http://lod.bco-dmo.org/id/dataset/688111
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
2017-04-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC project)
2017-04-21
publication
2017-04-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-28
publication
https://doi.org/10.26008/1912/bco-dmo.688111.1
Svetlana A. Maslakova
University of Oregon
principalInvestigator
Craig M. Young
University of Oregon
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: Maslakova, S. A., Young, C. (2021) DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-04-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.688111.1 [access date]
Bivalve larvae DNA barcode results Dataset Description: <p>This dataset&nbsp;provides the closest GenBank match for larval bivalve specimens resulting from DNA barcode sequencing, the percent match of the identification, and some information on the specimen collections.</p>
<p>NCBI GenBank accessions are not yet available&nbsp;[2017-04-21]. Please contact the PI for further information.</p>
<p><strong>Related datasets:</strong><br />
<a href="https://www.bco-dmo.org/dataset/659926" target="_blank">SEEPC</a><a href="https://www.bco-dmo.org/dataset/659926" target="_blank"> larval collections: MOCNESS</a><br />
<a href="http://www.bco-dmo.org/dataset/659965" target="_blank">SEEPC larval collections: SyPRID</a><br />
<a href="http://www.bco-dmo.org/dataset/659951">larval type codes</a></p> Methods and Sampling: <p>Bivalve larvae were collected either by MOCNESS or Sentry's SyPRID Sampler. The Multiple Opening and Closing Net Environmental Sensing System has 8 separate plankton nets which can be controlled from the ship, allowing for samples along discrete depth ranges. Sentry’s Precision Robotic Impeller Driven Sampler allows for the collection of larvae from just a few meters off the sea floor.&nbsp; DNA was extracted, purified, amplified, and sequenced using standard lab protocols and universal primers (except where indicated).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1030453 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1030453
completed
Svetlana A. Maslakova
University of Oregon
541-888-2581 X 309
P. O. Box 5389
Charleston
OR
97420
USA
svetlana@uoregon.edu
pointOfContact
Craig M. Young
University of Oregon
541-346-7274
Oregon Institute of Marine Biology P.O. Box 5389
Charleston
Oregon
97420
USA
cmyoung@uoregon.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
larva_id
larval_type
species
gene_id_pcent
cruise_id
date_collected
site
depth_range
date_extraction
comment
Applied Biosystems 3730xl DNA Analyzer
Bio-Rad C1000 Touch Thermal Cycler
theme
None, User defined
sample identification
sample description
species scientific name (binomial)
No BCO-DMO term
Cruise identfier
date
site
depth_range
comments
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
AUV Sentry
MOCNESS1
Thermal Cycler
instrument
BCO-DMO Standard Instruments
AT21-02
AT26-15
AT29-04
EN531
service
Deployment Activity
Barbados seeps, Intra-American Sea
Gulf of Mexico
Blake Ridge Diapir, Cape Fear Diapir, and United States Western Atlantic Margin
Blake Ridge, Cape Fear Diapir
place
Locations
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.
