http://lod.bco-dmo.org/id/dataset/873427
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
2022-04-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Genetic sequence identifiers for Etelis samples collected in the Indo-Pacific Ocean between 1997 and 2012
2022-04-21
publication
2022-04-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-05-10
publication
https://doi.org/10.26008/1912/bco-dmo.873427.1
Brian Bowen
University of Hawai'i
principalInvestigator
Kimberly R. Andrews
University of Hawai'i
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., Andrews, K. R. (2022) Genetic sequence identifiers for Etelis samples collected in the Indo-Pacific Ocean between 1997 and 2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-04-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.873427.1 [access date]
Methods and Sampling: <p>The holotype was purchased at Yanbu fish market after being collected by hook and line in a nearby area and was deposited at the National Museum of Marine Biology &amp; Aquarium (NMMB-P). Fifteen paratypes were obtained from Western Australia and deposited at the fish collection of California Academy of Sciences, San Francisco (CAS). These paratypes were part of a previous study using morphological and genetic data which revealed that two morphologically similar species were being identified as <em>E. carbunculus</em>, leading the authors to propose an undescribed species of<em>&nbsp;Etelis</em>&nbsp;(Andrews<em>&nbsp;et al.</em>&nbsp;2016). That study generated DNA sequence data from cytochrome <em>b</em>&nbsp;(cyt<em>b</em>) for the paratypes, and the sequences have been deposited in GenBank (Accession numbers MW151867- MW151881).&nbsp;See "Related Datasets" for links to the NCBI Popsets that contain these sequences.</p>
<p>&nbsp;[See Related Dataset "Etelis morphology"&nbsp;<span style="font-size:13px">https://www.bco-dmo.org/dataset/873174</span> for m<span style="font-size:13px">orphological measurements, meristics for the Etelis samples. </span>&nbsp;The column "Field_ID" can be used to relate the Etelis genetics and Etelis morphology datasets.<span style="font-size:13px">]</span></p>
<p>DNA sequences from cyt<em>b</em>&nbsp;and cytochrome oxidase I (COI) were obtained from the <em>E. boweni</em>&nbsp;holotype and four <em>E. radiosus</em>&nbsp;specimens from the Yanbu fish market using previously described protocols (Andrews <em>et al.</em>&nbsp;2016). The sequences were aligned with sequences used in phylogenetic analyses in Andrews <em>et al.</em>&nbsp;2016, including cyt<em>b</em>&nbsp;and COI sequences from six <em>E. boweni</em>&nbsp;and six <em>E. carbunculus</em>&nbsp;specimens collected across the Indo-Pacific, along with sequences from all other recognized <em>Etelis</em>&nbsp;species (six <em>E. coruscans</em>&nbsp;specimens, seven <em>E. radiosus</em>&nbsp;specimens, five <em>E. oculatus</em>&nbsp;specimens), and one specimen from each of two outgroups (<em>Pristipomoides filamentosus</em>&nbsp;and <em>Aphareus rutilans</em>). All sequences were then trimmed to a common length for each locus, for a total of 375 bp for cyt<em>b</em>&nbsp;and 599 bp for COI.<br />
<br />
Location: Indo-Pacific<br />
<br />
<span style="font-size:13px">Species List:</span></p>
<div><span style="font-size:13px">ScientificName,AphiaID,LSID</span></div>
<div><span style="font-size:13px">Aphareus rutilans,218468,urn:lsid:marinespecies.org:taxname:218468</span></div>
<div><span style="font-size:13px">Etelis boweni,1536489,urn:lsid:marinespecies.org:taxname:1536489</span></div>
<div><span style="font-size:13px">Etelis carbunculus,212545,urn:lsid:marinespecies.org:taxname:212545</span></div>
<div><span style="font-size:13px">Etelis coruscans,212544,urn:lsid:marinespecies.org:taxname:212544</span></div>
<div><span style="font-size:13px">Etelis oculatus,159789,urn:lsid:marinespecies.org:taxname:159789</span></div>
<div><span style="font-size:13px">Etelis radiosus,276518,urn:lsid:marinespecies.org:taxname:276518</span></div>
<div><span style="font-size:13px">Pristipomoides filamentosus,218511,urn:lsid:marinespecies.org:taxname:218511</span></div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558852 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1558852
completed
Brian Bowen
University of Hawai'i
808-236-7426
Hawaii Institute of Marine Biology 46-007 Lilipuna Road
Kaneohe
HI
96744
USA
bbowen@hawaii.edu
pointOfContact
Kimberly R. Andrews
University of Hawai'i
kimberlya@uidaho.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Field_ID
Species
Status
Sample_Location
cytb
COI
Reference
theme
None, User defined
sample identification
species
sample description
site
NCBI Genbank nucleotide accession
reference_paper
featureType
BCO-DMO Standard Parameters
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://osprey.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
29.8892
-120.1551564
-35
32
1997-01-01
2012-01-01
Central and West Pacific Ocean
0
BCO-DMO catalogue of parameters from Genetic sequence identifiers for Etelis samples collected in the Indo-Pacific Ocean between 1997 and 2012
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/873476.rdf
Name: Field_ID
Units: unitless
Description: <p>Field ID: sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/873477.rdf
Name: Species
Units: unitless
Description: <p>Species (Genus species)</p>
http://lod.bco-dmo.org/id/dataset-parameter/873478.rdf
Name: Status
Units: unitless
Description: <p>Status: specimen status</p>
