http://lod.bco-dmo.org/id/dataset/636335
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
2016-01-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Acropora palmata genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change project)
2016-01-22
publication
2016-01-22
revision
BCO-DMO Linked Data URI
2016-01-22
creation
http://lod.bco-dmo.org/id/dataset/636335
Iliana B. Baums
Pennsylvania State University
principalInvestigator
Dana E. Williams
University of Miami Rosenstiel School of Marine and Atmospheric Science
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: Baums, I. B., Williams, D. E. (2016) Acropora palmata genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2016.01.22) Version Date 2016-01-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636335 [access date]
Acropora palmata multilocus genotypes derived from five microsatellite markers Dataset Description: <p>Acropora palmata multilocus genotypes derived from five microsatellite markers.</p>
<p>&nbsp;</p> Methods and Sampling: <p>Adult Acropora palmata colonies were sampled (1 cm^2) with hammer and chisel and tissues were preserved in 96% non-denature Ethanol. DNA was extracted using the DNEasy tissue kit (Qiagen) following manufacturer’s instructions. Two multiplex Polymerase Chain Reactions (PCR) were performed per sample using fluorescently labeled primers to assay five loci containing AAT repeats. These five microsatellite loci have previously been demonstrated to be mendelian and coral-specific using controlled crosses (Baums et al., 2005). PCR products were visualized with an automated sequencer (ABI 3730). An internal size standard (Gene Scan 500-Liz, Applied Biosystems CA) ensured accurate sizing. Electropherograms were analyzed with GeneMapper Software 3.0 (Applied Biosystems, CA). Alleles were scored as PCR product size.</p>
<p>See Baums IB, Hughes CR, Hellberg MH (2005) for details.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1516763 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1516763
onGoing
Iliana B. Baums
Pennsylvania State University
814-867-0491
Department of Biology 208 Mueller Laboratory
University Park
PA
16802
USA
ibb3@psu.edu
pointOfContact
Dana E. Williams
University of Miami Rosenstiel School of Marine and Atmospheric Science
4600 Rickenbacker Causeway
Miami
FL
33149
USA
pointOfContact
asNeeded
Dataset Version: 2016.01.22
Unknown
region
reef
colony
sample
lat
lon
ID_database
ID_host_clonal
locus_166_allele1
locus_166_allele2
locus_181_allele1
locus_181_allele2
locus_182_allele1
locus_182_allele2
locus_192_allele1
locus_192_allele2
locus_207_allele1
locus_207_allele2
year
day_local
month_local
automated sequencer
theme
None, User defined
region
site
sample identification
replicate
latitude
longitude
individual
No BCO-DMO term
year
day_local
month_local
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Baums_FL_Keys_NMS
service
Deployment Activity
Multiple reefs throughout the Florida Keys National Marine Sanctuary, Key Largo Area
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.
RAPID: surviving climate change - the role of acclimatization in reef-building corals
https://osprey.bco-dmo.org/project/632663
RAPID: surviving climate change - the role of acclimatization in reef-building corals
<p><em>Description from NSF award abstract:</em><br />
August of 2014 was the warmest on record for the Florida Keys reef tract and by early September numerous corals species were severely stressed and looked bleached. This ongoing large-scale bleaching event provides an unprecedented opportunity to understand if prior stress exposure hardens individual coral colonies to future hot water events -- a process called acclimatization. This study combines long-term monitoring data of individual coral colonies with a stress experiment in the summer of 2015 to determine whether partially bleached colonies have acclimatized, to what extent, and by what means. The answers may fundamentally shape our understanding of how reefs might survive climate change. This is important because tropical coral reefs harbor more species then tropical rainforests and generate billions of dollars each year for local and national economies. The focal species of this project is the endangered elkhorn coral, Acropora palmata and results of the work can be used directly by managers when choosing coral colonies for conservation. The project will educate and train the public and public institutions on numerous levels. The scientists have partnered with the Coral Restoration Foundation, a non-for profit organization that delivers scientific knowledge and hands on experience in coral restoration to over 300 high school students per year. Postdoctoral scholars, and students are an integral part of this project and will receive training in field and laboratory work and lecture courses.</p>
<p>Acclimatization is a non-genetic process by which an individual heightens its tolerance after exposure to a stressor, such as temperature anomalies. Recent work has shown that acclimatization may be an important process by which corals may survive climate change. However, because reef-building corals harbor endosymbiotic Symbiodinium, discerning the relative contribution of host and symbiont to acclimatization can be difficult. The endangered Caribbean elkhorn coral, Acropora palmata, has an uncomplicated symbiosis: it associates with just one symbiont species (Symbiodinium fitti) and most colonies also harbor only one strain of S. fitti over space and time. August of 2014 was the warmest on record for the Florida Keys reef tract and by early September numerous corals species were severely stressed and looked bleached. This event provides an unprecedented opportunity to understand the role of acclimatization in reef corals. Initial surveys of A. palmata documented a range of bleaching response. This response varied between reefs but also within single, monoclonal stands of A. palmata. Thus, coral clone mates were observed to exhibit different bleaching susceptibilities despite indications that they share identical (clonal) symbiont communities, begging the question as to what mechanisms account for such differences. The answers may fundamentally shape our understanding of how reefs might survive climate change. Immediate support is requested to sample coral colonies while they are still bleached and for which long term performance histories exist. Results from this initial assessment are essential to inform the centerpiece of the proposal: a stress experiment to determine whether partially bleached colonies have acclimatized, to what extent, and by what means.</p>
