http://lod.bco-dmo.org/id/dataset/671927
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
2016-12-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sea spider Pallenopsis sampling sites and COI NCBI accessions from Table 1, Harder et al (2016) Polar Biology (Antarctic Inverts project)
2016-12-02
publication
2016-12-02
revision
BCO-DMO Linked Data URI
2016-12-02
creation
http://lod.bco-dmo.org/id/dataset/671927
Andrew Mahon
Central Michigan University
principalInvestigator
Kenneth M. Halanych
Auburn University
principalInvestigator
Scott Santos
Auburn University
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: Mahon, A., Halanych, K. M., Santos, S. (2016) Sea spider Pallenopsis sampling sites and COI NCBI accessions from Table 1, Harder et al (2016) Polar Biology (Antarctic Inverts project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-12-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/671927 [access date]
Sea spider Pallenopsis sampling sites and COI NCBI accessions Dataset Description: <p>This dataset was published as Table 1 from Harder et al (2016). It contains collection information and GenBank COI accession links for sea spider of the genus specimens Pallenopsis from the Southern Ocean and around the southern tip of S. America.</p>
<p><strong>Related Reference:</strong> Harder, A.M., K.M. Halanych and A.R. Mahon. Diversity and distribution within the sea spider genus Pallenopsis (Chelicerata: Pycnogonida) in the Western Antarctic as revealed by mitochondrial DNA. Polar Biol (2016) 39:677-688. DOI 10.1007/s00300-015-1823-8.</p> Methods and Sampling: <p>From Harder et al (2016):</p>
<p><em><strong>Sample collection</strong><br />
Samples were collected in 2006 and 2012-2013 aboard the RVIB Nathaniel B. Palmer and the ASRV Laurence M. Gould. Pycnogonids were obtained using a Blake trawl or epibenthic&nbsp;</em><em>sled,</em><em> and subsequently identified to genus level prior to preservation and shipment in ~95 % ethanol. Individuals were identified to species level according to standard pycnogonid taxonomic procedures (Child 1995; Weis and Melzer 2012b; Weis et al. 2014). In total, 64 specimens belonging to the genus </em><em>Pallenopsis</em><em> were collected and identified from 21 sampling sites, ranging from 53 16'S to 76 59'S and from 140 26'E to 37 26'W (Fig. 1). Sampling site locality information, including depth (when available), and GenBank accession numbers for all sequences generated for use in our analyses are provided in Table 1.</em></p>
<p><em><strong>Molecular techniques</strong><br />
A tissue sample was taken from each individual as a 1-cm piece from the first tibial segment, and DNA was extracted from these using a Qiagen DNeasy Blood &amp; Tissue Kit (Qiagen Inc., Valencia, CA) per manufacturer’s instructions. A ~650 bp portion of the cytochrome c oxidase subunit I (COI) gene was amplified using LCO-1490 (Folmer et al. 1994) and HCOoutout (Prendini et al. 2005). Each PCR mixture consisted of 1x PCR buffer, 0.75 U Taq DNA polymerase (5 PRIME Inc., Gaithersburg, MD), 2.5 mM Mg^+2, 10 nmol of each dNTP, 1 ul of template DNA, 0.5 uM of each primer, and water to 25 ul. The PCR cycling program began with an incubation at 94C for 2 min, followed by 38 cycles of 94C for 20 s, 46C for 30 s, and 65 C for 80 s, and concluded with a final extension at 65C for 7 min. Successful amplification was confirmed by visualizing PCR products on a 1% agarose gel stained with ethidium bromide. Target DNA was gel extracted and purified using a Qiagen QIAquick Gel Extraction Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s recommendations. Bidirectional Sanger sequencing of amplicons was performed at</em><em>High Throughput</em><em> Genomics Center (Seattle, WA). Obtained sequences were assembled and screened using Sequencher version 5.29 sequence analysis software (Gene Codes Corporation, Ann Arbor, MI), and aligned using Clustal W v1.8 (Thompson et al. 1994) in BioEdit v7.2.5 (Hall 1999). COI sequences were translated into amino acid sequences to further screen for sequencing error, including checking for frameshift mutations and stop codons.</em></p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1043745 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1043745
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1043670 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1043670
onGoing
Andrew Mahon
Central Michigan University
989-774-6777
Office of Research & Graduate St
Mount Pleasant
MI
48859-0001
USA
mahon2a@cmich.edu
pointOfContact
Kenneth M. Halanych
Auburn University
334-844-3222
101 Life Sciences Building Department of Biological Sciences, Auburn University
Auburn
AL
36849
USA
ken@auburn.edu
pointOfContact
Scott Santos
Auburn University
(334) 844-4830
101 Rouse Life Sciences
Auburn
AL
36849
santos@auburn.edu
pointOfContact
asNeeded
Unknown
species
lat
lon
locality_source
depth
GenBank_accession
accession_link
Blake trawl
theme
None, User defined
species
latitude
longitude
region
depth
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Beam Trawl
Epibenthic Sled
Thermal Cycler
instrument
BCO-DMO Standard Instruments
LMG1312
NBP1210
service
Deployment Activity
Western Antarctic
Ross Sea
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.