http://lod.bco-dmo.org/id/dataset-parameter/873479.rdf
Name: Sample_Location
Units: unitless
Description: <p>Sample location</p>
http://lod.bco-dmo.org/id/dataset-parameter/873480.rdf
Name: cytb
Units: unitless
Description: <p>cytb: NCBI GenBank accession number for cytochrome b sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/873481.rdf
Name: COI
Units: unitless
Description: <p>COI: NCBI GenBank accession number for cytochrome oxidase I sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/873482.rdf
Name: Reference
Units: unitless
Description: <p>Reference: specimen citation</p>
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
4959
https://darchive.mblwhoilibrary.org/bitstream/1912/28668/1/dataset-873427_etelis-genetics__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.873427.1
download
onLine
dataset
<p>The holotype was purchased at Yanbu fish market after being collected by hook and line in a nearby area and was deposited at the National Museum of Marine Biology &amp; Aquarium (NMMB-P). Fifteen paratypes were obtained from Western Australia and deposited at the fish collection of California Academy of Sciences, San Francisco (CAS). These paratypes were part of a previous study using morphological and genetic data which revealed that two morphologically similar species were being identified as <em>E. carbunculus</em>, leading the authors to propose an undescribed species of<em>&nbsp;Etelis</em>&nbsp;(Andrews<em>&nbsp;et al.</em>&nbsp;2016). That study generated DNA sequence data from cytochrome <em>b</em>&nbsp;(cyt<em>b</em>) for the paratypes, and the sequences have been deposited in GenBank (Accession numbers MW151867- MW151881).&nbsp;See "Related Datasets" for links to the NCBI Popsets that contain these sequences.</p>
<p>&nbsp;[See Related Dataset "Etelis morphology"&nbsp;<span style="font-size:13px">https://www.bco-dmo.org/dataset/873174</span> for m<span style="font-size:13px">orphological measurements, meristics for the Etelis samples. </span>&nbsp;The column "Field_ID" can be used to relate the Etelis genetics and Etelis morphology datasets.<span style="font-size:13px">]</span></p>
<p>DNA sequences from cyt<em>b</em>&nbsp;and cytochrome oxidase I (COI) were obtained from the <em>E. boweni</em>&nbsp;holotype and four <em>E. radiosus</em>&nbsp;specimens from the Yanbu fish market using previously described protocols (Andrews <em>et al.</em>&nbsp;2016). The sequences were aligned with sequences used in phylogenetic analyses in Andrews <em>et al.</em>&nbsp;2016, including cyt<em>b</em>&nbsp;and COI sequences from six <em>E. boweni</em>&nbsp;and six <em>E. carbunculus</em>&nbsp;specimens collected across the Indo-Pacific, along with sequences from all other recognized <em>Etelis</em>&nbsp;species (six <em>E. coruscans</em>&nbsp;specimens, seven <em>E. radiosus</em>&nbsp;specimens, five <em>E. oculatus</em>&nbsp;specimens), and one specimen from each of two outgroups (<em>Pristipomoides filamentosus</em>&nbsp;and <em>Aphareus rutilans</em>). All sequences were then trimmed to a common length for each locus, for a total of 375 bp for cyt<em>b</em>&nbsp;and 599 bp for COI.<br />
<br />
Location: Indo-Pacific<br />
<br />
<span style="font-size:13px">Species List:</span></p>
<div><span style="font-size:13px">ScientificName,AphiaID,LSID</span></div>
<div><span style="font-size:13px">Aphareus rutilans,218468,urn:lsid:marinespecies.org:taxname:218468</span></div>
<div><span style="font-size:13px">Etelis boweni,1536489,urn:lsid:marinespecies.org:taxname:1536489</span></div>
<div><span style="font-size:13px">Etelis carbunculus,212545,urn:lsid:marinespecies.org:taxname:212545</span></div>
<div><span style="font-size:13px">Etelis coruscans,212544,urn:lsid:marinespecies.org:taxname:212544</span></div>
<div><span style="font-size:13px">Etelis oculatus,159789,urn:lsid:marinespecies.org:taxname:159789</span></div>
<div><span style="font-size:13px">Etelis radiosus,276518,urn:lsid:marinespecies.org:taxname:276518</span></div>
<div><span style="font-size:13px">Pristipomoides filamentosus,218511,urn:lsid:marinespecies.org:taxname:218511</span></div>
Specified by the Principal Investigator(s)
<p>Maximum likelihood phylogenetic analysis was conducted with concatenated cyt<em>b</em>&nbsp;and COI sequences using the GTR-GAMMA model in RAxML (Stamatakis 2014) with sequence data partitioned by locus, and parameters and rates allowed to vary between partitions. We first conducted 50 maximum likelihood searches with distinct starting trees, and then performed 1,000 bootstrap replicates on the best-scoring tree. Sequence data generated for this study were deposited in GenBank (accession numbers MW138043- MW138047, MW151862- MW151866).<br />
<br />
<span style="font-size:13px">BCO-DMO Data Manager Processing Notes:</span></p>
<div><span style="font-size:13px">* Exact locations for these samples are not available due to fish market acquisition. The region is known ("Indo-Pacific").&nbsp; Bounding box coordinates were calculated in python using the multipolygon from marineregions.org (&nbsp;MRID:&nbsp;14289).</span></div>
<div><span style="font-size:13px">* A unique list of scientific names in this dataset were matched using the World Register of Marine Species taxa match tool.&nbsp; &nbsp;All names exactly matched the accepted synonym of a species name on 2022-04-22.<br />
* location names delimited with a column in the data changed to semicolon-delimited (for csv support).</span><br />
&nbsp;</div>
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