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Grid DAP Data | Sub- set | Table DAP Data | Make A Graph | W M S | Source Data Files | Acces- sible | Title | Sum- mary | FGDC, ISO, Metadata | Back- ground Info | RSS | E | Institution | Dataset ID |
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data | files | public | [dataset8- Oxynoe sequence data] - Molecular species delimitation and gene flow in Oxynoe (PLDvFST project) (Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions) | I M | background | BCO-DMO | bcodmo_dataset_715506 |
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 access. |
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 |
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/ |
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 |
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 |
attribute | NC_GLOBAL | metadata_source | String | https://www.bco-dmo.org/api/dataset/715506 |
attribute | NC_GLOBAL | param_mapping | String | {'715506': {}} |
attribute | NC_GLOBAL | parameter_source | String | https://www.bco-dmo.org/mapserver/dataset/715506/parameters |
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 | [dataset8- Oxynoe sequence data] - Molecular species delimitation and gene flow in Oxynoe (PLDvFST project) (Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions) |
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/ |
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/ |
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.