http://lod.bco-dmo.org/id/dataset/881853 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 2022-10-04 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in Moorea, French Polynesia in 2019 2022-10-04 publication 2022-10-04 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2022-10-12 publication https://doi.org/10.26008/1912/bco-dmo.881853.1 Scott Burgess Florida 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: Burgess, S. (2022) Genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in Moorea, French Polynesia in 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-10-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.881853.1 [access date] Methods and Sampling: &lt;p&gt;Tissue samples from 44 Pocillopora colonies were collected using SCUBA in August 2019 from six sites (LTER 1 – 6) and three depths (5, 10, and 20 m) around Mo’orea, French Polynesia. Tissue samples were stored in salt-saturated DMSO (dimethyl sulfoxide) buffer until DNA was extracted.&amp;nbsp; Genomic DNA was extracted from tissue using the OMEGA (BIO-TEK) E.Z.N.A. Tissue DNA Kit. Extractions were quantified using the Qubit dsDNA HS Assay Kit with the Qubit Fluorometer. ezRAD libraries were generated by digesting samples with the isoschizomer restriction enzymes MboI and Sau3AI (New England BioLab), which cleave at GATC cut sites, and libraries were generated with the KAPA HyperPrep Kit (Roche) using TruSeq DNA indexes (Illumina). Libraries were size selected at 350 – 700 bp and sequenced on the MiSeq platform as paired-end 300 bp runs at Florida State University.&amp;nbsp;&lt;/p&gt; 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 asNeeded Dataset Version: 1 Unknown BioProject BioSample geo_loc_name Collection_Date lat lon Depth Experiment Run Sample_ID Sample_Name SRA_Study Organism Isolate dev_stage Tissue Assay_Type AvgSpotLen Bases BioSampleModel Bytes DATASTORE_filetype Instrument Isolation_Source Library_Name LibraryLayout LibrarySelection LibrarySource mtORF_haplotype Platform Illumina MiSeq theme None, User defined NCBI BioProject accession NCBI BioSample accession site description date latitude longitude depth NCBI SRA experiment accession (SRX) NCBI SRA run accession (SRR) sample identification NCBI SRA study accession (SRP) taxon sample description file_size instrument featureType BCO-DMO Standard Parameters Automated DNA Sequencer 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 -149.924 -149.762 -17.583 -17.472 2019-08-01 2019-08-01 Moorea, French Polynesia 0 BCO-DMO catalogue of parameters from Genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in Moorea, French Polynesia in 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/881875.rdf Name: BioProject Units: unitless Description: <p>NCBI SRA BioProject ID</p> http://lod.bco-dmo.org/id/dataset-parameter/881876.rdf Name: BioSample Units: unitless Description: <p>NCBI SRA BioSample ID</p> http://lod.bco-dmo.org/id/dataset-parameter/881877.rdf Name: geo_loc_name Units: unitless Description: <p>Location where sample was collected</p> http://lod.bco-dmo.org/id/dataset-parameter/881878.rdf Name: Collection_Date Units: unitless Description: <p>Year and month of collection in format (YYYY-MM)</p> http://lod.bco-dmo.org/id/dataset-parameter/881879.rdf Name: lat Units: decimal degrees Description: <p>Latitude of site where sample collected</p> http://lod.bco-dmo.org/id/dataset-parameter/881880.rdf Name: lon Units: decimal degrees Description: <p>Longitude of site where sample collected</p> http://lod.bco-dmo.org/id/dataset-parameter/881881.rdf Name: Depth Units: meters (m) Description: <p>Depth of coral from which sample was taken</p> http://lod.bco-dmo.org/id/dataset-parameter/881882.rdf Name: Experiment Units: unitless Description: <p>NCBI SRA Experiment ID</p> http://lod.bco-dmo.org/id/dataset-parameter/881883.rdf Name: Run Units: unitless Description: <p>SRA Run ID</p> http://lod.bco-dmo.org/id/dataset-parameter/881884.rdf Name: Sample_ID Units: unitless Description: <p>Unique ID of the sample</p> http://lod.bco-dmo.org/id/dataset-parameter/881885.rdf Name: Sample_Name Units: unitless Description: <p>Sample name</p> http://lod.bco-dmo.org/id/dataset-parameter/881886.rdf