ERDDAP > info > bcodmo_dataset_788903

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data			files	public	Reef Fish genetic accession numbers at NCBI Genbank		I   M	background			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
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/788903
attribute	NC_GLOBAL	param_mapping	String	{'788903': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/788903/parameters
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.