<p>This is an NSF Collaborative Research project.</p>
Surviving Climate Change
largerWorkCitation
project
eng; USA
biota
oceans
Multiple reefs throughout the Florida Keys National Marine Sanctuary, Key Largo Area
2016-01-22
Florida Keys National Marine Sanctuary, Key Largo area
0
BCO-DMO catalogue of parameters from Acropora palmata genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change 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/636342.rdf
Name: region
Units: dimensionless
Description: <p>Region where coral colony was sampled.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636344.rdf
Name: reef
Units: dimensionless
Description: <p>Reef where coral colony was sampled.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636345.rdf
Name: colony
Units: dimensionless
Description: <p>Colony identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636346.rdf
Name: sample
Units: dimensionless
Description: <p>Sample identification number cosisting of colony identification number and replicate number (A-Z).</p>
http://lod.bco-dmo.org/id/dataset-parameter/636690.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude component of geographic sampling location, where positive is North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636692.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude component of geographic sampling location, where positive is East.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636879.rdf
Name: ID_database
Units: dimensionless
Description: <p>Baums Database access number</p>
http://lod.bco-dmo.org/id/dataset-parameter/636880.rdf
Name: ID_host_clonal
Units: dimensionless
Description: <p>Unique identifier of host genet</p>
http://lod.bco-dmo.org/id/dataset-parameter/636881.rdf
Name: locus_166_allele1
Units: base pairs
Description: <p>Allele size 1 for locus 166.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636882.rdf
Name: locus_166_allele2
Units: base pairs
Description: <p>Allele size 2 for locus 166.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636883.rdf
Name: locus_181_allele1
Units: base pairs
Description: <p>Allele size 1 for locus 181.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636884.rdf
Name: locus_181_allele2
Units: base pairs
Description: <p>Allele size 2 for locus 181.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636885.rdf
Name: locus_182_allele1
Units: base pairs
Description: <p>Allele size 1 for locus 182.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636886.rdf
Name: locus_182_allele2
Units: base pairs
Description: <p>Allele size 2 for locus 182.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636887.rdf
Name: locus_192_allele1
Units: base pairs
Description: <p>Allele size 1 for locus 192.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636888.rdf
Name: locus_192_allele2
Units: base pairs
Description: <p>Allele size 2 for locus 192.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636889.rdf
Name: locus_207_allele1
Units: base pairs
Description: <p>Allele size 1 for locus 207.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636890.rdf
Name: locus_207_allele2
Units: base pairs
Description: <p>Allele size 2 for locus 207.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636891.rdf
Name: year
Units: YYYY
Description: <p>year of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636892.rdf
Name: day_local
Units: DD
Description: <p>day of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636893.rdf
Name: month_local
Units: MM
Description: <p>month of sample collection.</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
7893
https://datadocs.bco-dmo.org/file/vmmwMOWTZKn5J/host_genotype.csv
host_genotype.csv
Primary data file for dataset ID 636335
download
https://osprey.bco-dmo.org/dataset/636335/data/download
download
onLine
dataset
<p>Adult Acropora palmata colonies were sampled (1 cm^2) with hammer and chisel and tissues were preserved in 96% non-denature Ethanol. DNA was extracted using the DNEasy tissue kit (Qiagen) following manufacturer’s instructions. Two multiplex Polymerase Chain Reactions (PCR) were performed per sample using fluorescently labeled primers to assay five loci containing AAT repeats. These five microsatellite loci have previously been demonstrated to be mendelian and coral-specific using controlled crosses (Baums et al., 2005). PCR products were visualized with an automated sequencer (ABI 3730). An internal size standard (Gene Scan 500-Liz, Applied Biosystems CA) ensured accurate sizing. Electropherograms were analyzed with GeneMapper Software 3.0 (Applied Biosystems, CA). Alleles were scored as PCR product size.</p>
<p>See Baums IB, Hughes CR, Hellberg MH (2005) for details.</p>
Specified by the Principal Investigator(s)
<p>Electropherograms of microsatellite alleles were scored for allele sizes (basepairs) in Genemapper vers. (Applied Biosystems) and transferred to spreadsheets.&nbsp;</p>
<p><strong>BCO-DMO Processing Notes:</strong></p>
<p>- As per PI, edited column "Region" to the value 'Florida' (previously, this column's valuess<br />
were all set to 'region'). &nbsp;It is expected that the dataset may grow with new regions in the<br />
future.</p>
<p>- Added PI-provided lat/lon for each "Reef" location.</p>
<p>- Each locus allele size was split into separate columns (i.e., allele size 1 was the first 3 digits,<br />
and allele size 2 were the second consecutive digits of a six digit column. &nbsp;These were separated into<br />
separate columns per allele size at each locus).</p>
<p>- Edited loci headers to include the word 'locus' and whether the column held values for<br />
allele size one or two (e.g., column headers for '166' was edited to 'locus_166_allele1' and locus_166_allele2'.</p>
<p>- Edited entire header to BCO-DMO format (e.g., lowercase names, underscores where needed)</p>
<p>- Edited lat/lon values to four decimal precision consistently.</p>
<p>- Edited spaces in reef names to underscores</p>
<p>- Split date into year, month, day fromat</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
automated sequencer
automated sequencer
PI Supplied Instrument Name: automated sequencer PI Supplied Instrument Description:Applied Biosystems 3730 DNA Analyzer 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.
Deployment: Baums_FL_Keys_NMS
Baums_FL_Keys_NMS
Florida Keys National Marine Sanctuary
shoreside
Baums_FL_Keys_NMS
Iliana B. Baums
Pennsylvania State University
Florida Keys National Marine Sanctuary
shoreside