Name: SRA_Study Units: unitless Description: <p>NCBI SRA Study ID</p> http://lod.bco-dmo.org/id/dataset-parameter/881887.rdf Name: Organism Units: unitless Description: <p>Genus of organism</p> http://lod.bco-dmo.org/id/dataset-parameter/881888.rdf Name: Isolate Units: unitless Description: <p>Isolate (Coral)</p> http://lod.bco-dmo.org/id/dataset-parameter/881889.rdf Name: dev_stage Units: unitless Description: <p>Developmental stage of the coral</p> http://lod.bco-dmo.org/id/dataset-parameter/881890.rdf Name: Tissue Units: unitless Description: <p>Tissue sampled</p> http://lod.bco-dmo.org/id/dataset-parameter/881891.rdf Name: Assay_Type Units: unitless Description: <p>Type of genomic library</p> http://lod.bco-dmo.org/id/dataset-parameter/881892.rdf Name: AvgSpotLen Units: unitless Description: <p>Average spot length</p> http://lod.bco-dmo.org/id/dataset-parameter/881893.rdf Name: Bases Units: unitless Description: <p>Size of genomic library</p> http://lod.bco-dmo.org/id/dataset-parameter/881894.rdf Name: BioSampleModel Units: unitless Description: <p>BioSample model</p> http://lod.bco-dmo.org/id/dataset-parameter/881895.rdf Name: Bytes Units: unitless Description: <p>Filesize in bytes for datastore file</p> http://lod.bco-dmo.org/id/dataset-parameter/881896.rdf Name: DATASTORE_filetype Units: unitless Description: <p>Type of file</p> http://lod.bco-dmo.org/id/dataset-parameter/881897.rdf Name: Instrument Units: unitless Description: <p>Sequencing instrument used to create library</p> http://lod.bco-dmo.org/id/dataset-parameter/881898.rdf Name: Isolation_Source Units: unitless Description: <p>Coral reef habitat type where sample was collected</p> http://lod.bco-dmo.org/id/dataset-parameter/881899.rdf Name: Library_Name Units: unitless Description: <p>Coral reef habitat type where sample was collected</p> http://lod.bco-dmo.org/id/dataset-parameter/881900.rdf Name: LibraryLayout Units: unitless Description: <p>Paired end read samples</p> http://lod.bco-dmo.org/id/dataset-parameter/881901.rdf Name: LibrarySelection Units: unitless Description: <p>Library selection (Reduced Representation)</p> http://lod.bco-dmo.org/id/dataset-parameter/881902.rdf Name: LibrarySource Units: unitless Description: <p>Within cell subunit</p> http://lod.bco-dmo.org/id/dataset-parameter/881903.rdf Name: mtORF_haplotype Units: unitless Description: <p>mitochondrial Open Reading Frame haplotype name</p> http://lod.bco-dmo.org/id/dataset-parameter/881904.rdf Name: Platform Units: unitless Description: <p>Platform (Illumina)</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 14081 https://darchive.mblwhoilibrary.org/bitstream/1912/29412/1/dataset-881853_pocillopora-sequences-2019__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.881853.1 download onLine dataset &lt;p&gt;Tissue samples from 44 Pocillopora colonies were collected using SCUBA in August 2019 from six sites (LTER 1 – 6) and three depths (5, 10, and 20 m) around Mo’orea, French Polynesia. Tissue samples were stored in salt-saturated DMSO (dimethyl sulfoxide) buffer until DNA was extracted.&amp;nbsp; Genomic DNA was extracted from tissue using the OMEGA (BIO-TEK) E.Z.N.A. Tissue DNA Kit. Extractions were quantified using the Qubit dsDNA HS Assay Kit with the Qubit Fluorometer. ezRAD libraries were generated by digesting samples with the isoschizomer restriction enzymes MboI and Sau3AI (New England BioLab), which cleave at GATC cut sites, and libraries were generated with the KAPA HyperPrep Kit (Roche) using TruSeq DNA indexes (Illumina). Libraries were size selected at 350 – 700 bp and sequenced on the MiSeq platform as paired-end 300 bp runs at Florida State University.&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;BCO-DMO Data manager processing notes:&lt;br /&gt; * Imported file&amp;nbsp;SraRunTable.txt which was generated by submitter using the NCBI run selector.&amp;nbsp;&amp;nbsp;&lt;br /&gt; * subset columns from the run selector results&lt;/p&gt; 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 Illumina MiSeq Illumina MiSeq PI Supplied Instrument Name: Illumina MiSeq 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.