LTER, Assistant Researcher)

Data Entities
Data Table Name:
Sampling overview
Description:
Table of samples taken.
Detailed Metadata

Data Entities

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-mcr/15/13/9fe07ac78534de7f7dcc4c5ebdd6e7ec
Name:Sampling overview
Description:Table of samples taken.
Number of Records:192
Number of Columns:9

Table Structure
Object Name:knb-lter-mcr.15_SymbiodiniumMooreaSamples.csv
Size:18 Kb
Authentication:8a4d0f16f5cd4a8507840d3456532acc Calculated By MD5
Character Encoding:ASCII
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 Field sample IDSpeciesCollected ByDateLocationSiteDepthSizeExtraction protocol
Column Name:Field_Sample_ID  
Species  
Collected_By  
Date  
Location  
Site  
Depth_Meters  
Size  
Extraction_protocol  
Definition:ID of an individual sampleGenus or species binomial.Name of the person who collected the dataDay of ObservationConstant value: MooreaName of the observation site at the location.Depth of observationSize of the observed object. The size can be an absolute value, a range, a minimum or maximumand and it has the unit attached.Reference to the protocol applied for DNA extraction.
Storage Type:       string  
          
Measurement Type:rationominalnominaldateTimenominalnominalrationominalnominal
Measurement Values Domain:
Unitnumber
Precision1
Typeinteger
DefinitionTaxonomic classification
DefinitionName of individual.
FormatYYYY-MM-DD
Precision1 Day
DefinitionLocation name
DefinitionSite name
Unitmeter
Precision1
Typeinteger
DefinitionSize.
DefinitionName of a protocol
Missing Value Code:              
Codena
Explnot applicable
Codena
Explnot applicable
Accuracy Report:                  
Accuracy Assessment:                  
Coverage:                  
Methods:                  

Data Package Usage Rights

Data collected under the auspices of the MCR LTER are available to the public after primary publication, or at most two years after the completion of the study unless proprietary restrictions are warranted. Use of MCR LTER data is subject to acceptance of the following conditions:

  • 1. The user agrees to provide valid name and contact information prior to downloading online data. This information will be used to contact the user in case of changes to the data, and may also be used by data set authors and MCR LTER project administrators to document data usage.
  • 2. The user agrees to cite the data set author and MCR LTER in all publications in which the data are used, as per the instructions in the data documentation. If no specific instructions are provided in the data documentation, the user is requested to include the following statement: "Data sets were provided by the Moorea Coral Reef Ecosystem LTER, funded by the US National Science Foundation (OCE-0417412)."
  • 3. The user agrees to provide one copy of any manuscript based on MCR LTER data to the data set author prior to submitting it for publication.
  • 4. The user agrees to send two hard copies of any published manuscript based on MCR LTER data to the following address: Dr. Andrew J. Brooks Deputy Program Director, MCR LTER Marine Science Institute University of California Santa Barbara, CA 93106-6150 The user also agrees to send one electronic copy (pdf format) to the following e-mail address: brooks@msi.ucsb.edu
  • 5. Users are prohibited from selling or redistributing any data provided by MCR LTER without explicit prior permission.
  • 6. Users are encouraged to contact original investigators responsible for data. Where appropriate, researchers whose projects are integrally dependent on MCR LTER data are encouraged to consider collaboration and/or co-authorship with original investigators.
  • 7. Extensive efforts are made to ensure that online data are accurate and up to date, but the authors and the MCR LTER will not take responsibility for any errors that may exist in data provided online. Furthermore, the user assumes all responsibility for errors in analysis or judgment resulting from use of the data.
  • 8. Any violation of the terms of this agreement will result in immediate forfeiture of the data and loss of access privileges to other MCR LTER data sets.

Keywords

By Thesaurus:
(No thesaurus)MCR, LTER
(No thesaurus)French Polynesia, Moorea
(No thesaurus)Moorea Coral Reef, Symbiodinium, Clades
NBII Biocomplexity ThesaurusInterspecific relationships, Interactions, Genetic diversity, Genotypes, Coral bleaching, Endosymbionts, Symbiosis, Coral Reefs
KNBMarine
LTER Core Research AreaDisturbance, Populations
MCR Core ActivityTime Series Program
MCR-LTER Working GroupPhysiology of Corals, Population and Community Dynamics

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Samples were collected on SCUBA from the LTER sites in Moorea. Sites include LTER 1 through LTER 6 at Fringing, Lagoon and Forereef plus Rose Garden.

Total DNA was extracted from the samples using the Dneasy Plant Mini Kit (Qiagen). Symbiodinium ITS2 and chloroplast 23S genes were amplified from all samples. Sequence and phylogenetic analysis is performed to determine the population structure of Symbiodinium from these corals.

