Dataset: Hawaiian reef fish genetic accessions 2016

Name: Reef Fish genetic accessions at NCBI Genbank from samples collected in the Indian Ocean, Pacific Ocean, and Red Sea from 2005 to 2015; related to 2016 publications
Published: 2017-12-18
Keywords: oceans

Cite This Dataset

Spatial Extent: N:30 E:35 S:-20 W:-180

Project:

Origins of Hawaiian Reef Fishes (Hawaiian Fish Origins)

Program:

Indo-Pac Research Coordination Network (Indo-Pac RCN)

Principal Investigator:

Brian Bowen (University of Hawaiʻi at Mānoa, HIMB)

Contact:

Brian Bowen (University of Hawaiʻi at Mānoa, HIMB)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-12-18

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Reef Fish genetic accessions at NCBI Genbank from samples collected in the Indian Ocean, Pacific Ocean, and Red Sea from 2005 to 2015; related to 2016 publications

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Description

This dataset contains GenBank accession numbers for various genomic and mtDNA loci sequences from reef fish. The fish were sampled in multiple locations in the Indian Ocean, Pacific Ocean, and the Red Sea between 2005 to 2015.

These data were published in the data sections of the following publications:

Coleman, R.R., J.A. Eble, J.D. DiBattista, L.A. Rocha, J.E. Randall, M.L. Berumen, B.W. Bowen. 2016. Regal phylogeography: range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Molecular Phylogenetics and Evolution 100:243 – 253. doi: 10.1016/j.ympev.2016.04.005.

DiBattista J.D., J. Whitney, M.T. Craig, J.-P. A. Hobbs, L.A. Rocha, K.A. Feldheim, M.L. Berumen, B.W. Bowen. 2016. Surgeons and suture zones: hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes. Molecular Phylogenetics and Evolution 101:203 – 215. doi: 10.1016/j.ympev.2016.04.036.

DiBattista, J.D., M.R. Gaither, J.-P. A. Hobbs, L.A. Rocha, B.W. Bowen. 2016. Angelfishes, paper tigers, and the devilish taxonomy of the Centropyge flavissima complex. Journal of Heredity 107:647 – 653. doi: 10.1093/jhered/esw062.

Tenggardjaja, K. A., Bowen, B. W., & Bernardi, G. (2014). Vertical and horizontal genetic connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and adjacent Johnston Atoll. PLoS One, 9 (12), e115493. doi: 10.1371/journal.pone.0115493

Tenggardjaja, K.A., B.W. Bowen, G. Bernardi. 2016. Reef fish dispersal in the Hawaiian Archipelago: comparative phylogeography of three endemic damselfishes. Journal of Marine Biology: Article ID 3251814. doi: 10.1155/2016/3251814.

Methods & Sampling

Methodology: Various genomic and mtDNA loci were sequenced from reef fishes.

Sampling and analytical procedures: Samples were taken as fine clips, then sequenced and analyzed to detect population structure and evolutionary genetic divergences. Species were collected with scuba gear, nets, and spears.

Raw sequence data was aligned with GENEIOUS R6 (Biomatters, LTD, Auckland, NZ) or GENEIOUS v.8.0.3 (Gene Codes, Ann Arbor, MI, USA). Sequence analyses were performed with BEAST v.2.2.0 and ARLEQUIN v. 3.5.

For details of these analyses, see the references listed in the "Description" section of this page.

Data Processing Description

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* added columns for max/min latitude and longitudes for species collections
* added column with DOIs for the journal references
* modified dataset so each row contains one range of accessions.
* replaced commas in the data with semicolons to support .csv format of data

Data Files

File
accessions.csv (Comma Separated Values (.csv), 2.79 KB) MD5:070ce4578de1ad420a8f0e3c3e1da4f0 Primary data file for dataset ID 716806

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1558852

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: ABI 3730XL Genetic Analyzer

Supplied Description:

ABI 3730XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA)

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sequence_Description	Description of type of sequence	unitless	sample_descrip
Journal_Publication_DOI	Digital object identifier (DOI) for the journal publications these accessions were published in	untiless	reference_paper
Journal_Publications	Journal publications these accessions were published in	untiless	reference_paper
Genbank_First_Accession_Link	Link to the first accession in the accession range at National Center for Biotechnology Information (NCBI) Genbank	unitless	external_link
Collection_Location	Location species were collected	unitless	site
Collection_Max_Lat	Maximum species collection latitude	decimal degrees	lat
Collection_Max_Lon	Maximum species collection longitude	decimal degrees	lon
Collection_Min_Lat	Minimum species collection latitude	decimal degrees	lat
Collection_Min_Lon	Minimum species collection longitude	decimal degrees	lon
Species_Names	Name of species sampled	unitless	taxon
Genbank_Accession_Range	Range of accession numbers at National Center for Biotechnology Information (NCBI) Genbank	unitless	accession_number
Sequence_Analysis_Method	Sequence method and instrument	unitless	instrument

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Database

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Dataset: Hawaiian reef fish genetic accessions 2016