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Title Sum-
Institution Dataset ID
   set  data        files  public Reef Fish genetic accession numbers at NCBI Genbank    ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_788903

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Arango et al. (2018) and Pyle et al. (2018) collectively describe 4 new
species, three damselfish and a basslet. Specimens were collected with hand
nets during deep dives using mixed-gas, closed-circuit rebreathers, and
brought to the surface alive with the aid of a hypodermic needle to vent gas
from the swim bladders. Methods for morphometric counts and measurements
follow standard procedures as detailed in Pyle et al. (2016; Zookeys 641:165).
DNA barcodes (COI) were produced with an ABI 3130XL genetic analyzer (Applied
Biosystems, Foster City, California) at the Hawai'i Institute of Marine
Biology EPSCoR Sequencing Facility.

Wilcox et al. (2018) and Tenggardjaja et al. (2018) are phylogeographic
surveys. Fish fin clips were collected on shallow reefs with conventional
SCUBA, using hand nets and pole spears. Tissue samples were preserved in salt-
saturated DMSO buffer. Various mitochondrial and nuclear loci were sequenced
for phylogeographic analyses. Collection data for Wilcox et al., including
lat-long information, is provided in Table S2 (see Supplemental Files below).
Locations for samples in Tenggardjaja et al. are limited to island sites (no
lat-long available). See paper\u00a0cited below for details.

In all cases the DNA sequences were aligned, edited and trimmed to a common
length using Geneious Pro DNA analysis software (v.5.6.6 and v.6.2; Kearse et
al. 2012; Bioinformatics 28: 1647\u20131649). Maximum Likelihood, Neighbor-
Joining, and Maximum Parsimony tree-building methods were implemented using
Mega v.5.2.2, and all sequences are available in GenBank. Where appropriate,
population genetic parameters were calculated with ARLEQUIN 3.5 (Excoffier and
Lischer 2010; Mol Ecol Resour 10:564\u2013567).
attribute NC_GLOBAL awards_0_award_nid String 658944
attribute NC_GLOBAL awards_0_award_number String OCE-1558852
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1558852 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Reef fish genetic accessions - 2019
PI: Brian Bowen (University of Hawaii)
Version date: 29-Jan-2020
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2020-01-29T21:23:01Z
attribute NC_GLOBAL date_modified String 2020-02-25T21:17:42Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.788903.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/788903 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String DNA barcodes (COI) were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 788940
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String ABI 3130XL
attribute NC_GLOBAL instruments_1_acronym String Hand Net
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Arango et al. (2018) and Pyle et al. (2018) used closed-circuit rebreather technology to access reefs and used hand nets to collect specimens. Wilcox et al. (2018) and Tenggardjaja et al. (2018) used conventional SCUBA to capture specimens with hand nets and pole spears.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 788939
attribute NC_GLOBAL instruments_1_description String A hand net (also called a scoop net or dip net) is a net or mesh basket held open by a hoop. They are used for scooping fish near the surface of the water.
attribute NC_GLOBAL instruments_1_instrument_name String Hand Net
attribute NC_GLOBAL instruments_1_instrument_nid String 682469
attribute NC_GLOBAL instruments_2_acronym String SCUBA
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Wilcox et al. (2018) and Tenggardjaja et al. (2018) used conventional SCUBA to capture specimens with hand nets and pole spears.
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 788941
attribute NC_GLOBAL instruments_2_description String The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.

