ERDDAP > info > bcodmo_dataset_768138

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 mail	Institution	Dataset ID
		data			files	public	[Palau lakes: invertebrate barcodes] - Specimen log with OTU identifiers collected from Palau marine lakes (Do Parallel Patterns Arise from Parallel Processes?)		I   M	background			BCO-DMO	bcodmo_dataset_768138

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	After completion of fieldwork, a subset of specimens from the transect surveys were chosen for DNA barcoding to confirm or amend field identifications. These specimens included (i) at least one specimen from each field-ID (except obvious species such as Mastigias papua) and (ii) several specimens representing the range of phenotypic variation of field-IDs that showed considerable variation or were challenging to distinguish (e.g. small sponge specimens of similar color and texture). Additionally, specimens from a previously collected voucher collection (indicated with \u201cV_\u201d in prefix of sequence ID) were barcoded and identified by taxonomic experts. Specimens from population genetic collections (indicated with \u201cPG_\u201d in prefix of sequence ID) were also barcoded. DNA was purified using a modified phenol-chloroform CTAB extraction protocol (1) or AcroPrep PALL 5053 glass fiber plates procedure (2, 3). We amplified the Cytochrome c Oxidase subunit I (COI) barcode locus using 0.5 \u00b5L of purified DNA in a 25-\u00b5L polymerase chain reaction (PCR) with 0.05 \u00b5L AMPLITAQ (Applied Biosystems, Foster City, California, USA), 2.5 \u00b5L 10x buffer (Applied Biosystems), 0.63 \u00b5L of 20 \u00b5M primers (Operon Biotechnologies Inc., Huntsville, Alabama, USA), 2.5 \u00b5L of 25 mM MgCl2 (Applied Biosystems), 0.5 \u00b5L of 10 mg/mL bovine serum albumin (BSA) and 0.5 \u00b5L of 10 mM dNTPs. Several primer sets were used (Table 1). Amplicons were sequenced at the University of California Berkeley DNA Sequencing Facility (Berkeley, California, USA). Base calls in electropherograms were visually checked and manually corrected for errors and forward and reverse reads were assembled in Sequencher 4.8 (GeneCodes, Ann Arbor, Michigan, USA). We used Basic Local Alignment Search Tool (BLASTn) to determine the higher level taxonomic assignment for each sequence (which we used to process batches of similar sequences) \u2014 ascidians, bivalves, bryozoans, cnidarians, crustaceans, echinoderms, gastropods, polychaetes, and poriferans. Sequences organized by these broad groups were then aligned using Muscle v3.8.425 (4). For each group, alignments were manually adjusted and trimmed to the same length in Mesquite v3.5 (5) to balance total individuals retained and sequence length. The resulting alignment lengths were: ascidians 395bp, bivalves 567bp, bryozoans 622bp, cnidarians 612bp, crustaceans 299bp, echinoderms 357bp, gastropods 562bp, polychaetes 509bp, and poriferans 688bp. Sequences were translated to amino acid sequence to confirm an open reading frame. Short sequences were excluded from further analysis, but percent pairwise identity with the closest match was recorded for each based on the shortest sequence. Pairwise sequence distance was calculated using dist.dna with Kimura\u2019s 2-parameter distance model of evolution (6) in the ape package v4.1 (7) in R (8). OTUs, or clusters of sequences, similar at 97% were identified using tclust in the spider package v1.5.0 (9) in R (8) for each taxonomic group, except for poriferans, which were clustered at 99% sequence similarity given their slow sequence evolution (10). 1\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Dawson MN, Raskoff KA, Jacobs DK (1998) Field preservation of marine invertebrate tissue for DNA analyses. Mol Mar Biol Biotechnol 7(2):145\u201352. 2\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Ivanova N V., Dewaard JR, Hebert PDN (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol Ecol Notes 6(4):998\u20131002. 3\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Schiebelhut LM, Abboud SS, G\u00f3mez Daglio LE, Swift HF, Dawson MN (2017) A comparison of DNA extraction methods for high-throughput DNA analyses. Mol Ecol Resour 17(4):721\u2013729. 4\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792\u20131797. 5\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Maddison WP, Maddison DR (2018) Mesquite: a modular system for evolutionary analysis. 6\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111\u2013120. 7\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Paradis E, Claude J, Strimmer K (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20(2):289\u2013290. 8\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 R Core Team (2018) R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria). 9\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 BROWN SDJ, et al. (2012) Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Mol Ecol Resour 12(3):562\u2013565. 10\. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Huang D, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66(2):167\u2013174. See Table 1.\u00a0Primers and thermocycle conditions used for PCR of macroinvertebrates by taxonomic group in Supplemental Documents, below. For the sequence alignment files (.fas) mentioned in the methods above, see the Supplemental Files section below.
