http://lod.bco-dmo.org/id/dataset/857058
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
2021-08-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
mtORF haplotype of each Pocillopora colony sampled at a given site and depth at Moorea, French Polynesia in August 2019
2021-08-03
publication
2021-08-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-08-11
publication
https://doi.org/10.26008/1912/bco-dmo.857058.1
Scott Burgess
Florida State University
principalInvestigator
Peter J. Edmunds
California State University Northridge
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: Burgess, S. (2021) mtORF haplotype of each Pocillopora colony sampled at a given site and depth at Moorea, French Polynesia in August 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.857058.1 [access date]
Pocillopora haplotypes at Moorea by site and depth Dataset Description: Methods and Sampling: <p>In August 2019, <em>Pocillopora</em> colonies were sampled from three depths (5, 10, and 20 m) at each of four sites (sites 1, 2, 4, and 5) on the fore reef of Mo'orea. Site locations and names correspond to that used by the Mo'orea Coral Reef Long-Term Ecological Research (MCR-LTER) program. At each depth at each site, 10-15 50x50 cm quadrats were randomly placed on the reef along the target depth contour until approximately 50 colonies had been sampled. Tissue from all <em>Pocillopora</em> colonies within the quadrat was sampled. Tissue (~ 5 mm diameter) was collected using small bone clippers, stored in salt-saturated dimethyl sulfoxide DMSO buffer. Genomic DNA was extracted from tissues using Chelex 100 (Bio-Rad, USA). DNA was then used for PCR amplification using the mitochondrial Open Reading Frame (mtORF) marker (Flot &amp; Tillier, 2007). A restriction fragment length polymorphism (RFLP) gel-based assay was used to distinguish <em>P. meandrina</em> and <em>P. eydouxi</em>. In GENEIOUS v.9.1.8 (Biomatters), forward mtORF sequences (855bp) were aligned and samples were identified to haplotype based on previously published sequences of mtORF haplotypes (see the attached Supplemental File 'Pocillopora_mtORF.fasta').</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829867 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829867
completed
Scott Burgess
Florida State University
850-645-9563
Department of Biological Science 319 Stadium Drive
Tallahassee
FL
32308
USA
sburgess@bio.fsu.edu
pointOfContact
Peter J. Edmunds
California State University Northridge
818-677-2502
Department of Biology 18111 Nordhoff Street
Northridge
CA
91330-8303
USA
peter.edmunds@csun.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Depth_m
Site
Tube_ID
Species_haplotype
PCR amplification
theme
None, User defined
depth
site
sample identification
species scientific name (binomial)
featureType
BCO-DMO Standard Parameters
Thermal Cycler
instrument
BCO-DMO Standard Instruments
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.
Collaborative research: Coral community resilience: testing the role of hidden diversity in pocilloporid corals at Moorea
https://osprey.bco-dmo.org/project/756178
Collaborative research: Coral community resilience: testing the role of hidden diversity in pocilloporid corals at Moorea
<p><em>NSF Award Abstract:</em><br />
While most coral reefs in the world are threatened by multiple disturbances that are driving coral cover downward, the coral reefs at Mo'orea, French Polynesia, provide a striking exception. However, it is not yet clear what makes the coral communities of Mo'orea an exception to the trend of global decline in coral cover, and what drives spatial variation in recovery patterns around the island. The most recent wave of recovery on the outer reefs is dominated by corals in the genus Pocillopora (the cauliflower coral). While the colonies of this coral all look similar to one another, they actually represent multiple 'hidden' species that are genetically divergent but visibly indistinguishable. The morphological similarity makes it hard to identify species in the field, and this often forces researchers to pool these corals into a single group, which has impeded a full understanding of coral recovery. The ecological differences among these hidden species remain poorly understood, but they may be a crucial factor keeping the ecosystem in a coral-dominated state. This project is studying how 'hidden diversity' provides a form of 'ecological insurance' that provides reef-building coral communities around this island with ecological and evolutionary options that buffer reefs from unpredictable and unfavorable environmental conditions. If multiple cryptic species exhibit a diversity of responses to disturbance and stress, then it increases the ability of the community to recover and re-organize after impacts compared to that if all the species responded the same way. By studying the reefs at Mo'orea, this project provides unique, important, and transferable knowledge to better understand fundamental mechanism driving coral community recovery following catastrophic damage, and will provide much-needed information to better manage coral reefs and favor them remaining in a coral-dominated state. A PhD student and a postdoctoral researcher at Florida State University (FSU) are being supported and mentored during the project, and a program of professional growth is being provided for a technician who will work on the project. The investigators are working with science educators from Florida schools to introduce marine biology clubs that will provide outreach opportunities for FSU and California State University Northridge participants to engage high school students and teachers in the research themes at the core of this project.</p>
