http://lod.bco-dmo.org/id/dataset/679922
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
2017-02-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
GenBank accessions and links for DNA sequences for three genes (COI, 16S, H3) from Elysia cornigera and E. timida (Gastropoda: Sacoglossa)in Krug et al (2011) Invert. Syst.(PLDvFST project)
2017-02-01
publication
2017-02-01
revision
BCO-DMO Linked Data URI
2017-02-01
creation
http://lod.bco-dmo.org/id/dataset/679922
Patrick Krug
California State University Los Angeles
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: Krug, P. (2017) GenBank accessions and links for DNA sequences for three genes (COI, 16S, H3) from Elysia cornigera and E. timida (Gastropoda: Sacoglossa)in Krug et al (2011) Invert. Syst.(PLDvFST project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-02-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/679922 [access date]
Elysia spp. accessions for COI, 16S, H3 Dataset Description: <p>Specimens of two species of Elysia (Gastropoda: Sacoglossa) were sequenced from the Caribbean (E. cornigera) and the Mediterranean (E. timida).</p>
<p><strong>Related Reference:</strong> Krug, P.J., Händeler, K., and J.E. Vendetti. 2012. Genes, morphology, development and photosynthetic ability support the resurrection of Elysia&nbsp;cornigera&nbsp;(Heterobranchia: Plakobranchoidea) as distinct from the solar-powered sea slug E.&nbsp;timida. Invertebrate Systematics, 25: 477–489. (<a href="http://dx.doi.org/10.1071/IS11026" target="_blank">doi: 10.1071/IS11026</a>)</p> Methods and Sampling: <p>Purified PCR products were directly cycle-sequenced in both directions using PCR primers and Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).&nbsp; Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software.</p>
<p>For full details on sampling and analytical methodology, see Krug et al (2012).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130072 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1130072
completed
Patrick Krug
California State University Los Angeles
3233432076
5151 State University Drive
Los Angeles
CA
900324221
pkrug@calstatela.edu
pointOfContact
asNeeded
Unknown
species
collection_locality
lat
lon
date_collected
NCBI_COI_accession
NCBI_16S_accession
NCBI_H3_accession
NCBI_COI_accession_link
NCBI_16S_accession_link
NCBI_H3_accession_link
theme
None, User defined
species scientific name (binomial)
site
latitude
longitude
date
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Krug_lab
service
Deployment Activity
lab
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.
Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions
https://osprey.bco-dmo.org/project/615835
Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions
<p>Dispersal is a critical life-history trait linking ecological and evolutionary processes. Transport of planktonic larvae affects colonization success and population persistence for benthic animals, and influences genetic subdivision of populations, local adaptation, and speciation. However, recent studies question the long-held assumption that pelagic larval duration (PLD) determines how far larvae are advected. This has applied significance, as oceanographic models used to predict exchange among marine protected areas often use PLD as the key larval parameter. The investigators' data for Caribbean gastropods show genetic breaks that are not congruent with model predictions, and levels of structure that are inconsistent with larval lifespan, highlighting a need for new theory.</p>
<p>This research will integrate molecular and larval ecology to test the link between dispersal and larval duration in a phylogenetic framework, and determine whether Individual Based Models (IBMs) accurately predict exchange for Caribbean reef ecosystems. The PI will collect multi-locus genetic data and quantify larval behavior for 14 related, ecologically similar species of sea slugs with PLDs from 0-30 days. The PI predicts that larval behavior explains why some species are under- or over-dispersed relative to their PLD; this work will reveal key parameters needed for biophysical-coupling models to predict connectivity for coastal invertebrates. The proposal will address 3 inter-related objectives: (1) Are genetic connectivity estimates from mtDNA and nuclear markers congruent, and consistent with model predictions? Data for mitochondrial and nuclear loci will be used to test for selection on mtDNA, estimate rates of gene flow and times of divergence, and assess levels of connectivity within each species. Matrices of model-predicted exchange will be compared with genetic similarity matrices to test whether breaks in gene flow occur where predicted. (2) Are genetic connectivity and PLD correlated? More broadly, the PI will test the assumption that larval period determines dispersal, using comparative methods in a phylogenetic framework to correct for effects of relatedness among species. The PI will compare models of trait evolution with Bayesian Markov chain Monte Carlo (MCMC) methods to determine if gene flow is correlated or uncorrelated with PLD, using a molecular phylogeny and multi-locus genetic data. (3) Does larval behavior explain genetic structure in species with long PLD? At least two of the focal species selected for this study are under-dispersed, with genetically isolated demes despite a 30-day PLD. Conversely, at least one short-PLD species has no genetic structure over large regions of the Caribbean. The PI will build on past work quantifying larval behavior to ask if species-specific differences in larval swimming facilitate local retention, making species deviate from expected connectivity patterns. The PI will also test whether pre-competent larvae respond to habitat cues in a way that influences dispersal, as occurs in fish. This work will reconcile life-history theory, oceanographic models, and genetics by mechanistically explaining breaks in connectivity; the results will deepen our understanding of how larval behavior can determine the pace of divergence among populations.</p>
<p> </p>
PLDvFST
largerWorkCitation
project
eng; USA
biota
oceans
lab
2017-02-01
Florida and Caribbean
0
BCO-DMO catalogue of parameters from GenBank accessions and links for DNA sequences for three genes (COI, 16S, H3) from Elysia cornigera and E. timida (Gastropoda: Sacoglossa)in Krug et al (2011) Invert. Syst.(PLDvFST 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/679933.rdf
Name: species
Units: unitless
Description: <p>species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/679934.rdf
Name: collection_locality
Units: unitless
Description: <p>collection location</p>
http://lod.bco-dmo.org/id/dataset-parameter/679935.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/679936.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/679937.rdf
Name: date_collected
Units: unitless
Description: <p>collection date formatted as m-yyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/679938.rdf
Name: NCBI_COI_accession
Units: unitless
Description: <p>COI gene GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/679939.rdf
Name: NCBI_16S_accession
Units: unitless
Description: <p>16S gene GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/679940.rdf
Name: NCBI_H3_accession
Units: unitless
Description: <p>H3 gene GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/679941.rdf
Name: NCBI_COI_accession_link
Units: unitless
Description: <p>link to COI gene GenBank accession page</p>
http://lod.bco-dmo.org/id/dataset-parameter/679942.rdf
Name: NCBI_16S_accession_link
Units: unitless
Description: <p>link to 16S gene GenBank accession page</p>
http://lod.bco-dmo.org/id/dataset-parameter/679943.rdf
Name: NCBI_H3_accession_link
Units: unitless
Description: <p>link to H3 gene 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
6257
https://datadocs.bco-dmo.org/file/N77GgxXs9qn55l/dataset2_Elysia_seqs.csv
dataset2_Elysia_seqs.csv
Primary data file for dataset ID 679922
download
https://osprey.bco-dmo.org/dataset/679922/data/download
download
onLine
dataset
<p>Purified PCR products were directly cycle-sequenced in both directions using PCR primers and Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).&nbsp; Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software.</p>
<p>For full details on sampling and analytical methodology, see Krug et al (2012).</p>
Specified by the Principal Investigator(s)
<p>Sequences were edited to remove primer sequences.</p>
<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 />
- nd (no data) was entered into all blank cells<br />
- converted latitude and longitude to decimal degrees<br />
- added column with species name and removed columns with species specimen count totals<br />
- added links to NCBI accessions</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:Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems). 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: Krug_lab
Krug_lab
Cal State LA
laboratory
Krug_lab
Patrick Krug
California State University Los Angeles
Cal State LA
laboratory