http://lod.bco-dmo.org/id/dataset/555354
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
2015-04-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
DNA sequence data deposited on GenBank for polychaetes used in the project studying the evolution and mechanics of burrowing in La Jolla, CA during 2011 (Burrowing polychaete mechanics project)
2015-04-03
publication
2015-04-03
revision
BCO-DMO Linked Data URI
2015-04-03
creation
http://lod.bco-dmo.org/id/dataset/555354
Gregory Rouse
University of California-San Diego Scripps
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: Rouse, G. (2015) DNA sequence data deposited on GenBank for polychaetes used in the project studying the evolution and mechanics of burrowing in La Jolla, CA during 2011 (Burrowing polychaete mechanics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-04-03) Version Date 2015-04-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/555354 [access date]
DNA sequence data deposited on GenBank for polychaetes used in the project studying the evolution and mechanics of burrowing. Dataset Description: <p><strong>Related References:</strong></p>
<p>Law, C, KM Dorgan, GW Rouse. 2014. Relating divergence in musculature within Opheliidae (Annelida) with different burrowing behaviors. Journal of Morphology 275:548-571.</p>
<p>&nbsp;Law, CJ, KM Dorgan, GW Rouse. 2013. Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data. Zootaxa 3608:67–74.</p> Methods and Sampling: <p>Specimens were collected by hand and sorted or sieved from sediments and preserved for DNA and morphology analysis.&nbsp;Armandia brevis (Moore, 1906) and Thoracophelia mucronata (Treadwell, 1914) were collected from Mission Bay, San Diego, California on June 9, 2011 and La Jolla Shores Beach, California on May 4, 2012, respectively.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029160 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029160
completed
Gregory Rouse
University of California-San Diego Scripps
858-534-7973
9500 Gilman Drive Mail Code: 0202
La Jolla
CA
92093
USA
grouse@ucsd.edu
pointOfContact
asNeeded
Dataset Version: 2015-04-03
Unknown
taxon
species
specimen_origin
lat
lon
gene
accession_number
DNA Sequencer
camera
microscope
Thermal Cycler
theme
None, User defined
taxon
species scientific name (binomial)
site
latitude
longitude
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Camera
Microscope - Optical
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Rouse_2011
service
Deployment Activity
nearshore La Jolla, CA
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.
Functional diversity of infaunal burrowers: Towards a mechanistic understanding of animal-sediment interactions
https://osprey.bco-dmo.org/project/555064
Functional diversity of infaunal burrowers: Towards a mechanistic understanding of animal-sediment interactions
<p><em>Description from NSF award abstract:</em><br />
Benthic communities comprise diverse and abundant organisms with important ecological and biogeochemical roles. They convert organic carbon into biomass that is transferred to higher trophic levels, regenerate nutrients, and determine the fate of pollutants and organic carbon buried in sediments. In many coastal environments, anthropogenic stresses, including eutrophication and resulting hypoxia, trawling and disturbance from fisheries, and pollutants have negative and often dramatic affects on species diversity. Assessing the ecological and biogeochemical impacts of changes in species diversity is nearly impossible, however, without understanding the functional roles of the species. In sedimentary environments, determining functionality is especially important for organisms closely associated sediments, such as infaunal deposit feeders that ingest sediments while living in and moving through them.</p>
<p>Burrowing behaviors and morphologies have been examined for individual species, but decades have passed since even broad burrowing behaviors were compared across diverse taxa. Moreover, such comparisons largely ignored the mechanical response of sediments, an omission similar to studying swimming without considering fluid mechanics. Since that time, there have been several major advances in the physics of animal-sediment interactions. Muddy sediments are elastic solids through which burrows are extended by fracture. In contrast, sands are granular materials whose mechanics are governed by gravitational forces acting on individual grains, rather than by adhesion and cohesion of the mucopolymeric matrix dominating mud mechanics. Use of gelatin as a clear analog for muds has enabled visualization of burrowing and analyses of forces and kinematics. This research will combine structural and anatomical studies and kinematic analyses of burrowing in gelatin and sand analogs with mechanical testing and numerical modeling of real sediments. Linkages would be made among anatomies, morphologies, and behaviors to burrowing function in sands versus muds. Polychaetous annelids, a diverse and abundant component of benthic communities, will be the focal taxon.</p>
<p>Functional groupings of burrowing infauna have been based on morphologies and trophic roles but advances in sediment mechanics suggest that similar morphologies may have different functions in sands versus muds (e.g., expansible structures extend cracks in muds but are anchors in sands). In addition, seemingly different morphologies may have analogous functions (e.g., the pharynx of Nereis virens and the muscular anterior of the cirratulid Cirriformia moorei both exert dorso-ventral stress to extend burrows by fracture). Linking functions to morphologies and behaviors of burrowers is important in understanding functional roles of infauna and resulting functional diversity of benthic communities. The diversity of burrowing mechanisms revealed in this study will enable generalizations about burrowing mechanics in different environments. Important characteristics of burrowing locomotion will be identified as those shared by diverse burrowers. How the different physical constraints of sand and mud specify burrowing mechanics and affect morphologies and behaviors of burrowers will be contrasted for closely related taxa from different environments.</p>
Burrowing polychaete mechanics
largerWorkCitation
project
eng; USA
biota
oceans
nearshore La Jolla, CA
2015-04-03
California
0
BCO-DMO catalogue of parameters from DNA sequence data deposited on GenBank for polychaetes used in the project studying the evolution and mechanics of burrowing in La Jolla, CA during 2011 (Burrowing polychaete mechanics 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/555444.rdf
Name: taxon
Units: unitless
Description: <p>polychaete family</p>
http://lod.bco-dmo.org/id/dataset-parameter/555445.rdf
Name: species
Units: unitless
Description: <p>taxonomic genus and species name with authority</p>
http://lod.bco-dmo.org/id/dataset-parameter/555446.rdf
Name: specimen_origin
Units: unitless
Description: <p>location of specimen collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/555447.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is postitive</p>
http://lod.bco-dmo.org/id/dataset-parameter/555448.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is postitive</p>
http://lod.bco-dmo.org/id/dataset-parameter/555494.rdf
Name: gene
Units: unitless
Description: <p>Type of gene sequenced:<br />
voucher_SIO=SIO voucher number<br />
rRNA_16S=GenBank accession number for 16S ribosomal RNA gene<br />
rRNA_18S=GenBank accession number for 18S ribosomal RNA gene<br />
rRNA_28S=GenBank accession number for 28S ribosomal RNA gene<br />
Histone_H3=GenBank accession number for; histone 3 gene<br />
ITS=GenBank accession number for 18S ribosomal RNA gene; internal transcribed spacer<br />
mtCOI=GenBank accession number for cytochrome oxidase subunit 1 gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/555495.rdf
Name: accession_number
Units: unitless
Description: <p>GenBank accession number</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
25293
https://datadocs.bco-dmo.org/file/4WW2r58H7ow68r/polych_accnums.csv
polych_accnums.csv
Primary data file for dataset ID 555354
download
https://osprey.bco-dmo.org/dataset/555354/data/download
download
onLine
dataset
<p>Specimens were collected by hand and sorted or sieved from sediments and preserved for DNA and morphology analysis.&nbsp;Armandia brevis (Moore, 1906) and Thoracophelia mucronata (Treadwell, 1914) were collected from Mission Bay, San Diego, California on June 9, 2011 and La Jolla Shores Beach, California on May 4, 2012, respectively.</p>
Specified by the Principal Investigator(s)
<p><strong>DNA Amplification and Sequencing:</strong><br />
Forty one specimens of 33 species were used for phylogenetic analyses: 25 opheliids, four polygordiids, and 10 scalibregmatids. The two outgroup taxa, a capitellid Notomastus sp. and an arenicolid A. marina were chosen based on Struck et al.’s (2011) annelid phylogeny (Table 1) with Notomastus sp. being used as the root terminal. Newly collected specimens [from Beaufort, NC (Ophelina sp1.); Costa Rica (Ophelina sp3.); Friday Harbor, WA (Notomastus sp., O. acuminata, Polygordius sp., and Scalibregma inflatum); Greenland (O. acuminata, O. cylindricaudata, and O. limacina); La Jolla, CA (A. brevis, Polyophthalmus sp., and T. mucronata); Lizard Island, Australia (Armandia sp1.); and off the Oregon coast (Ophelina sp2.)] were relaxed in 7.5% MgCl2 and fixed in 95% ethyl alcohol. Sequences for the remaining 26 species were accessed through GenBank (Table 1).</p>
<p>A Qiagen DNeasy tissue kit was used to extract genomic DNA from specimens according to the manufacturer’s instructions. Approximately 500 base pairs of the mitochondrial small subunit ribosomal DNA (16S) were amplified using the primers 16SarL and 16SbrL (Palumbi, 1996) with temperature profiles of 95C for 3 min, followed by 40 cycles of 95C for 40 s, 48C for 40 s, 68C for 50 s, and final extension at 68C for 5 min (see Supporting Information, Table S1).</p>
<p>Three nuclear loci were also sequenced. The small subunit ribosomal DNA (18S) was amplified using three primer sets: 1) 1F and 5R; 2) 3F and bi; and 3) a2.0 and 9R (Giribet et al., 1996, 1999). Temperature profiles for the 1F/5R and a2.0/9R primer sets were 95C for 3 min, followed by 40 cycles of 95C for 30 s, 52C for 30 s, 72C for 90 s, and final extension at 72C for 8 min. The temperature profile for the 3F/bi primer set was 95C for 3 min, followed by 40 cycles of 95C for 30 s, 49C for 30 s, 72C for 90 s, and final extension at 72C for 8 min. Approximately 930 base pairs of the large subunit ribosomal DNA (28S) were amplified using the primers Po28F1 and Po28R4 (Struck et al., 2006), and ~360 base pairs of the nuclear protein coding gene Histone H3 were amplified using the primers H3aF and H3aR (Colgan et al., 1998). Both genes were amplified using the same temperature profiles of 94C for 2 min, followed by 35 cycles of 94C for 45 s, 48C for 60 s, 72C for 90 s, and final extension at 72C for 10 min.</p>
<p>Amplification reactions (25 ml) were conducted containing 2 ml of DNA template, 1 ml of forward and reverse primers, 12.5 ml GoTaq Green Master Mix (Promega), and 8.5 ml H2O. ExoSAP-IT (Affymetrix) was used to purify PCR products. Sequencing was done by either Retrogen (San Diego, CA) or Eurofins MWG Operon (Louisville, KY). Sequences were edited using Geneious 5.5.6 (www.geneious.com) and aligned with MAFFT 3.8 (Katoh and Kuma, 2002) under default settings with no manual alterations. The combined molecular dataset consisted of 3,955 total characters, 1,075 of which were parsimony informative and 436 were uninformative.</p>
<p><strong>Phylogenetic Analysis:</strong><br />
Parsimony analyses on the combined genes (16S, 18S, 28S, and H3) were conducted in PAUP* 4.0b10 (Swofford, 2002) using a heuristic search with random stepwise addition of the terminals for 1,000 replicates, with tree bisection and reconnection. The character matrix was equally weighted, and gaps were treated as missing data. Clade support was assessed using jackknifing with 37% deletion of sites over 1,000 replicates with 10 random additions per iteration. Maximum likelihood analyses were performed in RAxML 7.2.8 (Stamatkis, 2006) as a four-gene partitioned dataset and under the General Time Reversible1Gamma (GTR1G) model. Bootstrap (thorough option) values were estimated using 100 pseudoreplicates under the same model.</p>
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
- replaced blanks with NA<br />
- transformed gene columns to rows<br />
- added html links to GenBank accession pages</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
DNA Sequencer
DNA Sequencer
PI Supplied Instrument Name: DNA Sequencer PI Supplied Instrument Description:Sequencing was done by either Retrogen (San Diego, CA) or Eurofins MWG Operon (Louisville, KY). 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.
camera
camera
PI Supplied Instrument Name: camera PI Supplied Instrument Description:Canon Powershot G9 camera attached to a Leica DMR microscope;
Canon T1i camera attached to an Olympus CX41 microscope Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
microscope
microscope
PI Supplied Instrument Name: microscope PI Supplied Instrument Description:Olympus CX41 compound microscope; Leica DMR microscope; Zeiss AxioObserver Z1 microscope with DIC filters and AxioVision software Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: 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)
Deployment: Rouse_2011
Rouse_2011
SIO_Rouse
laboratory
Rouse_2011
Gregory Rouse
University of California-San Diego Scripps
SIO_Rouse
laboratory