Dataset: Reef fish NCBI genetic sequence accession numbers

Name: Reef fish NCBI genetic sequence accession numbers for sequences from reef fish specimens collected in the Indo-Pacific and Pacific Ocean
Published: 2020-09-07
Keywords: oceans

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Cite This Dataset

Project:

Origins of Hawaiian Reef Fishes (Hawaiian Fish Origins)

Program:

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

Principal Investigator:

Brian Bowen (University of Hawaii at Manoa, HIMB)

Contact:

Mykle Hoban (University of Hawaii at Manoa, HIMB)

BCO-DMO Data Manager:

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

Version:

Version Date:

2020-09-07

Restricted:

Validated:

Current State:

Data not available

Reef fish NCBI genetic sequence accession numbers for sequences from reef fish specimens collected in the Indo-Pacific and Pacific Ocean

Abstract:

This dataset contains NCBI GenBank accession numbers for sequences from reef fish specimens collected in the Indo-Pacific, Pacific Ocean. These results were published in Hoban & Williams, 2020.

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Methods & Sampling

Hoban & Williams (2020) is a phylogeographic survey and taxonomic species description. Specimens were collected throughout the Central Pacific using rotenone and hand nets and/or pole spears. Fin clips were taken for genetic analysis and whole specimens were retained for taxonomic analysis. Specimens were sequenced at the mitochondrial COI marker for phylogeographic and phylogenetic analyses.

Instruments: Specimens were collected on SCUBA using pole spears and/or hand nets and rotenone. DNA barcodes were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California).

Data Processing Description

DNA sequences were trimmed, edited, and aligned using Geneious R6. Phylogeographic and population analyses were conducted using a modified version of the R package pegas and the package poppr. We used PartitionFinder 2. Phylogenetic analyses were performed using MrBayes 3.2.7 and verified with Tracer v1.7.1. Trees were visualized in FigTree and figures were produced using the R package ggtree.

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 3130XL genetic analyzer

Supplied Description:

DNA barcodes were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California)

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.

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Database

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Dataset: Reef fish NCBI genetic sequence accession numbers