Genetic connectivity and biogeographic patterns of Antarctic benthic invertebrates
https://osprey.bco-dmo.org/project/665837
Genetic connectivity and biogeographic patterns of Antarctic benthic invertebrates
<p><em>Extracted from the NSF award abstract:</em></p>
<p>The research will explore the genetics, diversity, and biogeography of Antarctic marine benthic invertebrates, seeking to overturn the widely accepted suggestion that benthic fauna do not constitute a large, panmictic population. The investigators will sample adults and larvae from undersampled regions of West Antarctica that, combined with existing samples, will provide significant coverage of the western hemisphere of the Southern Ocean. The objectives are: 1) To assess the degree of genetic connectivity (or isolation) of benthic invertebrate species in the Western Antarctic using high-resolution genetic markers. 2) To begin exploring planktonic larvae spatial and bathymetric distributions for benthic shelf invertebrates in the Bellinghausen, Amundsen and Ross Seas. 3) To continue to develop a Marine Antarctic Genetic Inventory (MAGI) that relates larval and adult forms via DNA barcoding. </p>
Antarctic Inverts
largerWorkCitation
project
eng; USA
biota
oceans
Western Antarctic; Ross Sea
2016-12-02
Antarctica
0
BCO-DMO catalogue of parameters from Sea spider Pallenopsis sampling sites and COI NCBI accessions from Table 1, Harder et al (2016) Polar Biology (Antarctic Inverts 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/671940.rdf
Name: species
Units: unitless
Description: <p>sea spider genus & species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/671941.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/671942.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/671943.rdf
Name: locality_source
Units: unitless
Description: <p>lacation of collection or reference source</p>
http://lod.bco-dmo.org/id/dataset-parameter/671944.rdf
Name: depth
Units: meters
Description: <p>depth collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/671945.rdf
Name: GenBank_accession
Units: unitless
Description: <p>NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671946.rdf
Name: accession_link
Units: unitless
Description: <p>link NCBI GenBank accession page</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
17338
https://datadocs.bco-dmo.org/file/GwwAJ61fqRYmLZ/Harder_2016_T1_sites.csv
Harder_2016_T1_sites.csv
Primary data file for dataset ID 671927
download
https://osprey.bco-dmo.org/dataset/671927/data/download
download
onLine
dataset
<p>From Harder et al (2016):</p>
<p><em><strong>Sample collection</strong><br />
Samples were collected in 2006 and 2012-2013 aboard the RVIB Nathaniel B. Palmer and the ASRV Laurence M. Gould. Pycnogonids were obtained using a Blake trawl or epibenthic&nbsp;</em><em>sled,</em><em> and subsequently identified to genus level prior to preservation and shipment in ~95 % ethanol. Individuals were identified to species level according to standard pycnogonid taxonomic procedures (Child 1995; Weis and Melzer 2012b; Weis et al. 2014). In total, 64 specimens belonging to the genus </em><em>Pallenopsis</em><em> were collected and identified from 21 sampling sites, ranging from 53 16'S to 76 59'S and from 140 26'E to 37 26'W (Fig. 1). Sampling site locality information, including depth (when available), and GenBank accession numbers for all sequences generated for use in our analyses are provided in Table 1.</em></p>
<p><em><strong>Molecular techniques</strong><br />
A tissue sample was taken from each individual as a 1-cm piece from the first tibial segment, and DNA was extracted from these using a Qiagen DNeasy Blood &amp; Tissue Kit (Qiagen Inc., Valencia, CA) per manufacturer’s instructions. A ~650 bp portion of the cytochrome c oxidase subunit I (COI) gene was amplified using LCO-1490 (Folmer et al. 1994) and HCOoutout (Prendini et al. 2005). Each PCR mixture consisted of 1x PCR buffer, 0.75 U Taq DNA polymerase (5 PRIME Inc., Gaithersburg, MD), 2.5 mM Mg^+2, 10 nmol of each dNTP, 1 ul of template DNA, 0.5 uM of each primer, and water to 25 ul. The PCR cycling program began with an incubation at 94C for 2 min, followed by 38 cycles of 94C for 20 s, 46C for 30 s, and 65 C for 80 s, and concluded with a final extension at 65C for 7 min. Successful amplification was confirmed by visualizing PCR products on a 