http://lod.bco-dmo.org/id/dataset/699954
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-05-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project)
2017-05-15
publication
2017-05-15
revision
BCO-DMO Linked Data URI
2017-05-15
creation
http://lod.bco-dmo.org/id/dataset/699954
Erica Goetze
University of Hawaiʻi at Mānoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Goetze, E. (2017) Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-05-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/699954 [access date]
H. longicornis SRA, accessions, collection info Dataset Description: <p>This data submission consists of specimen collection information and next-generation sequencing data (Illumina MiSeq v3 - 300bp PE reads) from pooled DNA libraries of three putative Haloptilus longicornis clades that have sympatric distributions in the North Atlantic Ocean. Specimens were collected during the 2010 Atlantic Meridional Transect cruise (AMT20). 113 total H. longicornis were pooled into three clades as defined by reciprocal monophly and fixed differences in mtDNA cytochrome oxidase c subunit II. The aim of this project is to utilize reduced representation genomic data to assess whether there is concordance between the three putative H. longicornis clades demarcated with mtCOII and clades determined using other regions of the genome. Earlier work indicates only two clades are detected using microsatellite loci, and this project will broaden the genomic scope of that investigation.</p>
<p>The sequences are archived at NCBI, BioProject&nbsp;PRJNA369182&nbsp;[https://www.ncbi.nlm.nih.gov/bioproject/PRJNA369182]</p>
<p>The publisher requires that this item is embargoed until <strong>2018-01-01</strong>. Please check back after <strong>2018-01-01</strong>.</p> Methods and Sampling: <p>If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.</p>
<p>From the cruise report: not yet available</p>
<p><strong>Sample collection.</strong> A total of 113 H. longicornis individuals from three putative clades were collected from five different locations in the North Atlantic Basin during the Atlantic Meridional Transect cruise in 2010 (AMT20) for this analysis. 81 individuals from putative clade 1 were collected from two sites, 20 individuals from putative clade 2 were collected from four sites (one of which was the same as one of the clade one locations), and 12 individuals from putative clade 3 were collected from the same four sites as the clade 2 individuals.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1338959 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1338959
onGoing
Erica Goetze
University of Hawaiʻi at Mānoa
808-956-7156
Department of Oceanography, University of Hawaii at Manoa 1000 Pope Road
Honolulu
HI
96822
United States
egoetze@hawaii.edu
pointOfContact
asNeeded
Unknown
bioproject_accession
biosample_accession
library_ID
title
sample_name
design_description
filename
cruise_id
station
lat_collection
lon_collection
date_collection
Illumina HiSeq 2500
WP2
theme
None, User defined
sample identification
No BCO-DMO term
file_name
Cruise identfier
station number
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Bongo Net
Thermal Cycler
instrument
BCO-DMO Standard Instruments
JC079
JC053
service
Deployment Activity
Southampton, UK to Punta Arenas, Chile
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Basin-scale genetics of marine zooplankton
https://osprey.bco-dmo.org/project/537991
Basin-scale genetics of marine zooplankton
<p><em>Description from NSF award abstract:</em><br />
Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.</p>
<p>Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the <a href="http://dmoserv3.whoi.edu/data_docs/Goetze/AMT24_cruise/GOETZE_AMT24_Cruise_Report.pdf" target="_blank">AMT24 zooplankton ecology cruise report (PDF)</a>.</p>
<p>Online science outreach blog at: <a href="https://atlanticplankton.wordpress.com" target="_blank">https://atlanticplankton.wordpress.com</a></p>
Plankton Population Genetics
largerWorkCitation
project
eng; USA
biota
oceans
Southampton, UK to Punta Arenas, Chile
2017-05-15
Atlantic Ocean, 46 N - 46 S
0
BCO-DMO catalogue of parameters from Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/699964.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699965.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699966.rdf
Name: library_ID
Units: unitless
Description: <p>NCBI Library identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/699967.rdf
Name: title
Units: unitless
Description: <p>NCBI sample title</p>
http://lod.bco-dmo.org/id/dataset-parameter/699968.rdf
Name: sample_name
Units: unitless
Description: <p>short sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/699969.rdf
Name: design_description
Units: unitless
Description: <p>NCBI Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.</p>
http://lod.bco-dmo.org/id/dataset-parameter/699970.rdf
Name: filename
Units: unitless
Description: <p>NCBI file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/699971.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/699972.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699973.rdf
Name: lat_collection
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/699974.rdf
Name: lon_collection
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/699975.rdf
Name: date_collection
Units: unitless
Description: <p>collection date formatted as yyyy-mm-dd</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/699954/data/download
download
onLine
dataset
<p>If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.</p>
<p>From the cruise report: not yet available</p>
<p><strong>Sample collection.</strong> A total of 113 H. longicornis individuals from three putative clades were collected from five different locations in the North Atlantic Basin during the Atlantic Meridional Transect cruise in 2010 (AMT20) for this analysis. 81 individuals from putative clade 1 were collected from two sites, 20 individuals from putative clade 2 were collected from four sites (one of which was the same as one of the clade one locations), and 12 individuals from putative clade 3 were collected from the same four sites as the clade 2 individuals.</p>
Specified by the Principal Investigator(s)
<p>Contact: Erica Goetze for any questions, or for subsequent use of these data.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
added conventional header with dataset name, PI name, version date<br />
modified parameter names to conform with BCO-DMO naming conventions<br />
combined SRA metadata with collection information<br />
converted latitude and longitude to decimal degrees</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
WP2
WP2
PI Supplied Instrument Name: WP2 PI Supplied Instrument Description:200µm mesh size; 0-300 meters vertical haul to collect copepods. Instrument Name: Bongo Net Instrument Short Name:Bongo Net Instrument Description: A Bongo Net consists of paired plankton nets, typically with a 60 cm diameter mouth opening and varying mesh sizes, 10 to 1000 micron. The Bongo Frame was designed by the National Marine Fisheries Service for use in the MARMAP program. It consists of two cylindrical collars connected with a yoke so that replicate samples are collected at the same time. Variations in models are designed for either vertical hauls (OI-2500 = NMFS Pairovet-Style, MARMAP Bongo, CalVET) or both oblique and vertical hauls (Aquatic Research). The OI-1200 has an opening and closing mechanism that allows discrete "known-depth" sampling. This model is large enough to filter water at the rate of 47.5 m3/minute when towing at a speed of two knots. More information: Ocean Instruments, Aquatic Research, Sea-Gear Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0009/
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: JC079
JC079
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel
JC079
Glen Tarran
Plymouth Marine Laboratory
http://dmoserv3.whoi.edu/data_docs/Goetze/AMT22_cruise/jc079.pdf
Report describing JC079
Cruise: JC053
JC053
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel
JC053
James Rees
Plymouth Marine Laboratory
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel