http://lod.bco-dmo.org/id/dataset/699234
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
2017-05-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Overview of population samples included in genetic analyses of Pleuromamma xiphias (Plankton Population Genetics)
2017-05-01
publication
2017-05-01
revision
BCO-DMO Linked Data URI
2017-05-01
creation
http://lod.bco-dmo.org/id/dataset/699234
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) Overview of population samples included in genetic analyses of Pleuromamma xiphias (Plankton Population Genetics). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 01 May 2017 ) Version Date 2017-05-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/699234 [access date]
Overview of population samples included in genetic analyses of Pleuromamma xiphias Dataset Description: <p>Overview of population samples that were included in genetic analyses of Pleuromamma xiphias from across the Atlantic Ocean. Specimens were collected on the Atlantic Meridional Transect 22 (AMT22) cruise on RRS James Cook from Oct-Nov 2012. Data columns include collection location and date, ocean biome, number of individuals sampled (N), number of haplotypes observed (H), the ratio of haplotypes to sample size (H/N), haplotype diversity (h) and nucleotide diversity (π) for each site. 'Pop' indicates whether the sample was included in population genetic analyses (Yes/No, see Goetze et al. 2016 for explanation).</p>
<p>These data are also published in Table 1 of:<br />
Goetze, E., Hüdepohl, P., Chang, C., Iacchei, M., Van Woudenberg, L., Peijnenburg, K. T. C. A. (2016) Ecological dispersal barrier across the equatorial Atlantic in a migratory planktonic copepod. <em>Progress in Oceanography – AMT special issue. </em>doi:&nbsp;<a href="http://dx.doi.org/10.1016/j.pocean.2016.07.001" target="_blank">10.1016/j.pocean.2016.07.001</a></p>
<p><strong>Refer to the related dataset</strong>&nbsp;"<a href="https://www.bco-dmo.org/dataset/699440" target="_blank">Pxiphias PopStructure mtDNA</a>" for data files generated by the genetic analyses.</p> Methods and Sampling: <p><strong>Refer to the following publication for complete methodology details:</strong><br />
Goetze, E., Hüdepohl, P., Chang, C., Iacchei, M., Van Woudenberg, L., Peijnenburg, K. T. C. A. (2016) Ecological dispersal barrier across the equatorial Atlantic in a migratory planktonic copepod.&nbsp;<em>Progress in Oceanography – AMT special issue.&nbsp;</em>doi:&nbsp;<a href="http://dx.doi.org/10.1016/j.pocean.2016.07.001" target="_blank">10.1016/j.pocean.2016.07.001</a></p>
<p><strong>In summary (excerpted from above):</strong><br />
Bulk plankton samples were collected on Atlantic Meridional Transect Cruise 22 (AMT22) between 10/13/2012 and 11/19/2012. Oblique tows were conducted with bongo nets (200 um, 333 um), towed between on average 324 m depth and the sea surface. A General Oceanics flowmeter (2030RC) mounted in the mouth of the 200 um net was used to measure seawater filtered during the tow. Plankton from the 200 um mesh net was bulk preserved immediately in 100% ethyl alcohol, the alcohol was changed to fresh within 12–24 h of collection, and samples were stored at -20 C. Plankton from the 333 um mesh net was sorted live at sea, and Pleuromamma xiphias specimens were preserved immediately in RNALater (Ambion), followed by cryopreservation in liquid nitrogen, and long-term storage at -80 C.</p>
<p>Specimens included in the genetic analyses in this study were collected at 18 stations, located between 39 38.82N and 40 4.39S latitude. The majority of genetic analyses focused on stations with sufficient sample size for population-level inference (N &gt; 42), including AMT22-09 through AMT22-29 and AMT22-45 through AMT22-68. Specimens used in genetic analyses were primarily RNALater-preserved, but some specimens were included from ethanol-preserved samples to achieve the minimum target sample size of 45 individuals per station. When a major genetic break across the equatorial region was identified, we included samples from stations AMT22-31 through AMT22-43 to assess the genetic composition of populations across this region. Population-level analyses were not conducted on these latter stations due to small sample sizes&nbsp;and