http://lod.bco-dmo.org/id/dataset/671459
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)
Hemichordata and Echinodermata NCBI accessions, Table 2, Cannon et al (2013) Biol. Bull. (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/671459
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) Hemichordata and Echinodermata NCBI accessions, Table 2, Cannon et al (2013) Biol. Bull. (Antarctic Inverts project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-12-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/671459 [access date]
Hemichordata and Echinodermata NCBI accessions Dataset Description: Methods and Sampling: <p><em>from Cannon et al (2013) Biol Bull:</em></p>
<p><strong>Collection:</strong><br />
Eleven specimens sequenced in this study were collected in September 2011 during Senckenberg’s German Center for Marine Biodiversity Research (DZMB) IceAGE expedition led by Dr. Saskia Brix aboard the R/V Meteor, which circled Iceland, crossing the Mid-Atlantic and Greenland-Scotland ridges. Cephalodiscus specimens were collected during two research expeditions to the Antarctic Peninsula aboard the R/V Lawrence M. Gould in 2001 and 2004. Antarctic enteropneusts were collected in January-February 2013 in the Amundsen and Ross Seas by the R/V Nathaniel B. Palmer. Enteropneusts from Norway were collected on the R/V Håkon Mosby or R/V Aurelia with the aid of Dr. Christiane Todt and the late Dr. Christoffer Schander. Balanoglossus sp. specimens from Mississippi were collected with the assistance of Dr. Richard Heard. Dr. Jon Norenburg and Dr. Darryl Felder provided material from Rhabdopleura sp. collected in the Gulf of Mexico on the R/V Pelican. Specimens were collected at depths ranging from the intertidal to over 2500 m, using diverse sampling methods (Table 1). Enteropneusts from Iceland were collected by decanting sediment through a 1-1.5-mm sieve, and were retained on either a 500- or 300-um sieve; enteropneusts from Antarctica and off Oregon were decanted from sediment directly onto a 250-um sieve. Freshly collected worms were preserved in 95%-100% ethanol, and when multiple specimens were available, voucher specimens were relaxed in 7.5% magnesium chloride and fixed in 4%-10% formalin for morphological studies.</p>
<p><strong>Molecular methods</strong><br />
Molecular laboratory methods followed Cannon et al. (2009). In addition to in-house sequencing on a CEQ8000 (Beckman-Coulter, Inc., Brea, CA), some PCR products were sent to Genewiz (South Plainfield, NJ). In the case of Rhabdopleura cf. normani from Bermuda, we were able to generate a full-length 18S rDNA sequence using publically available partial sequences (Genbank Accession numbers: U15664, JF900483, and JF900484) and 454 transcriptome data (Cannon and Halanych, unpubl.) prepared following the methods of Kocot et al. (2011). Assembled 454 contigs were formatted into a BLAST (Altschul et al., 1997) database, which was searched with a query composed of diverse hemichordate 18S sequences. Fragments with E-values below 1x10^30 were aligned to the partial 18S sequences as a backbone, and then assembled into a full-length 18S rDNA cofntig using the software package CLC Genomics Workbench ver. 5 (Aarhus, Denmark). As reported previously (Cannon et al. 2009), Stereobalanus canadensis (Enteropneusta, Harrimaniidae) has a highly divergent 18S rDNA sequence. Previously we had sequenced this acorn worm multiple times, but to further verify this sequence, genomic DNA was extracted from S. canadensis and sequenced via an Illumina MiSeq (San Diego, CA) at Auburn University. This work employed a 2x150-bp paired end run and the Nextera DNA sample kit. Scaffolds generated using the genome assembler Ray (Boisvert et al., 2010) were formatted into a BLAST database, and queried as above. A single 18S rDNA sequence was recovered, with 99.6% identity to our previously reported sequence; thus we have retained Stereobalanus canadensis in our analyses.</p>
<p>Taxon sampling and NCBI accession numbers for sequences used in phylogenetic analyses are given in Table 2. Representatives of each echinoderm class were used as outgroup taxa (Table 2). Sequences were aligned with MAFFT ver. 6.09b (Katoh et al., 2005) using the L-INS-i method, and uninformative sites were trimmed using the perl scripts Aliscore and Alicut (Misof and Misof, 2009). Models of evolution were selected under the Akaike Information Criterion (AIC) implemented by MrModelTest (Nylander, 2004). The best fitting model for both 16S and 18S rDNA, GTR+I+G, was used in maximum likelihood (ML) and Bayesian inference analyses (BI) of concatenated alignments. ML analyses were performed with RaxML version 7.3.9 (Stamatakis, 2006) using 5000 bootstrap replicates. Bayesian analyses were conducted using MrBayes ver. 3.2.0 (Ronquist and Huelsenbeck, 2003). Four independent BI analyses were run for each dataset for 5,000,000 generations with trees sampled every 100 generations using three heated and one cold chain. Plotting likelihood values versus generation number revealed that stationarity was reached after approximately 1,000,000 generations, and thus the first 25% of sampled trees was discarded as burn-in. Competing hypotheses of hemichordate phylogeny were evaluated using the SH-test (Shimodaira, 2002) as implemented in RAxML ver. 7.3.8 with the GTR+I+G model.</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
Dataset Version: 1
Unknown
phylum
family
taxon
new_seq
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
phylum
family
taxon
flag
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
NBP1210
Halanych_lab_2011-16
service
Deployment Activity
Ross Sea
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
Ross Sea; laboratory studies
2001-01-01
2013-12-31
Antarctica
0
BCO-DMO catalogue of parameters from Hemichordata and Echinodermata NCBI accessions, Table 2, Cannon et al (2013) Biol. Bull. (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/671479.rdf
Name: phylum
Units: unitless
Description: <p>taxonomic phylum</p>
http://lod.bco-dmo.org/id/dataset-parameter/671480.rdf
Name: family
Units: unitless
Description: <p>taxonomic family</p>
http://lod.bco-dmo.org/id/dataset-parameter/671481.rdf
Name: taxon
Units: unitless
Description: <p>more specific taxonomic group</p>
http://lod.bco-dmo.org/id/dataset-parameter/671482.rdf
Name: new_seq
Units: unitless
Description: <p>whether these are new sequences for this study</p>
http://lod.bco-dmo.org/id/dataset-parameter/671483.rdf
Name: accession_rDNA_18S
Units: unitless
Description: <p>18S NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671484.rdf
Name: accession_rDNA_16S
Units: unitless
Description: <p>16S NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671485.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/671486.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
22372
https://datadocs.bco-dmo.org/file/JEE1M65cKY1Zy9/Cannon_2013_T2.csv
Cannon_2013_T2.csv
Primary data file for dataset ID 671459
download
https://osprey.bco-dmo.org/dataset/671459/data/download
download
onLine
dataset
<p><em>from Cannon et al (2013) Biol Bull:</em></p>
<p><strong>Collection:</strong><br />
Eleven specimens sequenced in this study were collected in September 2011 during Senckenberg’s German Center for Marine Biodiversity Research (DZMB) IceAGE expedition led by Dr. Saskia Brix aboard the R/V Meteor, which circled Iceland, crossing the Mid-Atlantic and Greenland-Scotland ridges. Cephalodiscus specimens were collected during two research expeditions to the Antarctic Peninsula aboard the R/V Lawrence M. Gould in 2001 and 2004. Antarctic enteropneusts were collected in January-February 2013 in the Amundsen and Ross Seas by the R/V Nathaniel B. Palmer. Enteropneusts from Norway were collected on the R/V Håkon Mosby or R/V Aurelia with the aid of Dr. Christiane Todt and the late Dr. Christoffer Schander. Balanoglossus sp. specimens from Mississippi were collected with the assistance of Dr. Richard Heard. Dr. Jon Norenburg and Dr. Darryl Felder provided material from Rhabdopleura sp. collected in the Gulf of Mexico on the R/V Pelican. Specimens were collected at depths ranging from the intertidal to over 2500 m, using diverse sampling methods (Table 1). Enteropneusts from Iceland were collected by decanting sediment through a 1-1.5-mm sieve, and were retained on either a 500- or 300-um sieve; enteropneusts from Antarctica and off Oregon were decanted from sediment directly onto a 250-um sieve. Freshly collected worms were preserved in 95%-100% ethanol, and when multiple specimens were available, voucher specimens were relaxed in 7.5% magnesium chloride and fixed in 4%-10% formalin for morphological studies.</p>
<p><strong>Molecular methods</strong><br />
Molecular laboratory methods followed Cannon et al. (2009). In addition to in-house sequencing on a CEQ8000 (Beckman-Coulter, Inc., Brea, CA), some PCR products were sent to Genewiz (South Plainfield, NJ). In the case of Rhabdopleura cf. normani from Bermuda, we were able to generate a full-length 18S rDNA sequence using publically available partial sequences (Genbank Accession numbers: U15664, JF900483, and JF900484) and 454 transcriptome data (Cannon and Halanych, unpubl.) prepared following the methods of Kocot et al. (2011). Assembled 454 contigs were formatted into a BLAST (Altschul et al., 1997) database, which was searched with a query composed of diverse hemichordate 18S sequences. Fragments with E-values below 1x10^30 were aligned to the partial 18S sequences as a backbone, and then assembled into a full-length 18S rDNA cofntig using the software package CLC Genomics Workbench ver. 5 (Aarhus, Denmark). As reported previously (Cannon et al. 2009), Stereobalanus canadensis (Enteropneusta, Harrimaniidae) has a highly divergent 18S rDNA sequence. Previously we had sequenced this acorn worm multiple times, but to further verify this sequence, genomic DNA was extracted from S. canadensis and sequenced via an Illumina MiSeq (San Diego, CA) at Auburn University. This work employed a 2x150-bp paired end run and the Nextera DNA sample kit. Scaffolds generated using the genome assembler Ray (Boisvert et al., 2010) were formatted into a BLAST database, and queried as above. A single 18S rDNA sequence was recovered, with 99.6% identity to our previously reported sequence; thus we have retained Stereobalanus canadensis in our analyses.</p>
<p>Taxon sampling and NCBI accession numbers for sequences used in phylogenetic analyses are given in Table 2. Representatives of each echinoderm class were used as outgroup taxa (Table 2). Sequences were aligned with MAFFT ver. 6.09b (Katoh et al., 2005) using the L-INS-i method, and uninformative sites were trimmed using the perl scripts Aliscore and Alicut (Misof and Misof, 2009). Models of evolution were selected under the Akaike Information Criterion (AIC) implemented by MrModelTest (Nylander, 2004). The best fitting model for both 16S and 18S rDNA, GTR+I+G, was used in maximum likelihood (ML) and Bayesian inference analyses (BI) of concatenated alignments. ML analyses were performed with RaxML version 7.3.9 (Stamatakis, 2006) using 5000 bootstrap replicates. Bayesian analyses were conducted using MrBayes ver. 3.2.0 (Ronquist and Huelsenbeck, 2003). Four independent BI analyses were run for each dataset for 5,000,000 generations with trees sampled every 100 generations using three heated and one cold chain. Plotting likelihood values versus generation number revealed that stationarity was reached after approximately 1,000,000 generations, and thus the first 25% of sampled trees was discarded as burn-in. Competing hypotheses of hemichordate phylogeny were evaluated using the SH-test (Shimodaira, 2002) as implemented in RAxML ver. 7.3.8 with the GTR+I+G model.</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 phylum column<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)
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
Deployment: Halanych_lab_2011-16
Halanych_lab_2011-16
Auburn University lab
laboratory
Halanych_lab_2011-16
Kenneth M. Halanych
Auburn University
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel