http://lod.bco-dmo.org/id/dataset/715506
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
2017-09-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)
2017-09-22
publication
2017-09-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-06-12
publication
https://doi.org/10.1575/1912/bco-dmo.715506.1
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
documentDigital
Cite this dataset as: Krug, P. (2017) Molecular species delimitation and gene flow in Oxynoe (PLDvFST project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Dataset version 2017-09-22 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.715506.1 [access date]
Species names, sample codes, and collection details for sequenced taxa used in phylogenetic analyses. Dataset Description: <p>Species names, sample codes, and collection details for sequenced sea slugs in the family Oxynoidae that were used in phylogenetic analyses. Collections range from 1974 to 2014 from global locations near Florida, the Caribbean, and the East and West Pacific Ocean. Data are accessioned through the NCBI GenBank database.</p> Acquisition Description: <p>Purified PCR products were directly cycle-sequenced in both directions using PCR primers and Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego).&nbsp; Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software.&nbsp; Samples for morphological analysis were deposited in museum collections, sequences were archived in GenBank for public access.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130072 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1130072
completed
Patrick Krug
California State University Los Angeles
3233432076
5151 State University Drive
Los Angeles
CA
900324221
pkrug@calstatela.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
isolate_code
specimen_accession_numbers
collection_site
date
collector
accession_COI
accession_16S
accession_H3
Automated sequencer
theme
None, User defined
species
sample identification
accession number
site
date
person name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
PCR Thermal Cycler
instrument
BCO-DMO Standard Instruments
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://www.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
1974-07-01
2014-12-31
Florida and Caribbean
0
BCO-DMO catalogue of parameters from Molecular species delimitation and gene flow in Oxynoe (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/715514.rdf
Name: species
Units: unitless
Description: Species
http://lod.bco-dmo.org/id/dataset-parameter/715515.rdf
Name: isolate_code
Units: unitless
Description: Isolate code
http://lod.bco-dmo.org/id/dataset-parameter/715516.rdf
Name: specimen_accession_numbers
Units: unitless
Description: Accession numbers. 1AM = Australian Museum (Sydney, Australia) malacology collection; LACM = Los Angeles County Museum of Natural History malacology collection.
http://lod.bco-dmo.org/id/dataset-parameter/715517.rdf
Name: collection_site
Units: unitless
Description: Collection site
http://lod.bco-dmo.org/id/dataset-parameter/715518.rdf
Name: date
Units: unitless
Description: Date
http://lod.bco-dmo.org/id/dataset-parameter/715519.rdf
Name: collector
Units: unitless
Description: Collector's name. AAV = Angel A. Valdes; AH = Alicia Hermosillo; CDT = Cynthia D. Trowbridge; DH = Dai Herbert; DJM = Dustin J. Marshall; MAP = Mark A. Phuong; NGW = Nerida G. Wilson; PJK = Patrick Joseph Krug; RAE = Ryan A. Ellingson; YB = Yan Buske; YMH = Yayoi M. Hirano
http://lod.bco-dmo.org/id/dataset-parameter/715520.rdf
Name: accession_COI
Units: unitless
Description: COI gene GenBank accession number
http://lod.bco-dmo.org/id/dataset-parameter/715521.rdf
Name: accession_16S
Units: unitless
Description: 16S gene GenBank accession number
http://lod.bco-dmo.org/id/dataset-parameter/715522.rdf
Name: accession_H3
Units: unitless
Description: H3 gene GenBank accession number
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
https://www.bco-dmo.org/dataset/715506/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 Retrogen, Inc. (San Diego).&nbsp; Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software.&nbsp; Samples for morphological analysis were deposited in museum collections, sequences were archived in GenBank for public access.</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
Automated sequencer
Automated sequencer
PI Supplied Instrument Name: Automated sequencer PI Supplied Instrument Description:Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego) Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
PI Supplied Instrument Name: Instrument Name: PCR Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)