<p>This project will test the hypothesis that the presence of morphologically similar yet genetically divergent lineages of corals in the genus Pocillopora drives rapid recovery of coral communities dominated by Pocillopora on the outer reefs of Mo'orea, French Polynesia. By creating a diverse portfolio in the capacity of the Pocillopora community to recover and reorganize after disturbance, hidden ecological differences among coral lineages in their response to disturbance is expected to promote community resilience. A well-studied genetic marker will be used to distinguish coral colonies among different lineages. Field-based projects, co-located with Moorea Coral Reef-Long-Term Ecological Research (MCR-LTER) sites, will determine how pocilloporid lineages differ in their distribution and abundance, spatial and temporal patterns of annual recruitment, symbiont composition, and post-settlement growth and survival. These data will be used to build Integral Projection Models (IPMs) to compare population differences among lineages in their sensitivity to size-dependent perturbations, and their capacity for population growth following disturbance. Results from the field projects and IPMs will be synthesized to estimate response diversity as the multivariate dispersion of lineage dissimilarity, and to assess the extent to which it predicts variation among sites in the recovery rate of pocilloporid percent cover, estimated empirically from the MCR-LTER time series. The intellectual merits of this project lie in developing new and transferable understanding of: i) the ecological differences within an ecologically important coral genus, ii) why pocilloporids at Mo'orea are an exception to the global trend of declining coral cover, and iii) the potential for hidden response diversity to act as a fundamental mechanism determining the capacity for coral communities to reestablish and reorganize following disturbances.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Pocilloporid Coral Diversity
largerWorkCitation
project
eng; USA
oceans
-149.8333
-149.8333
-17.5333
-17.5333
2019-08-01
2019-08-31
Moorea, French Polynesia
0
BCO-DMO catalogue of parameters from mtORF haplotype of each Pocillopora colony sampled at a given site and depth at Moorea, French Polynesia in August 2019
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/857069.rdf
Name: Depth_m
Units: meters (m)
Description: <p>Sampling depth in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/857070.rdf
Name: Site
Units: unitless
Description: <p>Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program</p>
http://lod.bco-dmo.org/id/dataset-parameter/857071.rdf
Name: Tube_ID
Units: unitless
Description: <p>Coral colony identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/857072.rdf
Name: Species_haplotype
Units: unitless
Description: <p>mtORF haplotype ID</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
16185
https://darchive.mblwhoilibrary.org/bitstream/1912/27432/1/dataset-857058_pocillopora-haplotypes-moorea-site-and-depth__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.857058.1
download
onLine
dataset
<p>In August 2019, <em>Pocillopora</em> colonies were sampled from three depths (5, 10, and 20 m) at each of four sites (sites 1, 2, 4, and 5) on the fore reef of Mo'orea. Site locations and names correspond to that used by the Mo'orea Coral Reef Long-Term Ecological Research (MCR-LTER) program. At each depth at each site, 10-15 50x50 cm quadrats were randomly placed on the reef along the target depth contour until approximately 50 colonies had been sampled. Tissue from all <em>Pocillopora</em> colonies within the quadrat was sampled. Tissue (~ 5 mm diameter) was collected using small bone clippers, stored in salt-saturated dimethyl sulfoxide DMSO buffer. Genomic DNA was extracted from tissues using Chelex 100 (Bio-Rad, USA). DNA was then used for PCR amplification using the mitochondrial Open Reading Frame (mtORF) marker (Flot &amp; Tillier, 2007). A restriction fragment length polymorphism (RFLP) gel-based assay was used to distinguish <em>P. meandrina</em> and <em>P. eydouxi</em>. In GENEIOUS v.9.1.8 (Biomatters), forward mtORF sequences (855bp) were aligned and samples were identified to haplotype based on previously published sequences of mtORF haplotypes (see the attached Supplemental File 'Pocillopora_mtORF.fasta').</p>
Specified by the Principal Investigator(s)
<p>These data are published in Figures 2, 3, and 4 of Johnston et al. (2021). The&nbsp;R scripts and data used to perform analyses and prepare figures are available from Dryad (doi:&nbsp;<a href="http://dx.doi.org/10.5061/dryad.kwh70rz3p" target="_blank">10.5061/dryad.kwh70rz3p</a>).</p>
<p>BCO-DMO Processing:<br />
- renamed fields (columns) to conform with BCO-DMO naming conventions.</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
PCR amplification
PCR amplification
PI Supplied Instrument Name: PCR amplification 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)