http://lod.bco-dmo.org/id/dataset/671551
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
2016-12-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (Antarctic Inverts project)
2016-12-22
publication
2016-12-22
revision
BCO-DMO Linked Data URI
2016-12-22
creation
http://lod.bco-dmo.org/id/dataset/671551
Kenneth M. Halanych
Auburn University
principalInvestigator
Andrew Mahon
Central Michigan 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: Halanych, K. M., Mahon, A. (2016) GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (Antarctic Inverts project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-12-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/671551 [access date]
NCBI accessions Dataset Description: <p>This dataset was published as Supplementary Table 1 from Halanych et al (2013). It contains GenBank accession links of hemichordate and echinoderm specimens collected globally from 2001 to 2013.</p>
<p><strong>Related Reference:</strong>&nbsp;Halanych, K.M., J.T. Cannon, A.R. Mahon, B.J. Swalla, C.R. Smith. 2013. Tubicolous acorn worms from Antarctica. Nature Communications DOI://10.1038/ncomms3738</p>
<p><strong>Related Dataset:</strong>&nbsp;<a href="https://www.bco-dmo.org/dataset/671609" target="_blank">Halanych_2013: Video of acorn worm tubes</a></p> Methods and Sampling: <p>Scientific research expeditions were aboard the RVIB Nathaniel B. Palmer in 2008 to the Antarctic Peninsula and 2013 to the Ross Sea.&nbsp;Benthic samples were obtained from the Ross Sea by a Blake&nbsp;trawl with a 2-m opening. Sampled were sorted and preserved on deck. Sequencing&nbsp;and phylogenetic protocols of 18S and 16S ribosomal DNA used the standard&nbsp;procedures3. PCR amplification used primers 16Sar 50-CGCCTGTTTATCAAAAA&nbsp;CAT-30 and 16Sbr 50-CCGGTCTGAACTCAGATCACGT-30 for 16S ribosomal&nbsp;DNA and 18e 50-CTGGTTGATCCTGCCAGT-30 and 18 P 50-TAATGATCCTTCCGCAGGTTCACCT-30 .</p>
<p>Maximum likelihood and Bayesian analyses (both used the best fitting model GTR+I+G) were conducted with RaxML version 7.3.9 (ref. 19) (5,000 bootstrap replicates) and MrBayes version 3.2.0 (ref. 20) (four independent runs for 5,000,000 generations sampled every 100 generations), respectively.</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
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
Andrew Mahon
Central Michigan University
989-774-6777
Office of Research & Graduate St
Mount Pleasant
MI
48859-0001
USA
mahon2a@cmich.edu
pointOfContact
asNeeded
Unknown
taxon
species
accession_rDNA_18S
accession_rDNA_16S
link_accession_rDNA_18S
link_accession_rDNA_16S
Illumina MiSeq (San Diego, CA) at Auburn University
theme
None, User defined
taxon
species scientific name (binomial)
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Halanych_lab_2011-16
service
Deployment Activity
laboratory studies
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
laboratory studies
2016-12-22
Antarctica
0
BCO-DMO catalogue of parameters from GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (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/671598.rdf
Name: taxon
Units: unitless
Description: <p>more specific taxonomic group</p>
http://lod.bco-dmo.org/id/dataset-parameter/671599.rdf
Name: species
Units: unitless
Description: <p>taxonomic genus and species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/671600.rdf
Name: accession_rDNA_18S
Units: unitless
Description: <p>18S NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671601.rdf
Name: accession_rDNA_16S
Units: unitless
Description: <p>16S NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671602.rdf
Name: link_accession_rDNA_18S
Units: unitless
Description: <p>link to 18S NCBI GenBank accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/671603.rdf
Name: link_accession_rDNA_16S
Units: unitless
Description: <p>link to 16S NCBI GenBank accession</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
12731
https://datadocs.bco-dmo.org/file/N77Ggk3IVRpgOE/Halanych_2013_T1.csv
Halanych_2013_T1.csv
Primary data file for dataset ID 671551
download
https://osprey.bco-dmo.org/dataset/671551/data/download
download
onLine
dataset
<p>Scientific research expeditions were aboard the RVIB Nathaniel B. Palmer in 2008 to the Antarctic Peninsula and 2013 to the Ross Sea.&nbsp;Benthic samples were obtained from the Ross Sea by a Blake&nbsp;trawl with a 2-m opening. Sampled were sorted and preserved on deck. Sequencing&nbsp;and phylogenetic protocols of 18S and 16S ribosomal DNA used the standard&nbsp;procedures3. PCR amplification used primers 16Sar 50-CGCCTGTTTATCAAAAA&nbsp;CAT-30 and 16Sbr 50-CCGGTCTGAACTCAGATCACGT-30 for 16S ribosomal&nbsp;DNA and 18e 50-CTGGTTGATCCTGCCAGT-30 and 18 P 50-TAATGATCCTTCCGCAGGTTCACCT-30 .</p>
<p>Maximum likelihood and Bayesian analyses (both used the best fitting model GTR+I+G) were conducted with RaxML version 7.3.9 (ref. 19) (5,000 bootstrap replicates) and MrBayes version 3.2.0 (ref. 20) (four independent runs for 5,000,000 generations sampled every 100 generations), respectively.</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 />
- removed trailing blank spaces<br />
- replaced cells with hyphen with nd (no data)<br />
- added links to NCBI accession pages</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
Illumina MiSeq (San Diego, CA) at Auburn University
Illumina MiSeq (San Diego, CA) at Auburn University
PI Supplied Instrument Name: Illumina MiSeq (San Diego, CA) at Auburn University 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: 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)
Deployment: Halanych_lab_2011-16
Halanych_lab_2011-16
Auburn University lab
laboratory
Halanych_lab_2011-16
Kenneth M. Halanych
Auburn University
Auburn University lab
laboratory