http://lod.bco-dmo.org/id/dataset/927890
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
2024-05-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Growth and chlorophyll density of individual fragments of the coral Porites divaricata measured during a reciprocal transplant experiment conducted at three sites in Turneffe Atoll, Belize from February to July 2022
2024-05-20
publication
2024-05-20
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-05-28
publication
https://doi.org/10.26008/1912/bco-dmo.927890.1
Karina Scavo Lord
Boston University
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: Scavo Lord, K. (2024) Growth and chlorophyll density of individual fragments of the coral Porites divaricata measured during a reciprocal transplant experiment conducted at three sites in Turneffe Atoll, Belize from February to July 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-20 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.927890.1 [access date]
Coral trait variation Dataset Description: Methods and Sampling: <p><strong>Reciprocal transplant experiment:</strong><br />
In February 2022, 32 colonies (subclone/ramet) of the Caribbean thin finger coral, <em>Porites divaricata</em> (Taxonomy ID: 262287) were identified. 3 to 9 branch fragments were collected from every subclone (colony/ramet). 1 to 3 fragments from each ramet were moved to three designated sites: M1 (mangrove site 1), M2 (mangrove site 2), and R (reef site). 7 to 9 adjacent ropes were deployed at each site (seven ropes at M1 and R, and nine ropes at M2). Following a six-month period (February 2022 - July 2022), two traits were measured for each fragment: length change and red channel intensity, which serves as an inverse indicator of chlorophyll pigment density (Winters, Holzman, Blekhman, Beer, &amp; Loya, 2009).</p>
<p><strong>Trait Measurements:</strong><br />
To measure fragment growth, all fragments were photographed against a scale before and after transplantation, and their lengths were measured from base to apex using ImageJ software. The change in fragment length was determined by dividing the difference between the final and initial lengths by the initial length of the fragment. To measure red channel intensity, all fragments were collected at the end of the experiment and photographed against a laminated DKK color standard (DGK Color Tools) featuring an eleven-step gray scale with true white. Employing the methodology outlined by Winters et al. (2009), these photographs were used to estimate the chlorophyll density of each fragment. Initially, all images were standardized using the gray scale and the MATLAB macro CalibrateImageA. Subsequently, the MATLAB macro AnalyzeIntensity was employed to compute the mean red channel intensity for 20 swatches measuring 25 × 25 pixels for each fragment. Higher values of red channel intensity indicate lower levels of algal photosynthetic pigments (and hence, lower chlorophyll density) (Winters et al., 2009). The MATLAB scripts CalibrateImageA and AnalyzeIntensity are provided in the supplementary files in Winters et al., 2009.</p>
<p>See 'Related Datasets' for the environmental data from the coral transplant sites.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2126612 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2126612
completed
Karina Scavo Lord
Boston University
631-245-3393
2 Cummington Street
Boston
MA
02215
USA
kscavo@bu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample
origin
clone
subclone
sublcone_longitude
subclone_latitude
trans_site
rope
loc_grtn
age2
grtn
loc
len_in
len_fin
len_chg
len_ct
R_fin
Comment
theme
None, User defined
sample identification
site
longitude
latitude
sample description
age
length
image_analysis
comments
featureType
BCO-DMO Standard Parameters
Camera
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.