The samples were collected in April 2007 and there are plans to sample in future years to document long term change in the symbiont population.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Id:https://ror.org/0330j0z60
Creators:
Organization:Moorea Coral Reef LTER
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Web Address:
http://mcr.lternet.edu/
Individual: Ruth Gates
Organization:Moorea Coral Reef LTER
Position:Investigator
Address:
Hawaii Institute of Marine Biology/SOEST,
PO Box 1346,
University of Hawaii,
Kaneohe, HI 96744 USA
Phone:
808.236.7420 (voice)
Phone:
808.236.7443 (fax)
Email Address:
rgates@hawaii.edu
Web Address:
http://www.hawaii.edu/zoology/faculty/gates.htm
Web Address:
http://www.hawaii.edu/HIMB/faculty/gates.html
Id:http://orcid.org/0000-0003-4523-1403
Contacts:
Organization:Moorea Coral Reef LTER
Position:Information Manager
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Phone:
805.893.2071 (voice)
Email Address:
mcrlter@msi.ucsb.edu
Web Address:
http://mcr.lternet.edu/about/contact
Associated Parties:
Individual: Michael Stat
Organization:Moorea Coral Reef LTER
Role:Assistant Researcher
Individual: Benjamin Wheeler II
Organization:Moorea Coral Reef LTER
Role:Assistant Researcher

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2007-04-03
End:
2007-04-12
Geographic Region:
Description:Moorea, French Polynesia
Bounding Coordinates:
Northern:  -17.45Southern:  -17.62
Western:  -150.0Eastern:  -149.67
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Cnidaria
Classification:
Rank Name:Class
Rank Value:Anthozoa
Classification:
Rank Name:Order
Rank Value:Scleractinia
Classification:
Rank Name:Family
Rank Value:Acroporidae
Classification:
Rank Name:Genus
Rank Value:Acropora
Classification:
Rank Name:Genus
Rank Value:Astreopora
Classification:
Rank Name:Genus
Rank Value:Montipora
Classification:
Rank Name:Family
Rank Value:Agariciidae
Classification:
Rank Name:Genus
Rank Value:Gardinoseris
Classification:
Rank Name:Genus
Rank Value:Leptoseris
Classification:
Rank Name:Genus
Rank Value:Pachyseris
Classification:
Rank Name:Genus
Rank Value:Pavona
Classification:
Rank Name:Family
Rank Value:Faviidae
Classification:
Rank Name:Genus
Rank Value:Cyphastrea
Classification:
Rank Name:Genus
Rank Value:Leptastrea
Classification:
Rank Name:Genus
Rank Value:Montastrea
Classification:
Rank Name:Family
Rank Value:Fungiidae
Classification:
Rank Name:Genus
Rank Value:Fungia
Classification:
Rank Name:Genus
Rank Value:Herpolitha
Classification:
Rank Name:Family
Rank Value:Mussidae
Classification:
Rank Name:Genus
Rank Value:Lobophyllia
Classification:
Rank Name:Family
Rank Value:Pocilloporidae
Classification:
Rank Name:Genus
Rank Value:Pocillopora
Classification:
Rank Name:Family
Rank Value:Poritidae
Classification:
Rank Name:Genus
Rank Value:Porites
Classification:
Rank Name:Family
Rank Value:Siderastreidae
Classification:
Rank Name:Genus
Rank Value:Psammacora

Project

Parent Project Information:

Title:The Moorea Coral Reef (MCR) LTER
Personnel:
Individual: Russell Schmitt
Organization:Moorea Coral Reef LTER
Position:Lead Principal Investigator
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Phone:
805.893.3777 (fax)
Email Address:
schmitt@lifesci.ucsb.edu
Web Address:
http://mcr.lternet.edu/people/russell-j-schmitt
Role:Principal Investigator
Individual: Sally Holbrook
Organization:Moorea Coral Reef LTER
Position:Principal Investigator
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Phone:
805.893.3777 (fax)
Email Address:
holbrook@lifesci.ucsb.edu
Web Address:
http://mcr.lternet.edu/people/sally-holbrook
Role:Principal Investigator
Individual: Peter Edmunds
Organization:Moorea Coral Reef LTER
Position:Principal Investigator
Address:
Department of Biological Sciences, California State University,
18111 Nordhoff Street,
Northridge, CA 91330-8303 USA
Phone:
818.677.2502 (voice)
Email Address:
peter.edmunds@csun.edu
Web Address:
http://mcr.lternet.edu/people/peter-edmunds
Role:Principal Investigator
Individual: Robert Carpenter
Organization:Moorea Coral Reef LTER
Position:Principal Investigator
Address:
Department of Biological Sciences, California State University,
18111 Nordhoff Street,
Northridge, CA 91330-8303 USA
Phone:
818-677-3256 (voice)
Phone:
818-677-2034 (fax)
Email Address:
robert.carpenter@csun.edu
Web Address:
http://mcr.lternet.edu/people/robert-carpenter
Role:Principal Investigator
Funding:

NSF (LTER) MCR I #OCE-0417412

Maintenance

Maintenance:
Description:

Initially planned as a time series but not repeated.

Frequency:notPlanned
History:
scope:file format, metadata
old value:Changed from Excel to ASCII csv. Added taxonomicCoverage phylum to genus. Added missing value code. Added list of site names to methods.
change date:2011-02-03
scope:metadata
old value:Clarified these are only sample collection data, not sequencing results.
change date:2017-12-12
Other Metadata

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