Connectivity in western Atlantic seep populations: Oceanographic and life-history processes underlying genetic structure
https://osprey.bco-dmo.org/project/2270
Connectivity in western Atlantic seep populations: Oceanographic and life-history processes underlying genetic structure
<p>This project will evaluate connectivity on spatial scales that match those at which vent systems are being studied (3500 km), with a set of nested seeps (within the Barbados system) within which connectivity can be explored at more local spatial scales (30 to 130 km), and with species that span depth (600 m to 3600 m) and geographic ranges (30 km to 3500 km) and that have diverse life-history characteristics. Five deep-sea seep systems in the Intra- American Sea (IAS) are targeted: Blake Ridge, Florida Escarpment, Alaminos Canyon, Brine Pool, Barbados (El Pilar, Orenoque A, Orenoque B). The primary objective is to advance our general knowledge of connectivity in the deep sea. The focus is on species and processes occurring in the IAS, with attention to oceanographic circulation, life histories, and genetics. Questions that apply in shallow-water systems motivate this study:</p>
<p>1. What phylogeographic breaks occur in the system? It is important to distinguish between phylogeographic history and connectivity. A phylogeographic break with no shared alleles between populations implies a long history of isolation or possibly cryptic speciation.</p>
<p>2. Are populations connected by ongoing migration? This is the fundamental question about connectivity and the scale of genetic variation in marine species with planktonic larvae.</p>
<p>3. What biophysical processes underlie observed connectivities? Biological processes (e.g., larval distributions in the water column, timing of reproduction, and planktonic larval duration) and physical processes of transport and dispersion interact to determine connectivity.</p>
<p>The oceanographic model for the IAS will be improved and coupled to a Lagrangian larval transport model. The field program includes time-series sampling of larvae at seeps with records of current velocities, water column sampling to determine larval distribution potential, shipboard studies of larval biology and behavior, and sampling of benthic target species. Phylogenetic and population genetic tools will be used to explore historical and contemporary gene flow. Iterative interactions among the science teams will advance our understanding of connectivity in the deep sea and to develop effective and best methods for hypothesis testing under the constraints of working in a relatively inaccessible environment. Since their discovery, deep-sea chemosynthetic ecosystems have been novel systems within which to test the generality of paradigms developed for shallow-water species. This study will explore scale-dependent biodiversity and recruitment dynamics in deep-sea seep communities, and will identify key factors underlying population persistence and maintenance of biodiversity in these patchy systems.</p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/SEEPC/AT29-04_Zambon_map.kmz" target="_blank">Google Earth map</a> showing positions of stations, CTD, XBT, multibeam locations (KMZ file dlownload)</p>
SEEPC
largerWorkCitation
project
eng; USA
biota
oceans
Barbados seeps, Intra-American Sea; Gulf of Mexico; Blake Ridge Diapir, Cape Fear Diapir, and United States Western Atlantic Margin; Blake Ridge, Cape Fear Diapir
-95
-58
11
37
2011-06-01
2015-07-27
Western Atlantic, Gulf of Mexico, Intra-American Sea
0
BCO-DMO catalogue of parameters from DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC 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
http://lod.bco-dmo.org/id/dataset-parameter/688133.rdf
Name: larva_id
Units: unitless
Description: <p>larval specimen identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/688134.rdf
Name: larval_type
Units: unitless
Description: <p>morphotype based on gross larval morphology; BV = Bivalve</p>
http://lod.bco-dmo.org/id/dataset-parameter/688135.rdf
Name: species
Units: unitless
Description: <p>closest species match to the tested sequence in GenBank</p>
http://lod.bco-dmo.org/id/dataset-parameter/688136.rdf
Name: gene_id_pcent
Units: percent
Description: <p>gene(s) tested and how closely it matched the GenBank sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/688137.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/688138.rdf
Name: date_collected
Units: unitless
Description: <p>date collected and preserved (formatted as yyyy-mm-dd)</p>
http://lod.bco-dmo.org/id/dataset-parameter/688139.rdf
Name: site
Units: unitless
Description: <p>collection site: BAP=Barbados Acretionary Prism; WAM=Western Atlantic Margin; GOM=Gulf of Mexico</p>
http://lod.bco-dmo.org/id/dataset-parameter/688140.rdf
Name: depth_range
Units: meters
Description: <p>range of depths in which the larva was collected (formatted as yyyy-mm-dd)</p>
http://lod.bco-dmo.org/id/dataset-parameter/688141.rdf
Name: date_extraction
Units: unitless
Description: <p>date the DNA was extracted; purified; and amplified for each larva</p>