Reference: http://oceanexplorer.noaa.gov/technology/diving/diving.html
attribute NC_GLOBAL instruments_2_instrument_name String Self-Contained Underwater Breathing Apparatus
attribute NC_GLOBAL instruments_2_instrument_nid String 713363
attribute NC_GLOBAL instruments_2_supplied_name String SCUBA
attribute NC_GLOBAL keywords String accession, analysis, bco, bco-dmo, biological, chemical, collection, Collection_Location, data, dataset, description, dmo, doi, erddap, genbank, Genbank_Accession_Range, journal, Journal_Publication_DOI, Journal_Publications, management, method, name, oceanography, office, preliminary, publication, publications, range, sequence, Sequence_Analysis_Method, Sequence_Description, species, Species_Name
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/788903/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/788903 (external link)
attribute NC_GLOBAL param_mapping String {'788903': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/788903/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Hawaii at Manoa
attribute NC_GLOBAL people_0_affiliation_acronym String HIMB
attribute NC_GLOBAL people_0_person_name String Brian Bowen
attribute NC_GLOBAL people_0_person_nid String 552882
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Shannon Rauch
attribute NC_GLOBAL people_1_person_nid String 51498
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Hawaiian Fish Origins
attribute NC_GLOBAL projects_0_acronym String Hawaiian Fish Origins
attribute NC_GLOBAL projects_0_description String Project summary:
This research is designed to resolve the origins of Hawaiian reef fishes. All living inhabitants of the Hawaiian archipelago necessarily originate elsewhere, due to the volcanic history of the island arc. Hawaii also has the highest endemism (native species) in the Pacific, with 25% of the 625 near-shore fish species found nowhere else. Where did these fishes come from? Two prominent hypotheses regarding the origins of Hawaiian marine species maintain that colonists arrive either from the south (via the Line Islands and Johnston Atoll) or from the west (via Japan). Previous research has shown that Hawaiian endemic limpets (genus Cellana) colonized from Japan (Bird et al. 2011 Mol. Ecol. 20:2128 – 2141). Andrews et al. (2014; PLoS One 9: e91665) report evidence for a colonization pathway from the south (Johnston Atoll) to the middle of the archipelago in the Papahanaumokuakea Marine National Monument (PMNM). In this project, we will sample locations to the south of Hawaii (Johnston and Line Islands) and to the west of Hawaii (Ogasawara and Ryukyu Islands) for a suite of 20 reef fishes in order to resolve the origins of Hawaiian biodiversity.  Advanced rebreather technology allows dives with longer bottom time and more efficient sample collection, and our program is pioneering the applications of this advance diving technology. To test alternate hypotheses in the lab, we will employ both population genetics (shifts in genotype frequencies) and phylogenetics (DNA sequence divergence) for more ancient separations. Restriction-digest associated DNA sequencing (RAD-seq) is the best method for studies of phylogeography, phylogenetics, and population biology because it provides high coverage of homologous portions of the genome from multiple individuals for comparatively low cost and effort. We use the ezRAD approach developed in the shared Bowen-Toonen Lab.
Description from NSF award abstract:
The Hawaiian Islands are the product of a volcanic hot spot in the middle of the North Pacific. Hence every living thing on this isolated archipelago has origins elsewhere. This project will investigate the origins of Hawaiian reef fishes, which are important both as a food source and a cultural touchstone in native Hawaiian communities. Two prominent hypotheses maintain that marine fish originally arrived from the south (Line Islands and Johnston Atoll) or from the west (Japan). To test these hypotheses, this research will augment existing specimens from Hawaii with expeditions to Johnston Atoll (closest shallow habitat to the south), the northern Line Islands (Palmyra), southern Line Islands (Christmas Island), and Ryukyu Islands and Ogasawara Islands in Japan. Advanced genetic techniques will be used to resolve the closest relatives to the Hawaiian fish species and the pathways by which reef species colonize Hawaii and help establish patterns of biodiversity. In cases where Hawaiian species are closely related to widespread sister species, this project will detect hotspots of genetic divergence. Because this research will reveal the sources of Hawaiian marine biodiversity, results can be used to help define priorities for reef protection. The project will support two graduate students and train at least two more in all aspects of the project from rebreather diving, specimen collection and curation, information management, and advanced genetic techniques. There will be outreach efforts to schools through existing programs, and expedition teams will include a videographer to provide footage for the award-winning Voice of the Sea program, broadcast locally. Expeditions will also include an outreach specialist to handle media reports and promote awareness and concern for reefs in the communities surrounding study sites. 
The investigators will sample a suite of 20 reef fishes at locations to the south (Johnston and Line Islands) and west (Ogasawara and Ryukyu Islands) of Hawaii to resolve the origins of Hawaiian biodiversity. The investigators will employ both population genetics (shifts in genotype frequencies) and phylogenetics (DNA sequence divergence) for more ancient separations to test their hypotheses. Restriction-digest associated DNA sequencing (RAD-seq) will be employed for the phylogeography, phylogenetics, and population biology studies because it provides high coverage of homologous portions of the genome from multiple individuals for comparatively low cost and effort.
attribute NC_GLOBAL projects_0_end_date String 2019-03
attribute NC_GLOBAL projects_0_geolocation String Central and West Pacific Ocean
attribute NC_GLOBAL projects_0_name String Origins of Hawaiian Reef Fishes
attribute NC_GLOBAL projects_0_project_nid String 635745
attribute NC_GLOBAL projects_0_start_date String 2016-04
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String Sequence_Analysis_Method
attribute NC_GLOBAL summary String Reef Fish genetic accession numbers at NCBI Genbank.
attribute NC_GLOBAL title String Reef Fish genetic accession numbers at NCBI Genbank
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Species_Name   String  
attribute Species_Name bcodmo_name String species
attribute Species_Name description String Species name
attribute Species_Name long_name String Species Name
attribute Species_Name units String unitless
variable Sequence_Description   String  
attribute Sequence_Description bcodmo_name String sample_descrip
attribute Sequence_Description description String Description of the type of sequence
attribute Sequence_Description long_name String Sequence Description
attribute Sequence_Description units String unitless
variable Collection_Location   String  
attribute Collection_Location bcodmo_name String site
attribute Collection_Location description String Locations where species were collected
attribute Collection_Location long_name String Collection Location
attribute Collection_Location units String unitless
variable Sequence_Analysis_Method   String  
attribute Sequence_Analysis_Method bcodmo_name String sample_descrip
attribute Sequence_Analysis_Method description String Sequencing and analysis methods
attribute Sequence_Analysis_Method long_name String Sequence Analysis Method
attribute Sequence_Analysis_Method units String unitless
variable Journal_Publications   String  
attribute Journal_Publications bcodmo_name String reference_paper
attribute Journal_Publications description String Relevant publications
attribute Journal_Publications long_name String Journal Publications
attribute Journal_Publications units String unitless
variable Journal_Publication_DOI   String  
attribute Journal_Publication_DOI bcodmo_name String reference_paper
attribute Journal_Publication_DOI description String DOI of the relevant publication
attribute Journal_Publication_DOI long_name String Journal Publication DOI
attribute Journal_Publication_DOI units String unitless
variable Genbank_Accession_Range   String  
attribute Genbank_Accession_Range bcodmo_name String accession number
attribute Genbank_Accession_Range description String Genbank Accession numbers
attribute Genbank_Accession_Range long_name String Genbank Accession Range
attribute Genbank_Accession_Range units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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