low abundance&nbsp;in this region, but sequences from these animals were included in the haplotype network. DNA was extracted from individual P. xiphias adults using the DNeasy Blood &amp; Tissue kit (Qiagen), following the manufacturer’s protocol, with the exception of longer elution incubation times (Goetze, 2011). The second of two elutions for each individual was used in this study. Polymerase Chain Reaction (PCR) amplification of a 681-bp fragment of mtCOI was conducted with primers and PCR and sequencing protocols as described in (Goetze, 2011). Forward and reverse sequences from each individual were aligned and checked for errors in Geneious (v7.1.8, Biomatters). Consensus sequences for all individuals were aligned using MUSCLE (Edgar, 2004), and unique mtCOI haplotypes were identified using FABox (<a href="http://users-birc.au.dk/biopv/php/fabox/" target="_blank">http://users-birc.au.dk/biopv/php/fabox/</a>). MtCOI sequences representing unique haplotypes are available under GenBank accession numbers KT429028–KT429159. A minimum spanning haplotype network was inferred for all mtCOI sequences using Population Analysis with Reticulate Trees (PopART; <a href="http://popart.otago.ac.nz" target="_blank">http://popart.otago.ac.nz</a>), in order to investigate geographic patterns in the distribution of haplotypes across the Atlantic.</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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029478 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029478
completed
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
Dataset Version: 01 May 2017
Unknown
ID
cruise_station
latitude
longitude
date
ocean_biome
pop
N
H
H_N
h
pi
bongo net
PCR
theme
None, User defined
sample identification
station number
latitude
longitude
date
site description
particulate organic phosphorus
number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Bongo Net
Thermal Cycler
instrument
BCO-DMO Standard Instruments
JC079
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
-42.3712545
-22.4662575
-40.0732082
39.6470388
2012-10-16
2012-11-17
Atlantic Ocean, 46 N - 46 S
0
BCO-DMO catalogue of parameters from Overview of population samples included in genetic analyses of Pleuromamma xiphias (Plankton Population Genetics)
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/699245.rdf
Name: ID
Units: unitless
Description: <p>Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/699246.rdf
Name: cruise_station
Units: unitless
Description: <p>Cruise and station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699247.rdf
Name: latitude
Units: decimal degrees
Description: <p>Station latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/699248.rdf
Name: longitude
Units: decimal degrees
Description: <p>Station longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/699249.rdf
Name: date
Units: unitless
Description: <p>Date of collection formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/699250.rdf
Name: ocean_biome
Units: unitless
Description: <p>Description of ocean biome at the sampling station.</p>
http://lod.bco-dmo.org/id/dataset-parameter/699251.rdf
Name: pop
Units: unitless
Description: <p>'pop' indicates whether the sample was included in population genetic analyses (Yes/No)</p>
http://lod.bco-dmo.org/id/dataset-parameter/699252.rdf
Name: N
Units: unitless
Description: <p>Number of individuals sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/699253.rdf
Name: H
Units: unitless
Description: <p>Number of haplotypes observed</p>
http://lod.bco-dmo.org/id/dataset-parameter/699254.rdf
Name: H_N
Units: unitless
Description: <p>The ratio of haplotypes to sample size (H/N)</p>
http://lod.bco-dmo.org/id/dataset-parameter/699255.rdf
Name: h
Units: unitless
Description: <p>Haplotype diversity</p>
http://lod.bco-dmo.org/id/dataset-parameter/699256.rdf
Name: pi
Units: unitless
Description: <p>Nucleotide diversity</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
1618
https://datadocs.bco-dmo.org/file/P66GkZ7hvy7rok/genetic_samples.csv
genetic_samples.csv
Primary data file for dataset ID 699234
download
https://osprey.bco-dmo.org/dataset/699234/data/download
download
onLine
dataset
<p><strong>Refer to the following publication for complete methodology details:</strong><br />