http://lod.bco-dmo.org/id/dataset-parameter/688142.rdf
Name: comment
Units: unitless
Description: <p>overall results for each larva</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
31778
https://darchive.mblwhoilibrary.org/bitstream/1912/27183/1/dataset-688111_seepc-bivalve-dna-barcoding-results__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.688111.1
download
onLine
dataset
<p>Bivalve larvae were collected either by MOCNESS or Sentry's SyPRID Sampler. The Multiple Opening and Closing Net Environmental Sensing System has 8 separate plankton nets which can be controlled from the ship, allowing for samples along discrete depth ranges. Sentry’s Precision Robotic Impeller Driven Sampler allows for the collection of larvae from just a few meters off the sea floor.&nbsp; DNA was extracted, purified, amplified, and sequenced using standard lab protocols and universal primers (except where indicated).&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- renamed some parameters to BCO-DMO standard<br />
- replaced blanks, '?',&nbsp; '-' with 'nd' (no data)<br />
- reformatted date from m/d/yyyy to yyyy-mm-dd<br />
- removed 'm' from depth values<br />
- converted lat and lon to decimal degrees<br />
- removed or replaced special characters<br />
- added cruise_id and year columns</p>
<p>Version: 2017-02-13 [added EN531 collection data]<br />
Replaces version: 2016-09-30</p>
<p>&nbsp;</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
Applied Biosystems 3730xl DNA Analyzer
Applied Biosystems 3730xl DNA Analyzer
PI Supplied Instrument Name: Applied Biosystems 3730xl DNA Analyzer PI Supplied Instrument Description:The sequencing was done by Sequetech in California Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: PI Supplied Instrument Description:Fitted out with the SyPRID (Sentry’s Precision Robotic Impeller Driven) Sampler Instrument Name: AUV Sentry Instrument Short Name:AUV Sentry Instrument Description: The autonomous underwater vehicle (AUV) Sentry is a fully autonomous underwater vehicle capable of exploring the ocean down to 6,000 meters (19,685 feet) depth. Sentry builds on the success of its predecessor the ABE, with improved speed, range, and maneuverability.
Sentry's hydrodynamic shape also allows faster ascents and descents. Sentry carries a superior science sensor suite and an increased science payload enabling it to be used for both mid-water and near-seabed oceanographic investigations. Sentry produces bathymetric, sidescan, subbottom, and magnetic maps of the seafloor and is capable of taking digital bottom photographs in a variety of deep-sea terrains such as mid-ocean ridges, deep-sea vents, and cold seeps at ocean margins. Sentry is uniquely able to operate in extreme terrain, including volcano caldera and scarps. Sentry's navigation system uses a doppler velocity log and inertial navigation system, aided by acoustic navigation systems (USBL or LBL). The USBL system also provides acoustic communications, which can be used to obtain the vehicle state and sensor status as well as to retask the vehicle while on the bottom. In addition its standard sensors, Sentry has carried a variety of science-supplied sensors, including the Nakamura redox potential probe, ACFR 3-D imaging system, and the Tethys in-situ mass spectrometer.
Sentry can be used to locate and quantify hydrothermal fluxes. Sentry is also capable of a much wider range of oceanographic applications due to its superior sensing suite, increased speed and endurance, improved navigation, and acoustic communications. Sentry can be used as a stand alone vehicle or in tandem with Alvin or an ROV to increase the efficiency of deep-submergence investigations.
More information is available from the operator site at URL: https://ndsf.whoi.edu/sentry/
PI Supplied Instrument Name: PI Supplied Instrument Description:MOCNESS plankton system with 300 um mesh nets. Instrument Name: MOCNESS1 Instrument Short Name:MOC1 Instrument Description: The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
Bio-Rad C1000 Touch Thermal Cycler
Bio-Rad C1000 Touch Thermal Cycler
PI Supplied Instrument Name: Bio-Rad C1000 Touch Thermal Cycler Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: AT21-02
AT21-02
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT21-02
Cindy Van Dover
Duke University
http://dmoserv3.whoi.edu/data_docs/SEEPC/AT21-02_CruiseREPORT.pdf
Report describing AT21-02
Cruise: AT26-15
AT26-15
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT26-15
Cindy Van Dover
Duke University
Cruise: AT29-04
AT29-04
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT29-04
Cindy Van Dover
Duke University
http://dmoserv3.whoi.edu/data_docs/SEEPC/AT29-04_SeepC_cruise_report.pdf
Report describing AT29-04
Cruise: EN531
EN531
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN531
Ruoying He
North Carolina State University - Marine, Earth and Atmospheric Sciences
http://dmoserv3.whoi.edu/data_docs/SEEPC/Cruise.Report.EN531-08-14.2013.pdf
Report describing EN531
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel