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     data        files  public Barcoded specimen log with sequence name and OTU identifier collected from Palau marine lakes    ?         M   background (external link) RSS Subscribe 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 (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 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/ (external link)
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 (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_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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/768138 (external link)
attribute NC_GLOBAL param_mapping String {'768138': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/768138/parameters (external link)
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/ (external link)
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 Barcoded specimen log with sequence name and OTU identifier collected from Palau marine lakes
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/ (external link)
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/ (external link)
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/ (external link)
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.


 
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