OCE-PRF: Drivers of phenotypic diversity and adaptation in asexually propagating coral populations
https://osprey.bco-dmo.org/project/880237
OCE-PRF: Drivers of phenotypic diversity and adaptation in asexually propagating coral populations
<p><em>NSF Award Abstract:</em><br />
This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).</p>
<p>In this era of rapid environmental change and degradation, the survival of marine organisms will depend largely upon their ability to tolerate increasing environmental stress. However, the processes that drive resilience (e.g., the relative contribution of genetic versus environmental factors) remain largely a mystery. Corals are a major focus of current studies on organismal resilience because they are undergoing a worldwide decline, and they are so important for both the health of the oceans and the welfare of coastal communities. Corals often occupy and build habitats through asexual reproduction (production of clones), and it is widely assumed that such asexual populations may lack sufficient genetic diversity to respond to diverse environmental stressors. However, few previous studies have quantified the effects of asexual reproduction on the ability of corals to respond to environmental change. This research explores the different mechanisms that contribute to differences in coral stress response among two predominately clonal populations of the Caribbean thin finger coral (<em>Porites divaricata</em>) dwelling in distinct habitat types (mangroves vs. reef). This research will illuminate the drivers of organismal resilience, potentially impacting ongoing coral conservation and restoration efforts. It will also broaden the participation of underrepresented groups by encouraging active participation by local community members, students and scientists at the University of Belize, as well as providing unique training opportunities for next-generation scientists at the interface of field marine ecology and genomics. Importantly, these results will be communicated to a wide audience through diverse venues, including technical reports and management recommendations provided for government agencies and non-profit Belizean conservation organizations, popular articles and curricular materials for the community at large, and peer-reviewed manuscripts and presentations targeted to the scientific community.</p>
<p>Among conservation biologists and ecologists, there is an urgent effort underway to understand the causes of diversity in traits impacting organismal survival and reproduction. If we are to understand how natural populations will respond to environmental change, it is critical to understand how genetic, epigenetic, and environmental factors impact resilience. Such studies have advanced significantly in many plant species, but they are only just beginning to be applied to animals like corals. As in many plants, the model species used here - Caribbean thin finger coral (<em>Porites divaricata</em>) - reproduces primarily asexually, allowing us to compare the performance of clones in different environments and isolate the effects of genotype, epigenetics (namely DNA methylation), environment, and somatic mutations on variation in stress-related coral traits. Specially, combining fully-crossed reciprocally transplanted coral ramets across mangrove and reef sites with genomic and methylation sequencing data, this research will evaluate 1) the role of intra-genet variation accumulated during asexual reproduction in facilitating adaptation in the mangrove population, relative to roles of between-genet variation and phenotypic plasticity, 2) assess the role of new DNA methylation states, and 3) measure the rate of accumulation of new DNA methylation marks and base-changes during asexual reproduction. Results from this research effort will advance our understanding of the role of mechanisms like DNA methylation and somatic mutations in driving phenotypic variation in critical stress-response traits and how these mutations accumulate over time, provide insight into how such mechanisms are generated and inherited across asexual generations, build upon the sparse understanding of the role of novel habitat types, i.e. mangroves, in coral ecology and evolution; and generate novel molecular resources including the first reference genome assembly for the non-model coral, <em>P. divaricata</em>.</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>
Adaptation in asexual coral populations
largerWorkCitation
project
eng; USA
oceans
-87.815167
-87.81111
17.28717
17.288681
2022-02-01
2022-07-31
Caribbean
0
BCO-DMO catalogue of parameters from Growth and chlorophyll density of individual fragments of the coral Porites divaricata measured during a reciprocal transplant experiment conducted at three sites in Turneffe Atoll, Belize from February to July 2022
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/927896.rdf
Name: sample
Units: unitless
Description: <p>Tag number of transplant</p>
http://lod.bco-dmo.org/id/dataset-parameter/927897.rdf
Name: origin
Units: unitless
Description: <p>Site from which sample was collected (originated): M2 = mangrove site 2, M1= mangrove site 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/927898.rdf
Name: clone
Units: unitless
Description: <p>Color indicating which genotype the sample belongs to, each color represents a different genotype</p>
http://lod.bco-dmo.org/id/dataset-parameter/927899.rdf
Name: subclone
Units: unitless
Description: <p>Character string representing which coral colony (or subclone) each sample belongs to</p>
http://lod.bco-dmo.org/id/dataset-parameter/927900.rdf
Name: sublcone_longitude
Units: decimal degrees
Description: <p>Longitude of where coral colony (subclone) was collected; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/927901.rdf
