ERDDAP > info > bcodmo_dataset_715506

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data			files	public	Molecular species delimitation and gene flow in Oxynoe (PLDvFST project)		I   M	background			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 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	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/
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.