http://lod.bco-dmo.org/id/dataset/666350
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
2016-11-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Multilocus microsatellite genotypes of Acropora palmata from the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project)
2016-11-30
publication
2016-11-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-24
publication
https://doi.org/10.26008/1912/bco-dmo.666350.1
Iliana B. Baums
Pennsylvania State 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: Baums, I. B. (2021) Multilocus microsatellite genotypes of Acropora palmata from the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-11-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.666350.1 [access date]
Mutations at microsatellite loci of Acropora palmata Dataset Description: Methods and Sampling: <p>Adult Acropora palmata colonies were sampled (1 cm2) 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.&nbsp; 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><strong>References:</strong></p>
<p>Baums IB, Devlin-Durante MK, LaJeunesse TC (2014) New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies. Molecular Ecology 23, 4203-4215.</p>
<p>Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Marine Ecology - Progress Series 288, 115-127 for details on PCR amplification.</p>
<p>Devlin-Durante MK, Miller MW, Caribbean Acropora Research G, Precht WF, Baums IB. How old are you? Genet age estimates in a clonal animal. Mol Ecol. 2016. doi: 10.1111/mec.13865 for details on how mutations were scored.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1537959 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1537959
completed
Iliana B. Baums
Pennsylvania State University
814-867-0491
Department of Biology 208 Mueller Laboratory
University Park
PA
16802
USA
ibb3@psu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
region
database_id
genet_id
mutant_id
locus
size_bp
allele
automated sequencer (ABI 3730)
ABI 3730
theme
None, User defined
region
sample identification
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Baums_Carib
service
Deployment Activity
Caribbean and North-West Atlantic
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.
Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?
https://osprey.bco-dmo.org/project/663794
Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?
<p><em>NSF Award Abstract:</em><br />
Reef-building acroporid corals form the foundation of shallow tropical coral communities throughout the Caribbean. Yet, the once dominant staghorn coral (Acropora cervicornis) and the elkhorn coral (A. palmata) have decreased by more than 90% since the 1980s, primarily from disease. Their continuing decline jeopardizes the ability of coral reefs to provide numerous societal and ecological benefits, including economic revenue from seafood harvesting and tourism and shoreline protection from extreme wave events caused by storms and hurricanes. Despite their protection under the U.S. Endangered Species Act since 2006, threats to the survival of reef-building acroporid corals remain pervasive and include disease and warming ocean temperatures that may lead to further large-scale mortality. However, hybridization among these closely related species is increasing and may provide an avenue for adaptation to a changing environment. While hybrids were rare in the past, they are now thriving in shallow habitats with extreme temperatures and irradiance and are expanding into the parental species habitats. Additional evidence suggests that the hybrid is more disease resistant than at least one of the parental species. Hybridization may therefore have the potential to rescue the threatened parental species from extinction through the transfer of adapted genes via hybrids mating with both parental species, but extensive gene flow may alter the evolutionary trajectory of the parental species and drive one or both to extinction. This collaborative project is to collect genetic and ecological data in order to understand the mechanisms underlying increasing hybrid abundance. The knowledge gained from this research will help facilitate more strategic management of coral populations under current and emerging threats to their survival. This project includes integrated research and educational opportunities for high school, undergraduate and graduate students, and a postdoctoral researcher. Students in the United States Virgin Islands will take part in coral spawning research and resource managers will receive training on acroporid reproduction to apply to coral restoration techniques.</p>
<p>Current models predict the demise of reefs in the next 200 years due to increasing sea surface temperatures and ocean acidification. It is thus essential to identify habitats, taxa and evolutionary mechanisms that will allow some coral species to maintain their role as foundation fauna. Hybridization can provide an avenue for adaptation to changing conditions. Corals hybridize with some frequency and results may range from the introduction of a few alleles into existing parent species via introgression, to the birth of a new, perhaps better adapted genetic lineage. The only widely accepted coral hybrid system consists of the once dominant but now threatened Caribbean species, Acropora cervicornis and A. palmata. In the past, hybrid colonies originating from natural crosses between elkhorn and staghorn corals were rare, and evidence of hybrid reproduction was limited to infrequent matings with the staghorn coral. Recent field observations suggest that the hybrid is increasing and its ecological role is changing throughout