Goetze, E., Hüdepohl, P., Chang, C., Iacchei, M., Van Woudenberg, L., Peijnenburg, K. T. C. A. (2016) Ecological dispersal barrier across the equatorial Atlantic in a migratory planktonic copepod.&nbsp;<em>Progress in Oceanography – AMT special issue.&nbsp;</em>doi:&nbsp;<a href="http://dx.doi.org/10.1016/j.pocean.2016.07.001" target="_blank">10.1016/j.pocean.2016.07.001</a></p>
<p><strong>In summary (excerpted from above):</strong><br />
Bulk plankton samples were collected on Atlantic Meridional Transect Cruise 22 (AMT22) between 10/13/2012 and 11/19/2012. Oblique tows were conducted with bongo nets (200 um, 333 um), towed between on average 324 m depth and the sea surface. A General Oceanics flowmeter (2030RC) mounted in the mouth of the 200 um net was used to measure seawater filtered during the tow. Plankton from the 200 um mesh net was bulk preserved immediately in 100% ethyl alcohol, the alcohol was changed to fresh within 12–24 h of collection, and samples were stored at -20 C. Plankton from the 333 um mesh net was sorted live at sea, and Pleuromamma xiphias specimens were preserved immediately in RNALater (Ambion), followed by cryopreservation in liquid nitrogen, and long-term storage at -80 C.</p>
<p>Specimens included in the genetic analyses in this study were collected at 18 stations, located between 39 38.82N and 40 4.39S latitude. The majority of genetic analyses focused on stations with sufficient sample size for population-level inference (N &gt; 42), including AMT22-09 through AMT22-29 and AMT22-45 through AMT22-68. Specimens used in genetic analyses were primarily RNALater-preserved, but some specimens were included from ethanol-preserved samples to achieve the minimum target sample size of 45 individuals per station. When a major genetic break across the equatorial region was identified, we included samples from stations AMT22-31 through AMT22-43 to assess the genetic composition of populations across this region. Population-level analyses were not conducted on these latter stations due to small sample sizes&nbsp;and low abundance&nbsp;in this region, but sequences from these animals were included in the haplotype network. DNA was extracted from individual P. xiphias adults using the DNeasy Blood &amp; Tissue kit (Qiagen), following the manufacturer’s protocol, with the exception of longer elution incubation times (Goetze, 2011). The second of two elutions for each individual was used in this study. Polymerase Chain Reaction (PCR) amplification of a 681-bp fragment of mtCOI was conducted with primers and PCR and sequencing protocols as described in (Goetze, 2011). Forward and reverse sequences from each individual were aligned and checked for errors in Geneious (v7.1.8, Biomatters). Consensus sequences for all individuals were aligned using MUSCLE (Edgar, 2004), and unique mtCOI haplotypes were identified using FABox (<a href="http://users-birc.au.dk/biopv/php/fabox/" target="_blank">http://users-birc.au.dk/biopv/php/fabox/</a>). MtCOI sequences representing unique haplotypes are available under GenBank accession numbers KT429028–KT429159. A minimum spanning haplotype network was inferred for all mtCOI sequences using Population Analysis with Reticulate Trees (PopART; <a href="http://popart.otago.ac.nz" target="_blank">http://popart.otago.ac.nz</a>), in order to investigate geographic patterns in the distribution of haplotypes across the Atlantic.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- converted lat and lon from degrees and decimal minutes to decimal degrees;<br />
- changed date format to yyyy-mm-dd.</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
bongo net
bongo net
PI Supplied Instrument Name: bongo net PI Supplied Instrument Description:Oblique tows were conducted with bongo nets (200 um, 333 um), towed between on average 324 m depth and the sea surface. 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/
PCR
PCR
PI Supplied Instrument Name: PCR PI Supplied Instrument Description:Polymerase Chain Reaction (PCR) amplification of a 681-bp fragment of mtCOI was conducted with primers and PCR and sequencing protocols as described in (Goetze, 2011). 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
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel