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Dataset Title:  Molecular species delimitation and gene flow in Oxynoe (PLDvFST project) Subscribe RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_715506)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 species (unitless) ?          "L. viridis (Pease,..."    "Oxynoe viridis (Pe..."
 isolate_code (unitless) ?          "Lo_sou_09Cur01"    "Ovir_11How26"
 specimen_accession_numbers (unitless) ?          "-"    "LACM 3427"
 collection_site (unitless) ?          "Annes Beach, Flori..."    "Zanpa, Okinawa, Ja..."
 date (unitless) ?          "2003"    "Oct 2010"
 collector (unitless) ?          "AAV"    "unknown"
 accession_COI (unitless) ?          "-"    "KY581383"
 accession_16S (unitless) ?          "-"    "KY610380"
 accession_H3 (unitless) ?          "-"    "KY611442"
 
Server-side Functions ?
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  species {
    String bcodmo_name "species";
    String description "Species";
    String long_name "Species";
    String units "unitless";
  }
  isolate_code {
    String bcodmo_name "sample";
    String description "Isolate code";
    String long_name "Isolate Code";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  specimen_accession_numbers {
    String bcodmo_name "accession number";
    String description "Accession numbers. 1AM = Australian Museum (Sydney, Australia) malacology collection; LACM = Los Angeles County Museum of Natural History malacology collection.";
    String long_name "Specimen Accession Numbers";
    String units "unitless";
  }
  collection_site {
    String bcodmo_name "site";
    String description "Collection site";
    String long_name "Collection Site";
    String units "unitless";
  }
  date {
    String bcodmo_name "date";
    String description "Date";
    String long_name "Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  }
  collector {
    String bcodmo_name "person";
    String 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";
    String long_name "Collector";
    String units "unitless";
  }
  accession_COI {
    String bcodmo_name "accession number";
    String description "COI gene GenBank accession number";
    String long_name "Accession COI";
    String units "unitless";
  }
  accession_16S {
    String bcodmo_name "accession number";
    String description "16S gene GenBank accession  number";
    String long_name "Accession 16 S";
    String units "unitless";
  }
  accession_H3 {
    String bcodmo_name "accession number";
    String description "H3 gene GenBank accession number";
    String long_name "Accession H3";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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
access.";
    String awards_0_award_nid "615834";
    String awards_0_award_number "OCE-1130072";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1130072";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Dataset 8- Oxynoe sequence data (PLDvFST) 
  PI: Patrick Krug (Cal State LA) 
  Version: 2017-09-25";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2017-09-22T20:25:10Z";
    String date_modified "2019-06-12T18:59:57Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.715506.1";
    String history 
"2020-08-11T10:19:20Z (local files)
2020-08-11T10:19:20Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_715506.html";
    String infoUrl "https://www.bco-dmo.org/dataset/715506";
    String institution "BCO-DMO";
    String instruments_0_acronym "Automated Sequencer";
    String instruments_0_dataset_instrument_description "Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego)";
    String instruments_0_dataset_instrument_nid "715704";
    String instruments_0_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.";
    String instruments_0_instrument_name "Automated DNA Sequencer";
    String instruments_0_instrument_nid "649";
    String instruments_0_supplied_name "Automated sequencer";
    String instruments_1_acronym "Thermal Cycler";
    String instruments_1_dataset_instrument_nid "715705";
    String instruments_1_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)";
    String instruments_1_instrument_name "PCR Thermal Cycler";
    String instruments_1_instrument_nid "471582";
    String keywords "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";
    String license "https://www.bco-dmo.org/dataset/715506/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/715506";
    String param_mapping "{'715506': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/715506/parameters";
    String people_0_affiliation "California State University Los Angeles";
    String people_0_affiliation_acronym "Cal State LA";
    String people_0_person_name "Patrick Krug";
    String people_0_person_nid "615837";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI BCO-DMO";
    String people_1_person_name "Nancy Copley";
    String people_1_person_nid "50396";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Megan Switzer";
    String people_2_person_nid "708683";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "PLDvFST";
    String projects_0_acronym "PLDvFST";
    String projects_0_description 
"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.";
    String projects_0_end_date "2016-07";
    String projects_0_geolocation "Florida and Caribbean";
    String projects_0_name "Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions";
    String projects_0_project_nid "615835";
    String projects_0_start_date "2011-09";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)";
    String title "Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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