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Dataset Title:  Reef Fish genetic accession numbers at NCBI Genbank Subscribe RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_788903)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Files
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
   or a List of Values ?
   Maximum ?
 
 Species_Name (unitless) ?          "Abudefduf vaigiensis"    "Tosanoides annepat..."
 Sequence_Description (unitless) ?          "Glyceraldehyde-3-p..."    "mtDNA cytochrome b"
 Collection_Location (unitless) ?          "1341 22.74N 12050 ..."    "Multiple Indo-Paci..."
 Sequence_Analysis_Method (unitless) ?      
   - +  ?
 Journal_Publications (unitless) ?          "Arango et al. 2019"    "Wilcox et al. 2018"
 Journal_Publication_DOI (unitless) ?          "10.1007/s00227-018..."    "10.3897/zookeys.83..."
 Genbank_Accession_Range (unitless) ?          "BOLD Accession Num..."    "MH687779-MH687868"
 
Server-side Functions ?
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Species_Name {
    String bcodmo_name "species";
    String description "Species name";
    String long_name "Species Name";
    String units "unitless";
  }
  Sequence_Description {
    String bcodmo_name "sample_descrip";
    String description "Description of the type of sequence";
    String long_name "Sequence Description";
    String units "unitless";
  }
  Collection_Location {
    String bcodmo_name "site";
    String description "Locations where species were collected";
    String long_name "Collection Location";
    String units "unitless";
  }
  Sequence_Analysis_Method {
    String bcodmo_name "sample_descrip";
    String description "Sequencing and analysis methods";
    String long_name "Sequence Analysis Method";
    String units "unitless";
  }
  Journal_Publications {
    String bcodmo_name "reference_paper";
    String description "Relevant publications";
    String long_name "Journal Publications";
    String units "unitless";
  }
  Journal_Publication_DOI {
    String bcodmo_name "reference_paper";
    String description "DOI of the relevant publication";
    String long_name "Journal Publication DOI";
    String units "unitless";
  }
  Genbank_Accession_Range {
    String bcodmo_name "accession number";
    String description "Genbank Accession numbers";
    String long_name "Genbank Accession Range";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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).";
    String awards_0_award_nid "658944";
    String awards_0_award_number "OCE-1558852";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1558852";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Reef fish genetic accessions - 2019 
  PI: Brian Bowen (University of Hawaii) 
  Version date: 29-Jan-2020";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2020-01-29T21:23:01Z";
    String date_modified "2020-02-25T21:17:42Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.788903.1";
    String history 
"2020-08-13T17:58:54Z (local files)
2020-08-13T17:58:54Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_788903.html";
    String infoUrl "https://www.bco-dmo.org/dataset/788903";
    String institution "BCO-DMO";
    String instruments_0_acronym "Automated Sequencer";
    String instruments_0_dataset_instrument_description "DNA barcodes (COI) were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California).";
    String instruments_0_dataset_instrument_nid "788940";
    String instruments_0_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.";
    String instruments_0_instrument_name "Automated DNA Sequencer";
    String instruments_0_instrument_nid "649";
    String instruments_0_supplied_name "ABI 3130XL";
    String instruments_1_acronym "Hand Net";
    String instruments_1_dataset_instrument_description "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.";
    String instruments_1_dataset_instrument_nid "788939";
    String instruments_1_description "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.";
    String instruments_1_instrument_name "Hand Net";
    String instruments_1_instrument_nid "682469";
    String instruments_2_acronym "SCUBA";
    String instruments_2_dataset_instrument_description "Wilcox et al. (2018) and Tenggardjaja et al. (2018) used conventional SCUBA to capture specimens with hand nets and pole spears.";
    String instruments_2_dataset_instrument_nid "788941";
    String instruments_2_description 
"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";
    String instruments_2_instrument_name "Self-Contained Underwater Breathing Apparatus";
    String instruments_2_instrument_nid "713363";
    String instruments_2_supplied_name "SCUBA";
    String keywords "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";
    String license "https://www.bco-dmo.org/dataset/788903/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/788903";
    String param_mapping "{'788903': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/788903/parameters";
    String people_0_affiliation "University of Hawaii at Manoa";
    String people_0_affiliation_acronym "HIMB";
    String people_0_person_name "Brian Bowen";
    String people_0_person_nid "552882";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI BCO-DMO";
    String people_1_person_name "Shannon Rauch";
    String people_1_person_nid "51498";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "Hawaiian Fish Origins";
    String projects_0_acronym "Hawaiian Fish Origins";
    String projects_0_description 
"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.";
    String projects_0_end_date "2019-03";
    String projects_0_geolocation "Central and West Pacific Ocean";
    String projects_0_name "Origins of Hawaiian Reef Fishes";
    String projects_0_project_nid "635745";
    String projects_0_start_date "2016-04";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "Sequence_Analysis_Method";
    String summary "Reef Fish genetic accession numbers at NCBI Genbank.";
    String title "Reef Fish genetic accession numbers at NCBI Genbank";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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