http://lod.bco-dmo.org/id/dataset/671822
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
2016-12-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Outgroup species, description reference, and GenBank accession numbers from Table 2, from Janosik & Halanych (2013) (Antarctic Inverts project)
2016-12-27
publication
2016-12-27
revision
BCO-DMO Linked Data URI
2016-12-27
creation
http://lod.bco-dmo.org/id/dataset/671822
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) Outgroup species, description reference, and GenBank accession numbers from Table 2, from Janosik & Halanych (2013) (Antarctic Inverts project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-12-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/671822 [access date]
Outgroup species and accessions Dataset Description: <p>This dataset was published as Table 2 from Janosik et al (2013). It contains a list of outgroup species with their description reference and NCBI GenBank accession numbers.</p>
<p><strong>Related Reference:</strong> Janosik, A.M., and K.M. Halanych,. 2013. Seeing stars: a molecular and morphological investigation of the evolutionary history of Odontasteridae (Asteroidea) with description of a new species from the Galapagos Islands. Marine Biology.160:821-841. DOI 10.1007/s00227-012-2136-x</p>
<p><strong>Related Datasets:</strong><br />
<a href="https://www.bco-dmo.org/dataset/671804">Janosik_2013_T1: Odontasteridae species collection information</a><br />
<a href="https://www.bco-dmo.org/dataset/671850">Janosik_2013_T3: matrix of Odontasteridea morphological characters</a></p>
<p>&gt;</p>
<p>&nbsp;</p> Methods and Sampling: <p>From Janosik&nbsp;et al (2013):</p>
<p><em><strong>Specimen collection</strong><br />
Specimens were obtained from the Division of Echinoderms, Smithsonian Institution National Museum of Natural History (USNM) in Washington, DC, the Department of Invertebrate Zoology, California Academy of Sciences (</em><em>CASIZ</em><em>), San Francisco, California, and the National Institute of Water and Atmospheric Research (NIWA), New Zealand (Table 1). Most specimens were dried. Antarctic species were collected during two five-week research cruises aboard the R/V Laurence M. Gould in November/December of 2004 and May/June of 2006. Images of D. </em><em>clarki</em><em> were provided by NIWA.</em></p>
<p><em><strong>Molecular data</strong><br />
Molecular methods follow Janosik et al. (2011). DNA extraction of specimens was performed by using DNeasy Tissue Kit (Qiagen). Two mitochondrial DNA markers (16S and COI) were utilized to estimate the evolutionary history of Odontasteridae. Specifically, a 508-bp region of the mitochondrial 16S gene was amplified using the 16SarL and 16SbrH primers and protocols of Palumbi et al. (1991). For the same individuals, a 627-bp region of the COI gene was amplified using primers designed to work with Odontaster COI-Ast 22F (5'-TTYTCNACNAAACA YAAGGA-3') and COI-Ast722R (5'-GGRTGNCCRAAR AAYCARAA-3') (Janosik et al. 2011). Amplified products were purified with either a Qiagen QIAquick Gel Extraction Kit (Qiagen Inc.) or a Montage PCR Filter Units (Millipore) according to the manufacturer’s directions. Purified products were then sequenced bidirectionally on a Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter). Sequences were edited and aligned using Sequencher 4.6 (Gene CodesCorporation) andBioedit v.7.0.8 (Hall 1999). COI sequences were translated according to the echinoderm mitochondrial DNA code to aid in proofreading. Genbank accession number is listed in Table 2.</em></p>
<p><em>Based on current understandings of sea star relationships (Blake 1987; Mah and Foltz 2011), Bathybiaster loripes, Chaetaster moorei, Crossaster papposus, Luidia foliolata, Mediaster aequalis, and Solaster stimpsoni were selected for the outgroup, and these sequences were downloaded from GenBank (www.ncbi.nlm.nih.gov/ genbank/) (Table 2).</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
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
reference
NCBI_accession
link_NCBI_accession
Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter)
theme
None, User defined
taxon
reference_paper
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
2016-12-27
Antarctica
0
BCO-DMO catalogue of parameters from Outgroup species, description reference, and GenBank accession numbers from Table 2, from Janosik & Halanych (2013) (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/671832.rdf
Name: taxon
Units: unitless
Description: <p>taxonomic genus and species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/671833.rdf
Name: reference
Units: unitless
Description: <p>published taxonomic description of the species</p>
http://lod.bco-dmo.org/id/dataset-parameter/671834.rdf
Name: NCBI_accession
Units: unitless
Description: <p>NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671835.rdf
Name: link_NCBI_accession
Units: unitless
Description: <p>link to 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
1333
https://datadocs.bco-dmo.org/file/933jorkSYBLvJK/Janosik_2013_T2.csv
Janosik_2013_T2.csv
Primary data file for dataset ID 671822
download
https://osprey.bco-dmo.org/dataset/671822/data/download
download
onLine
dataset
<p>From Janosik&nbsp;et al (2013):</p>
<p><em><strong>Specimen collection</strong><br />
Specimens were obtained from the Division of Echinoderms, Smithsonian Institution National Museum of Natural History (USNM) in Washington, DC, the Department of Invertebrate Zoology, California Academy of Sciences (</em><em>CASIZ</em><em>), San Francisco, California, and the National Institute of Water and Atmospheric Research (NIWA), New Zealand (Table 1). Most specimens were dried. Antarctic species were collected during two five-week research cruises aboard the R/V Laurence M. Gould in November/December of 2004 and May/June of 2006. Images of D. </em><em>clarki</em><em> were provided by NIWA.</em></p>
<p><em><strong>Molecular data</strong><br />
Molecular methods follow Janosik et al. (2011). DNA extraction of specimens was performed by using DNeasy Tissue Kit (Qiagen). Two mitochondrial DNA markers (16S and COI) were utilized to estimate the evolutionary history of Odontasteridae. Specifically, a 508-bp region of the mitochondrial 16S gene was amplified using the 16SarL and 16SbrH primers and protocols of Palumbi et al. (1991). For the same individuals, a 627-bp region of the COI gene was amplified using primers designed to work with Odontaster COI-Ast 22F (5'-TTYTCNACNAAACA YAAGGA-3') and COI-Ast722R (5'-GGRTGNCCRAAR AAYCARAA-3') (Janosik et al. 2011). Amplified products were purified with either a Qiagen QIAquick Gel Extraction Kit (Qiagen Inc.) or a Montage PCR Filter Units (Millipore) according to the manufacturer’s directions. Purified products were then sequenced bidirectionally on a Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter). Sequences were edited and aligned using Sequencher 4.6 (Gene CodesCorporation) andBioedit v.7.0.8 (Hall 1999). COI sequences were translated according to the echinoderm mitochondrial DNA code to aid in proofreading. Genbank accession number is listed in Table 2.</em></p>
<p><em>Based on current understandings of sea star relationships (Blake 1987; Mah and Foltz 2011), Bathybiaster loripes, Chaetaster moorei, Crossaster papposus, Luidia foliolata, Mediaster aequalis, and Solaster stimpsoni were selected for the outgroup, and these sequences were downloaded from GenBank (www.ncbi.nlm.nih.gov/ genbank/) (Table 2).</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 />
-&nbsp;removed special 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
Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter)
Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter)
PI Supplied Instrument Name: Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter) PI Supplied Instrument Description:Purified products were then sequenced bidirectionally 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