Data Set Citation:
When using this data, please cite the data package:
NCEAS 12595: Edmunds: Tropical coral reefs of the future: Modeling ecological outcomes from the analyses of current and historical trends , National Center for Ecological Analysis and Synthesis , and Franklin E. 2011.
GeoSymbio: Symbiodinium-host symbioses
nceas.977.4 (https://knb.ecoinformatics.org:443/knb/metacat/nceas.977.4/nceas)
General Information:
Title:GeoSymbio: Symbiodinium-host symbioses
Identifier:nceas.977
Abstract:
A global Symbiodinium data set using genetic, taxonomic, collection event, and reference information of DNA sequences of the Internal Transcribed Spacer-2 (ITS2) region of the nuclear ribosomal array. This data corresponds to the supplemental information from Franklin EC, Stat M, Pochon X, Putnam H, Gates RD. 2011. GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses. Molecular Ecology Resources. DOI: 10.1111/j.1755-0998.2011.03081.x
Keywords:None:
  • Symbiodinium
  • GeoSymbio
  • Ecoinformatics
  • Symbioses
  • Biogeography
  • Bioinformatics
  • Hybrid web application
Publication Date:2011-11-01
Data Table, Image, and Other Data Details:
Metadata download: Ecological Metadata Language (EML) File
Data Table:Symbiodinium data.csv ( View Metadata | Download File download)
Data Table:References.csv ( View Metadata | Download File download)

Involved Parties

Data Set Creators:
Organization:NCEAS 12595: Edmunds: Tropical coral reefs of the future: Modeling ecological outcomes from the analyses of current and historical trends
Organization:National Center for Ecological Analysis and Synthesis
Individual: Erik Franklin
Organization:Hawaii Institute of Marine Biology
Address:
Hawaii Institute of Marine Biology University of Hawaii PO Box 1346,
Kaneohe, Hawaii 96744 USA
Phone:
808-440-8607
Email Address:
erikcf@hawaii.edu
Data Set Contacts:
Individual: Erik Franklin
Organization:Hawaii Institute of Marine Biology
Address:
Hawaii Institute of Marine Biology University of Hawaii PO Box 1346,
Kaneohe, Hawaii 96744 USA
Phone:
808-440-8607
Email Address:
erikcf@hawaii.edu
Associated Parties:
Individual: Erik Franklin
Individual: Michael Stat
Individual: Xavier Pochon
Individual: Hollie Putnam
Individual: Ruth Gates
Metadata Providers:
Individual: Xueying Han

Data Set Characteristics

Geographic Region:
Geographic Description:All major tropical oceans
Bounding Coordinates:
West:  -180.0000  degrees
East:  180.0000  degrees
North:  35.0000  degrees
South:  -35.0000  degrees
Time Period:
Begin:
1982
End:
2010
Taxonomic Range:
Classification:
Rank Name:Genus
Rank Value:Symbiodinium

Sampling, Processing and Quality Control Methods

Step by Step Procedures
Step 1:  
Description:

Data Sources

Data were mined from the US National Center for Biotechnology Information’s GenBank. DNA sequences of Symbiodinium were used to organize the organisms into clades and types based on partial 5.8S, complete ITS2 and partial 28S rDNA, referred to here on as ITS2 types. For Symbiodinium ITS2 sequences, GenBank possessed a multitude of redundant entries, often incomplete descriptions of associated attributes and mismatched fields in the submitted data. Comparison of ITS2 sequences from 79 published studies identified redundancies between records with synonymous sequences but different ITS2 type nomenclature. Identical sequences (i.e. 100% residue similarity) with different accession numbers were identified as synonyms with the first published record as the ‘parent’ accession number. The source literature identified in the GenBank record was then searched to confirm or ascertain the following descriptive characteristics for each sequence: host taxa, location, collection year and laboratory methodology. The accurate mapping of the location of Symbiodinium occurrences required manual data mining of the primary literature sources identified in each GenBank accession, with a cross-check of location in GEOnet Names (http://earth-info.nga.mil/gns/html) and Google Earth (http://www.google.com/earth).

Sampling Area And Frequency:
The data compilation yielded 4833 records in 34 variables that described bioinformatic and ecoinformatic attributes including host taxonomy, genetic sequence, methodology, collection event and scientific references for all nine Symbiodinium clades with hosts from 20 taxonomic orders in all major tropical oceans between 1982 and 2010.
Sampling Description:
NA

Data Set Usage Rights

no restrictions
Access Control:
Auth System:knb
Order:denyFirst
Metadata download: Ecological Metadata Language (EML) File