Name: subclone_latitude
Units: decimal degrees
Description: <p>Latitude of where coral colony (subclone) was collected; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/927902.rdf
Name: trans_site
Units: unitless
Description: <p>Site where each sample was transplanted to : M2 = mangrove site 2, M1= mangrove site 1, R = reef</p>
http://lod.bco-dmo.org/id/dataset-parameter/927903.rdf
Name: rope
Units: unitless
Description: <p>Rope number that each sample was strung on at the transplanted site</p>
http://lod.bco-dmo.org/id/dataset-parameter/927904.rdf
Name: loc_grtn
Units: unitless
Description: <p>Character string indicating whether the colony was transplanted to its home or away site and whether it is an early generation subclone (old) or young generation (young) subclone</p>
http://lod.bco-dmo.org/id/dataset-parameter/927905.rdf
Name: age2
Units: years
Description: <p>Age of the coral subclone/colony in years</p>
http://lod.bco-dmo.org/id/dataset-parameter/927906.rdf
Name: grtn
Units: unitless
Description: <p>Indicates whether subclone/colony is early generation (old) or late generation (young)</p>
http://lod.bco-dmo.org/id/dataset-parameter/927907.rdf
Name: loc
Units: unitless
Description: <p>Indicates whether the sample was transplanted to its home site or away site</p>
http://lod.bco-dmo.org/id/dataset-parameter/927908.rdf
Name: len_in
Units: centimeters (cm)
Description: <p>Initial length of fragment at time of transplanting (start of transplant experiment)</p>
http://lod.bco-dmo.org/id/dataset-parameter/927909.rdf
Name: len_fin
Units: centimeters (cm)
Description: <p>Final length of fragment at the end of the transplant experiment. NA indicates that sample did not survive to the end of the fragmentation experiment to be measured.</p>
http://lod.bco-dmo.org/id/dataset-parameter/927910.rdf
Name: len_chg
Units: centimeters (cm)
Description: <p>Change of length of fragment over the duration of the transplant experiment. NA indicates that sample did not survive to the end of the fragmentation experiment to be measured.</p>
http://lod.bco-dmo.org/id/dataset-parameter/927911.rdf
Name: len_ct
Units: centimeters (cm)
Description: <p>Change of length of fragment over the duration of the transplant experiment divided by the initial length of fragment. NA indicates that sample did not survive to the end of the fragmentation experiment to be measured.</p>
http://lod.bco-dmo.org/id/dataset-parameter/927912.rdf
Name: R_fin
Units: unitless
Description: <p>Red channel intensity value of sample; measured as intensity of red color in image, 0-255</p>
http://lod.bco-dmo.org/id/dataset-parameter/927913.rdf
Name: Comment
Units: unitless
Description: <p>Notes or comments</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
20789
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/64a8ddb7-0e83-4421-add9-a231b5342025/content
download
https://doi.org/10.26008/1912/bco-dmo.927890.1
download
onLine
dataset
<p><strong>Reciprocal transplant experiment:</strong><br />
In February 2022, 32 colonies (subclone/ramet) of the Caribbean thin finger coral, <em>Porites divaricata</em> (Taxonomy ID: 262287) were identified. 3 to 9 branch fragments were collected from every subclone (colony/ramet). 1 to 3 fragments from each ramet were moved to three designated sites: M1 (mangrove site 1), M2 (mangrove site 2), and R (reef site). 7 to 9 adjacent ropes were deployed at each site (seven ropes at M1 and R, and nine ropes at M2). Following a six-month period (February 2022 - July 2022), two traits were measured for each fragment: length change and red channel intensity, which serves as an inverse indicator of chlorophyll pigment density (Winters, Holzman, Blekhman, Beer, &amp; Loya, 2009).</p>
<p><strong>Trait Measurements:</strong><br />
To measure fragment growth, all fragments were photographed against a scale before and after transplantation, and their lengths were measured from base to apex using ImageJ software. The change in fragment length was determined by dividing the difference between the final and initial lengths by the initial length of the fragment. To measure red channel intensity, all fragments were collected at the end of the experiment and photographed against a laminated DKK color standard (DGK Color Tools) featuring an eleven-step gray scale with true white. Employing the methodology outlined by Winters et al. (2009), these photographs were used to estimate the chlorophyll density of each fragment. Initially, all images were standardized using the gray scale and the MATLAB macro CalibrateImageA. Subsequently, the MATLAB macro AnalyzeIntensity was employed to compute the mean red channel intensity for 20 swatches measuring 25 × 25 pixels for each fragment. Higher values of red channel intensity indicate lower levels of algal photosynthetic pigments (and hence, lower chlorophyll density) (Winters et al., 2009). The MATLAB scripts CalibrateImageA and AnalyzeIntensity are provided in the supplementary files in Winters et al., 2009.</p>
<p>See 'Related Datasets' for the environmental data from the coral transplant sites.</p>
Specified by the Principal Investigator(s)
- Imported original files "GPSCoords_Data.xlsx" (site locations) and "TraitVariation_Data.xlsx" (trait variation data) into the BCO-DMO system.
- Added Latitude and Longitude columns from the site locations list to the trait dataset by matching on Subclone_ID number.
- Moved the comment "could not get value from photo" which was in the R_fin column to a Comment column
- Saved the final file as "927890_v1_coral_trait_variation.csv".
Specified by BCO-DMO Data Managers
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
PI Supplied Instrument Name: Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/