attribute	NC_GLOBAL	awards_0_award_nid	String	55103
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1241255
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1241255
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	PaPaPro barcoding: surveyed specimens and vouchers M. Dawson (UC-Merced) version date: 2019-05-13
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	2019-05-16T13:22:49Z
attribute	NC_GLOBAL	date_modified	String	2020-03-05T13:50:02Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.768138.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/768138
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	768177
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_1_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	768178
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	array, array-data, bco, bco-dmo, biological, chemical, class, code, comprehensive, crrf, CRRF_ID, data, dataset, dmo, erddap, family, genus, lake, lake_code, large, management, name, oceanography, office, order, otu, OTU_id, phylum, preliminary, sequence, SequenceName, species, stewardship, system
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/768138/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/768138
attribute	NC_GLOBAL	param_mapping	String	{'768138': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/768138/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of California-Merced
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UC Merced
attribute	NC_GLOBAL	people_0_person_name	String	Michael N Dawson
attribute	NC_GLOBAL	people_0_person_nid	String	51577
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	project	String	PaPaPro
attribute	NC_GLOBAL	projects_0_acronym	String	PaPaPro
attribute	NC_GLOBAL	projects_0_description	String	This project will survey the taxonomic, genetic, and functional diversity of the organisms found in marine lakes, and investigate the processes that cause gains and losses in this biodiversity. Marine lakes formed as melting ice sheets raised sea level after the last glacial maximum and flooded hundreds of inland valleys around the world. Inoculated with marine life from the surrounding sea and then isolated to varying degrees for the next 6,000 to 15,000 years, these marine lakes provide multiple, independent examples of how environments and interactions between species can drive extinction and speciation. Researchers will survey the microbes, algae, invertebrates, and fishes present in 40 marine lakes in Palau and Papua, and study how diversity has changed over time by retrieving the remains of organisms preserved in sediments on the lake bottoms. The project will test whether the number of species, the diversity of functional roles played by organisms, and the genetic diversity within species increase and decrease in parallel; whether certain species can greatly curtail diversity by changing the environment; whether the size of a lake determines its biodiversity; and whether the processes that control diversity in marine organisms are similar to those that operate on land. Because biodiversity underlies the ecosystem services on which society depends, society has a great interest in understanding the processes that generate and retain biodiversity in nature. This project will also help conserve areas of economic importance. Marine lakes in the study region are important for tourism, and researchers will work closely with governmental and non-governmental conservation and education groups and with diving and tourism businesses to raise awareness of the value and threats to marine lakes in Indonesia and Palau.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-12
attribute	NC_GLOBAL	projects_0_geolocation	String	Western Pacific; Palau; Indonesia (West Papua)
attribute	NC_GLOBAL	projects_0_name	String	Do Parallel Patterns Arise from Parallel Processes?
attribute	NC_GLOBAL	projects_0_project_nid	String	2238
attribute	NC_GLOBAL	projects_0_project_website	String	http://marinelakes.ucmerced.edu/
attribute	NC_GLOBAL	projects_0_start_date	String	2013-01
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	List of all barcoded specimens of collected invertebrates with sequence name and OTU identifier collected from Palau marine lakes. FASTA files for major invertebrate groups are included in supplemental files.
attribute	NC_GLOBAL	title	String	[Palau lakes: invertebrate barcodes] - Specimen log with OTU identifiers collected from Palau marine lakes (Do Parallel Patterns Arise from Parallel Processes?)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	OTU_id		String
attribute	OTU_id	bcodmo_name	String	sample
attribute	OTU_id	description	String	Operational Taxonomic Unit identifier. The first four-letters describe the taxon: ASCI: Ascidiacea BIVA: MolluscaBivalvia BRYO: Bryozoa CNID: Cnidaria CRUS: Crustacea ECHI: Echinodermata GAST: MolluscaGastropoda POLY: Polychaeta PORI: Porifera
attribute	OTU_id	long_name	String	OTU Id
attribute	OTU_id	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	OTU_id	units	String	unitless
variable	ID		String
attribute	ID	bcodmo_name	String	taxon
attribute	ID	description	String	Identification of specimens in OTU
attribute	ID	long_name	String	ID
attribute	ID	units	String	unitless
variable	lake_code		String
attribute	lake_code	bcodmo_name	String	site
attribute	lake_code	description	String	3-letter code for sampled lake name
attribute	lake_code	long_name	String	Lake Code
attribute	lake_code	units	String	unitless
variable	SequenceName		String
attribute	SequenceName	bcodmo_name	String	sample
attribute	SequenceName	description	String	This is the name of the DNA sequences in the alignment (a prefix of "PG_" has been added for individuals that were taken from the popgen dataset; a prefix of "V_" has been added for individuals in the voucher dataset identified by taxonomic experts)
attribute	SequenceName	long_name	String	Sequence Name
attribute	SequenceName	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	SequenceName	units	String	unitless
variable	Phylum		String
attribute	Phylum	bcodmo_name	String	phylum
attribute	Phylum	description	String	Phylum assigned by taxonomic expert
attribute	Phylum	long_name	String	Phylum
attribute	Phylum	units	String	unitless
variable	Class		String
attribute	Class	bcodmo_name	String	class
attribute	Class	description	String	Class assigned by taxonomic expert
attribute	Class	long_name	String	Class
attribute	Class	units	String	unitless
variable	Order		String
attribute	Order	bcodmo_name	String	order
attribute	Order	description	String	Order assigned by taxonomic expert
attribute	Order	long_name	String	Order
attribute	Order	units	String	unitless
variable	Family		String
attribute	Family	bcodmo_name	String	family
attribute	Family	description	String	Family assigned by taxonomic expert
attribute	Family	long_name	String	Family
attribute	Family	units	String	unitless
variable	Genus		String
attribute	Genus	bcodmo_name	String	genus
attribute	Genus	description	String	Genus assigned by taxonomic expert
attribute	Genus	long_name	String	Genus
attribute	Genus	units	String	unitless
variable	Species		String
attribute	Species	bcodmo_name	String	species_epithet
attribute	Species	description	String	Species assigned by taxonomic expert
attribute	Species	long_name	String	Species
attribute	Species	units	String	unitless
variable	CRRF_ID		String
attribute	CRRF_ID	bcodmo_name	String	sample
attribute	CRRF_ID	description	String	internal ID number for voucher sample
attribute	CRRF_ID	long_name	String	CRRF ID
attribute	CRRF_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	CRRF_ID	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.