http://lod.bco-dmo.org/id/dataset/788903
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2020-01-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Reef Fish genetic accession numbers at NCBI Genbank
2020-01-29
publication
2020-01-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-02-25
publication
https://doi.org/10.1575/1912/bco-dmo.788903.1
Brian Bowen
University of Hawaii at Manoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Bowen, B. (2020) Reef Fish genetic accession numbers at NCBI Genbank. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-01-29 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.788903.1 [access date]
Hawaiian Reef Fish Genetic Accessions Dataset Description: Methods and Sampling: <p>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.</p>
<p>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&nbsp;cited below for details.</p>
<p>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: 1647–1649). 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 10:564–567).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558852 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1558852
completed
Brian Bowen
University of Hawaii at Manoa
808-236-7426
Hawaii Institute of Marine Biology 46-007 Lilipuna Road
Kaneohe
HI
96744
USA
bbowen@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Species_Name
Sequence_Description
Collection_Location
Sequence_Analysis_Method
Journal_Publications
Journal_Publication_DOI
Genbank_Accession_Range
ABI 3130XL
SCUBA
theme
None, User defined
species
sample description
site
reference_paper
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Hand Net
Self-Contained Underwater Breathing Apparatus
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Indo-Pac Research Coordination Network
https://indopacificnetwork.wikispaces.com/
Indo-Pac Research Coordination Network
Description from NSF award abstract:
The objective of this Research Coordination Network project is to develop an international network of researchers who use genetic methodologies to study the ecology and evolution of marine organisms in the Indo-Pacific to share data, ideas and methods. The tropical Indian and Pacific Oceans encompass the largest biogeographic region on the planet, the Indo-Pacific. It spans over half of the Earth's circumference and includes the exclusive economic zones of over 50 nations and territories. The Indo-Pacific is also home to our world's most diverse marine environments. The enormity and diversity of the Indo-Pacific poses tremendous logistical, political and financial obstacles to individual researchers and laboratories attempting to study the marine biology of the region. Genetic methods can provide invaluable information for our understanding of processes ranging from individual dispersal to the composition and assembly of entire marine communities.
The project will:
(1) assemble a unique, open access database of population genetic data and associated metadata that is compatible with the developing genomic and biological diversity standards for data archiving,
(2) facilitate open communication and collaboration among researchers from across the region through international workshops, virtual communication and a collaborative website,
(3) promote training in the use of genetic methodologies in ecology and evolution for researchers from developing countries through these same venues, and
(4) use the assembled database to address fundamental questions about the evolution of species and the reservoirs of genetic diversity in the Indo-Pacific.
The network will provide a model for international collaborative networks and genetic databasing in biodiversity research that extends beyond the results of this Research Coordination Network effort.
Indo-Pac RCN
largerWorkCitation
program
Origins of Hawaiian Reef Fishes
https://www.bco-dmo.org/project/635745
Origins of Hawaiian Reef Fishes
<p><em>Project summary:</em><br />
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 <em>Cellana</em>) 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.</p>
<p><strong>Description from NSF award abstract:</strong><br />
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. </p>
<p>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.</p>
Hawaiian Fish Origins
largerWorkCitation
project
eng; USA
oceans
2020-01-29
Central and West Pacific Ocean
0
BCO-DMO catalogue of parameters from Reef Fish genetic accession numbers at NCBI Genbank
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/788954.rdf
Name: Species_Name
Units: unitless
Description: Species name
http://lod.bco-dmo.org/id/dataset-parameter/788955.rdf
Name: Sequence_Description
Units: unitless
Description: Description of the type of sequence
http://lod.bco-dmo.org/id/dataset-parameter/788956.rdf
Name: Collection_Location
Units: unitless
Description: Locations where species were collected
http://lod.bco-dmo.org/id/dataset-parameter/788957.rdf
Name: Sequence_Analysis_Method
Units: unitless
Description: Sequencing and analysis methods
http://lod.bco-dmo.org/id/dataset-parameter/788958.rdf
Name: Journal_Publications
Units: unitless
Description: Relevant publications
http://lod.bco-dmo.org/id/dataset-parameter/788959.rdf
Name: Journal_Publication_DOI
Units: unitless
Description: DOI of the relevant publication
http://lod.bco-dmo.org/id/dataset-parameter/788960.rdf
Name: Genbank_Accession_Range
Units: unitless
Description: Genbank Accession numbers
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2401
https://darchive.mblwhoilibrary.org/bitstream/1912/25433/1/dataset-788903_reef-fish-genetic-accessions-2019__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.788903.1
download
onLine
dataset
<p>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.</p>
<p>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&nbsp;cited below for details.</p>
<p>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: 1647–1649). 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 10:564–567).</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ABI 3130XL
ABI 3130XL
PI Supplied Instrument Name: ABI 3130XL PI Supplied Instrument Description:DNA barcodes (COI) were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California). Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument 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.
PI Supplied Instrument Name: PI Supplied 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. Instrument Name: Hand Net Instrument Short Name:Hand Net Instrument 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.
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:Wilcox et al. (2018) and Tenggardjaja et al. (2018) used conventional SCUBA to capture specimens with hand nets and pole spears. Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument 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