the Caribbean. These hybrids appear to be less affected by the disease that led to the mass mortality of their parental species in recent decades. Hybrids are also found thriving in shallow habitats with high temperatures and irradiance suggesting they may be less susceptible to future warming scenarios. At the same time, they are expanding into the deeper parental species habitats. Preliminary genetic data indicate that hybrids are now mating with each other, demonstrating the potential for the formation of a new species. Further, hybrids appear to be capable of mating with both staghorn and elkhorn coral, perhaps leading to gene flow between the parent species via the hybrid. Research is proposed to address how the increase in hybridization and perhaps subsequent introgression will affect the current ecological role and the future evolutionary trajectory of Caribbean acroporids. Specifically, this collaborative project aims to answer the following questions: 1) What is the historic rate, direction, and degree of introgression across species ranges and genomes? Linkage block analysis based on genome-wide SNP genotyping across three replicate hybrid zones will answer this question. 2) What is the current extent and future potential of later generation hybrid formation? Morphometric and genetic analyses combined with in vitro fertilization assays will be used. 3) What mechanisms allow hybrids to thrive in hot, shallow waters? A series of manipulative in situ and ex situ experiments will determine whether biotic or abiotic factors favor hybrid survival in shallow waters. 4) Are hybrids more disease resistant than the parentals species? Disease transmission assays in reciprocal transplant experiments and histological analysis to determine the extent of disease will be conducted. A multidisciplinary approach will be taken that combines traditional and cutting edge technology to provide a detailed analysis of the evolutionary ecology of Caribbean corals.</p>
<p><em>Note: </em>PI Nicole Fogarty's original award OCE-1538469 was issued while at Nova Southeastern University. This was replaced by OCE-1929979 upon moving to the University of North Carolina Wilmington.</p>
Coral Hybridization
largerWorkCitation
project
eng; USA
biota
oceans
Caribbean and North-West Atlantic
-88.199
-64.677
12.0831
26.7075
2016-11-30
Caribbean and North-West Atlantic
0
BCO-DMO catalogue of parameters from Multilocus microsatellite genotypes of Acropora palmata from the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization 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/666358.rdf
Name: region
Units: unitless
Description: <p>sampling region</p>
http://lod.bco-dmo.org/id/dataset-parameter/666359.rdf
Name: database_id
Units: unitless
Description: <p>Baums lab sample Database ID (unique for each sample)</p>
http://lod.bco-dmo.org/id/dataset-parameter/666360.rdf
Name: genet_id
Units: unitless
Description: <p>Genets are identified by their Genet ID. All samples that share all ancestral alleles at five microsatellite loci were assigned the same genet ID. See methods for how ancestral alleles were determined.</p>
http://lod.bco-dmo.org/id/dataset-parameter/666361.rdf
Name: mutant_id
Units: unitless
Description: <p>A Unique ID given to each unique multilocus genotype. This multilocus genotype includes all alleles (diploid ancestral and additional mutations).</p>
http://lod.bco-dmo.org/id/dataset-parameter/666362.rdf
Name: locus
Units: basepairs
Description: <p>the microsatellite locus that had a mutated allele (166; 181; 182; 192; 207)</p>
http://lod.bco-dmo.org/id/dataset-parameter/666363.rdf
Name: size_bp
Units: basepairs
Description: <p>size of allele?</p>
http://lod.bco-dmo.org/id/dataset-parameter/841625.rdf
Name: allele
Units: unitless
Description: <p>allele identifier</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
2031958
https://darchive.mblwhoilibrary.org/bitstream/1912/26738/1/dataset-666350_acropora-palmata-genotypes-clonal-age__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.666350.1
download
onLine
dataset
<p>Adult Acropora palmata colonies were sampled (1 cm2) 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.&nbsp; 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><strong>References:</strong></p>
<p>Baums IB, Devlin-Durante MK, LaJeunesse TC (2014) New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies. Molecular Ecology 23, 4203-4215.</p>
<p>Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Marine Ecology - Progress Series 288, 115-127 for details on PCR amplification.</p>
<p>Devlin-Durante MK, Miller MW, Caribbean Acropora Research G, Precht WF, Baums IB. How old are you? Genet age estimates in a clonal animal. Mol Ecol. 2016. doi: 10.1111/mec.13865 for details on how mutations were scored.</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.</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 />
- nd (no data) was entered into all blank cells<br />
- replaced spaces and / with underscores<br />
- converted the submitted multilevel table to a flat table</p>
<p>VERSIONS: 2017-21-26: Replaced version 1 (2016-11-30) with version 2 (2017-10-19). There was a&nbsp;shift in 1 basepair at locus 181 for some of the data.</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 (ABI 3730)
automated sequencer (ABI 3730)
PI Supplied Instrument Name: automated sequencer (ABI 3730) 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.
ABI 3730
ABI 3730
PI Supplied Instrument Name: ABI 3730 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)
Deployment: Baums_Carib
Baums_Carib
Penn_State_U
laboratory
Penn_State_U
laboratory