17970 Coral genetic (Taxonomic and genetic identification of deep-sea corals in bycatch and field surveys -linked to groundfish survey dataset) Data Set Published / External 17775 CB (Conservation Biology) Division Project Completed 2018-02-22 Data for this project resides in the West Coast Groundfish Bottom Trawl Survey Database. Deep-sea corals are often components of trawling bycatch, though their brittle skeleton and slow growth make them particularly vulnerable to such impacts. An understanding of the population structure of deep-sea corals will be critical to ascertaining the effects of habitat loss and genetic connections between distant populations, both of which are important to the 2006 Magnuson-Stevens Act directive and the NMFS federal mandate. An initial species inventory of deep-sea corals off the United States coastline is a necessary first step toward a comprehensive understanding of the ecology and distribution of this diverse species assemblage. Quantifying species distributions from bycatch data and fisheries independent surveys requires accurate species-level identifications of the corals found in tows; however, the taxonomic identification of corals to the species level is often problematic. In some cases morphologically similar specimens may only be distinguished from one another using microscopic skeletal structures. In other cases, the taxonomic delineations of some families are so confused that accurate species-level designations are currently impossible. The use of genetic information combined with morphology is likely the best approach to decipher evolutionary patterns in these species. A collection of genetic barcodes for all verified voucher specimens of deep sea corals in our collections. Also includes SEM images for some species. Addresses Legal Mandate Raw/field data, Laboratory data, Other Loaded by batch 4257, 01-30-2013 17:10 Subject to Public Access to Research Results (PARR): Yes Theme by-catch Theme deep sea coral Spatial Northern CA Current System Instrument DNA Sequencer Platform Unknown Physical Collection Device Northwest Fisheries Science Center Seattle WA USA Data Set Other Other DNA Sequencer Platform Not Applicable Unknown Physical Collection Device 51593 Deep Sea Corals PARR 02.21.18 Published / External Planned This is a table referencing DNA sequences generated from deep sea corals collected by a number of agencies. All sequences are published in one of two databases, and those accession numbers are included here. The Genbank Database can be accessed here: https://www.ncbi.nlm.nih.gov/genbank/. The National Coral Database can be accessed here: https://deepseacoraldata.noaa.gov/. Spreadsheet Yes PARR This is a table referencing DNA sequences generated from deep sea corals collected by a number of agencies. All sequences are published in one of two databases, and those accession numbers are included here. The Genbank Database can be accessed here: https://www.ncbi.nlm.nih.gov/genbank/. The National Coral Database can be accessed here: https://deepseacoraldata.noaa.gov/. 1 Barcode or Agency ID text No No Active Barcode or other identifier given to the specimen from the original agency doing the collection. Units for values are N/A. text N/A N/A 2 Agency of Specimen Origin text No No Active Agency responsible for the original specimen collection. Units for values are N/A. text N/A N/A 3 Verified Species ID by Morphology text No No Active Species identification determined by a taxonomic expert, based on morphology of the specimen. Units for values are N/A. text N/A N/A 4 Morphologist of ID Designation text No No Active Taxonomic expert responsible for the morphological identification. Units for values are N/A. text N/A N/A 5 Genetic Species ID by DNA Sequence text No No Active Species identification based on DNA sequence information. Units for values are N/A. text N/A N/A 6 Database for Sequences text No No Active Database(s) containing DNA sequence information from these specimens. Units for values are N/A. text N/A N/A 7 Genbank Accession Number text No No Active Accession number(s) for DNA sequences published in Genbank. Units for values are N/A. text N/A N/A 8 National Coral Database Accession Number text No No Active Accession number for DNA sequences included in the National Coral Database. Units for values are N/A. text N/A N/A Data Steward 2015-10-01 Person Everett, Meredith meredith.everett@noaa.gov 2725 Montlake Boulevard East Seattle WA 98112 USA Distributor 2015-10-01 Organization Northwest Fisheries Science Center NWFSC nmfs.nwfsc.metadata@noaa.gov https://ror.org/05r7z1k40 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov NWFSC Home Online Resource Metadata Contact 2015-10-01 Organization Northwest Fisheries Science Center NWFSC nmfs.nwfsc.metadata@noaa.gov https://ror.org/05r7z1k40 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov NWFSC Home Online Resource Originator 2015-10-01 Person Berntson, Ewann A Ewann.Berntson@noaa.gov 2725 Montlake Boulevard East Seattle WA 98112 360-871-8333 Point of Contact 2015-10-01 Person Everett, Meredith meredith.everett@noaa.gov 2725 Montlake Boulevard East Seattle WA 98112 USA -122.3062 -122.3062 47.6449 47.6449 Northern CA Current System: US-Canada to US-Mexico 55 -1280 m Continuing 2009-01-01 -122.5547 -122.3062 47.6449 47.569 Montlake Genetics Continuing 2009-01-01 Unclassified Contact one of the project leads NA https://www.webapps.nwfsc.noaa.gov/apex/parr/deep_sea_corals_parr_022118/data/page/ 2015-10-01 Organization Northwest Fisheries Science Center https://ror.org/05r7z1k40 Deep Sea Corals PARR 02.21.18 (RESTful) This is a table referencing DNA sequences generated from deep sea corals collected by a number of agencies. All sequences are published in one of two databases, and those accession numbers are included here. The Genbank Database can be accessed here: https://www.ncbi.nlm.nih.gov/genbank/. The National Coral Database can be accessed here: https://deepseacoraldata.noaa.gov/. https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/tables/table/deep_sea_corals_parr_022118 2015-10-01 Organization Northwest Fisheries Science Center https://ror.org/05r7z1k40 Deep Sea Corals PARR 02.21.18 This is a table referencing DNA sequences generated from deep sea corals collected by a number of agencies. All sequences are published in one of two databases, and those accession numbers are included here. The Genbank Database can be accessed here: https://www.ncbi.nlm.nih.gov/genbank/. The National Coral Database can be accessed here: https://deepseacoraldata.noaa.gov/. https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/105225 Deep Sea Coral voucher sequence dataset Online Resource Web site NWFSC Dataset Information page. A collection of genetic barcodes for all verified voucher specimens of deep sea corals in our collections. Also includes SEM images for some species. Spreadsheet High Sequencing quality checks Yes 15 No No No 0 days No Delay Other 365 The Northwest Fisheries Science Center facilitates backup and recovery of all data and IT components which are managed by IT Operations through the capture of static (point-in-time) backup data to physical media. Once data is captured to physical media (every 1-3 days), a duplicate is made and routinely (weekly) transported to an offsite archive facility where it is maintained throughout the data's applicable life-cycle. DNA extraction and sequencing, morphological identifications made, SEM images, QA/QC, phylogenetic analysis 51593 Entity gov.noaa.nmfs.inport:17970 SysAdmin InPortAdmin 2013-01-30T17:10:31 SysAdmin InPortAdmin 2026-03-04T19:17:17 2019-06-04 Northwest Fisheries Science Center NWFSC 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov 1001 Public No No 2019-06-04 1 Year 2020-06-04