1% agarose gel stained with ethidium bromide. Target DNA was gel extracted and purified using a Qiagen QIAquick Gel Extraction Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s recommendations. Bidirectional Sanger sequencing of amplicons was performed at</em><em>High Throughput</em><em> Genomics Center (Seattle, WA). Obtained sequences were assembled and screened using Sequencher version 5.29 sequence analysis software (Gene Codes Corporation, Ann Arbor, MI), and aligned using Clustal W v1.8 (Thompson et al. 1994) in BioEdit v7.2.5 (Hall 1999). COI sequences were translated into amino acid sequences to further screen for sequencing error, including checking for frameshift mutations and stop codons.</em></p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added links to NCBI accession pages<br />
- converted lat and lon to decimal degrees<br />
- replaced '-' with nd (no data)<br />
- replaced special characters with ascii characters</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Sequencing performed at High Throughput Genomics Center (Seattle, WA) 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.
Blake trawl
Blake trawl
PI Supplied Instrument Name: Blake trawl Instrument Name: Beam Trawl Instrument Short Name:Beam trawl Instrument Description: A beam trawl consists of a cone-shaped body ending in a bag or codend, which retains the catch. In these trawls the horizontal opening of the net is provided by a beam, made of wood or metal, which is up to 12 m long. The vertical opening is provided by two hoop-like trawl shoes mostly made from steel. No hydrodynamic forces are needed to keep a beam trawl open. The beam trawl is normally towed on outriggers, one trawl on each side.
While fishing for flatfish the beam trawl is often equipped with tickler chains to disturb the fish from the seabed. For operations on very rough fishing grounds they can be equipped with chain matrices. Chain matrices are rigged between the beam and the groundrope and prevent boulders/stones from being caught by the trawl. Shrimp beam trawls are not so heavy and have smaller mesh sizes. A bobbin of groundrope with rubber bobbins keeps the shrimp beam trawl in contact with the bottom and gives flatfish the opportunity to escape.
Close bottom contact is necessary for successful operation. To avoid bycatch of most juvenile fishes selectivity devices are assembled (sieve nets, sorting grids, escape holes). While targeting flatfish the beam trawls are towed up to seven knots, therefore the gear is very heavy; the largest gears weighs up to 10 ton. The towing speed for shrimp is between 2.5 and 3 knots.
(from: http://www.fao.org/fishery/geartype/305/en) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/24/
PI Supplied Instrument Name: Instrument Name: Epibenthic Sled Instrument Short Name: Instrument Description: An epibenthic sled is a semi-quantitative bottom-sampling device designed to trawl just above the bottom at the sediment water interface (the epibenthic zone). The sled consists of a rectangular steel frame with a mesh net (often more than one) attached to it. Towed along the ocean floor, its weight scrapes into the benthos, collecting any organisms on the surface or in the first few centimeters of sediment. It also collects the organisms in the water column just above the benthos.
Descriptions from WHOI and Census of Marine Life. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/24/
PI Supplied Instrument Name: 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: LMG1312
LMG1312
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
LMG1312
Kenneth M. Halanych
Auburn University
http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/OA_Antarctic_organisms/727518.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/OA_Antarctic_organisms/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/OA_Antarctic_organisms/mg_ca_ratios%7D
Report describing LMG1312
Cruise: NBP1210
NBP1210
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel
NBP1210
Kenneth M. Halanych
Auburn University
http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/OA_Antarctic_organisms/727518.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/OA_Antarctic_organisms/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/OA_Antarctic_organisms/mg_ca_ratios%7D
Report describing NBP1210
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel