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Title Sum-
Institution Dataset ID
     data        files  public Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)    ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_715506

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String 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).\u00a0 Chromatograms were edited and primer sequences removed
in GeneiousPro 4.8 software.\u00a0 Samples for morphological analysis were
deposited in museum collections, sequences were archived in GenBank for public
attribute NC_GLOBAL awards_0_award_nid String 615834
attribute NC_GLOBAL awards_0_award_number String OCE-1130072
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1130072 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Dataset 8- Oxynoe sequence data (PLDvFST)
PI: Patrick Krug (Cal State LA)
Version: 2017-09-25
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2017-09-22T20:25:10Z
attribute NC_GLOBAL date_modified String 2019-06-12T18:59:57Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.715506.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/715506 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego)
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 715704
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String Automated sequencer
attribute NC_GLOBAL instruments_1_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 715705
attribute NC_GLOBAL instruments_1_description String 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)
attribute NC_GLOBAL instruments_1_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_1_instrument_nid String 471582
attribute NC_GLOBAL keywords String accession, accession_16S, accession_COI, accession_H3, bco, bco-dmo, biological, chemical, code, coi, collection, collection_site, collector, data, dataset, date, dmo, erddap, isolate, isolate_code, management, numbers, oceanography, office, preliminary, site, species, specimen, specimen_accession_numbers
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/715506/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/715506 (external link)
attribute NC_GLOBAL param_mapping String {'715506': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/715506/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String California State University Los Angeles
attribute NC_GLOBAL people_0_affiliation_acronym String Cal State LA
attribute NC_GLOBAL people_0_person_name String Patrick Krug
attribute NC_GLOBAL people_0_person_nid String 615837
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Megan Switzer
attribute NC_GLOBAL people_2_person_nid String 708683
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String PLDvFST
attribute NC_GLOBAL projects_0_acronym String PLDvFST
attribute NC_GLOBAL projects_0_description String 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.
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.
attribute NC_GLOBAL projects_0_end_date String 2016-07
attribute NC_GLOBAL projects_0_geolocation String Florida and Caribbean
attribute NC_GLOBAL projects_0_name String Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions
attribute NC_GLOBAL projects_0_project_nid String 615835
attribute NC_GLOBAL projects_0_start_date String 2011-09
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)
attribute NC_GLOBAL title String Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable species   String  
attribute species bcodmo_name String species
attribute species description String Species
attribute species long_name String Species
attribute species units String unitless
variable isolate_code   String  
attribute isolate_code bcodmo_name String sample
attribute isolate_code description String Isolate code
attribute isolate_code long_name String Isolate Code
attribute isolate_code nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute isolate_code units String unitless
variable specimen_accession_numbers   String  
attribute specimen_accession_numbers bcodmo_name String accession number
attribute specimen_accession_numbers description String Accession numbers. 1AM = Australian Museum (Sydney, Australia) malacology collection; LACM = Los Angeles County Museum of Natural History malacology collection.
attribute specimen_accession_numbers long_name String Specimen Accession Numbers
attribute specimen_accession_numbers units String unitless
variable collection_site   String  
attribute collection_site bcodmo_name String site
attribute collection_site description String Collection site
attribute collection_site long_name String Collection Site
attribute collection_site units String unitless
variable date   String  
attribute date bcodmo_name String date
attribute date description String Date
attribute date long_name String Date
attribute date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date units String unitless
variable collector   String  
attribute collector bcodmo_name String person
attribute collector description String 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
attribute collector long_name String Collector
attribute collector units String unitless
variable accession_COI   String  
attribute accession_COI bcodmo_name String accession number
attribute accession_COI description String COI gene GenBank accession number
attribute accession_COI long_name String Accession COI
attribute accession_COI units String unitless
variable accession_16S   String  
attribute accession_16S bcodmo_name String accession number
attribute accession_16S description String 16S gene GenBank accession number
attribute accession_16S long_name String Accession 16 S
attribute accession_16S units String unitless
variable accession_H3   String  
attribute accession_H3 bcodmo_name String accession number
attribute accession_H3 description String H3 gene GenBank accession number
attribute accession_H3 long_name String Accession H3
attribute accession_H3 units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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