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Title: Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes.
Creator: Hill, Malcolm S., Hill, April L., Lopez, Jose V., Peterson, Kevin J., Pomponi, Shirley A., Diaz, Maria Cristina, Thacker, Robert W., Adamska, Maja, Boury-Esnault, Nicole, Cárdenas, Paco, Chaves-Fonnegra, Andia, Danka, Elizabeth, De Laine, Bre-Onna, Formica, Dawn, Hajdu, Eduardo, Lobo-Hajdu, Gisele, Klontz, Sarah, Morrow, Christine C., Patel, Jignasa, Picton, Bernard, Pisani, Davide, Pohlmann, Deborah, Redmond, Niamh E., Reed, John K., Richey, Stacy, Riesgo, Ana, Rubin, Ewelina, Russell, Zach, Rützler, Klaus, Sperling, Erik A., di Stefano, Michael, Tarver, James E., Collins, Allen G., Lin, Senjie
Abstract/Description: Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea,...
Show moreBackground: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A wellsupported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.
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Date Issued: 2013-01-23
PURL: http://purl.flvc.org/fau/fd/FAUIR000044
Format: Citation

Title: Sediment produced from abrasion of the branching stony coral Oculina Varicosa.
Creator: Hoskin, Charles M., Geier, J. C., Reed, John K.
Date Issued: 1983
PURL: http://purl.flvc.org/fau/fd/FA00007144
Subject Headings: Corals, Oculinidae, Stony corals, Scleractinia, Sediment
Format: Document (PDF)

Title: Sediments from a living shelf-edge reef and adjacent area off central eastern Florida.
Creator: Hoskin, Charles M., Reed, John K., Mook, David H.
Date Issued: 1987
PURL: http://purl.flvc.org/fau/fd/FA00007444
Subject Headings: East Florida, Oculinidae, Sediments (Geology), Coral reefs and islands--Florida
Format: Document (PDF)

Title: Semi-annual report. South Atlantic shelf-edge MPAs and Oculina Experimental Closed Area. Summary of accomplishments, April 2015 to September 30, 2015. Project ID#: NA14NMF441049. Report to SAFMC and NOAA.
Creator: Harter, Stacey, David, Andrew, Reed, John K., Harbor Branch Oceanographic Institute
Date Issued: 2015
PURL: http://purl.flvc.org/fau/fd/FA00007517
Subject Headings: Marine parks and reserves, Deep sea corals, Oculinidae, Benthos Habitat
Format: Document (PDF)

Title: South Atlantic MPAs and deepwater coral HAPCs: Characterization of Benthic Habitat and Biota; NOAA Ship Pisces 2013 cruise. NOAA CIOERT Report.
Creator: Reed, John K., Harter, Stacey, Farrington, Stephanie, David, Andrew, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007514
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, NOAA Ship Pisces
Format: Document (PDF)

Title: South Atlantic MPAs and Deepwater Coral HAPCs: Characterization of Benthic Habitat and Fauna.
Creator: Harter, Stacey, David, Andrew, Reed, John K., Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007507
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, Benthic animals, Underwater exploration
Format: Document (PDF)

Title: South Atlantic MPAs and Deepwater Coral HAPCs: Characterization of Benthic Habitat and Fauna.
Creator: Harter, Stacey, David, Andrew, Reed, John K., Harbor Branch Oceanographic Institute
Date Issued: 2013
PURL: http://purl.flvc.org/fau/fd/FA00007506
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, Benthic animals, Underwater exploration
Format: Document (PDF)

Title: South Atlantic MPAs and deepwater coral HAPCs: Characterization of benthic habitat and fauna.
Creator: Harter, Stacey, David, Andrew, Reed, John K.
Date Issued: 2013
PURL: http://purl.flvc.org/fcla/dt/3359866
Subject Headings: Marine protected areas, Benthos--Habitat, Benthic animals
Format: Document (PDF)

Title: South Atlantic MPAs and deepwater coral HAPCs: Characterization of benthic habitat and fauna.
Creator: Harter, Stacey, David, Andrew, Reed, John K.
Date Issued: 2012
PURL: http://purl.flvc.org/fcla/dt/3359861
Subject Headings: Groupers--Atlantic Coast (U.S.), Tilefish, Marine protected areas, Benthos
Format: Document (PDF)

Title: South Atlantic MPAs and deepwater coral HAPCs: Characterization of benthic habitat, benthic macrobiota, and fish communities; NOAA Ship Nancy Foster 2014 cruise. NOAA CIOERT Report.
Creator: Reed, John K., Farrington, Stephanie, Harter, Stacey, Harbor Branch Oceanographic Institute
Date Issued: 2015
PURL: http://purl.flvc.org/fau/fd/FA00007515
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, Fish communities
Format: Document (PDF)

Title: South Atlantic MPAs and deepwater coral HAPCs: Characterization of fish communities, benthic habitat, and benthic macrobiota. Final Report for 2012-2014 NOAA Cruises. A NOAA CIOERT Report.
Creator: Harter, Stacey, Reed, John K., Farrington, Stephanie, David, Andrew, Harbor Branch Oceanographic Institute
Date Issued: 2015
PURL: http://purl.flvc.org/fau/fd/FA00007516
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, Fish communities, South Atlantic Fishery Management Council (U.S.)
Format: Document (PDF)

Title: South Atlantic MPAs and Deepwater Coral HAPCs:Characterization of Benthic Habitat and FaunaNOAA Ship Pisces Cruise 12-03UNCW Super Phantom ROVJuly 6-19, 2012.
Creator: Reed, John K., Harter, Stacey, Farrington, Stephanie, David, Andrew, Harbor Branch Oceanographic Institute
Date Issued: 2013
PURL: http://purl.flvc.org/fau/fd/FA00007505
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, Benthic animals, Underwater exploration
Format: Document (PDF)

Title: South Atlantic MPAs and Oculina HAPC: Characterization of Benthic Habitat and Biota.
Creator: Harter, Stacey, Reed, John K., David, Andrew, Farrington, Stephanie, Harbor Branch Oceanographic Institute
Abstract/Description: A 14-day research cruise was conducted May 30 to June 12, 2021 by NOAA National Marine Fisheries on the NOAA Ship Pisces with the UNCW Mohawk ROV with a pre-cruise Shelter in Place (SIP. Other collaborators involved include: the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) at Harbor Branch Oceanographic Institute, Florida Atlantic University (HBOI-FAU), and University of North Carolina at Wilmington (UNCW). Harbor Branch Oceanographic Institute Technical...
Show moreA 14-day research cruise was conducted May 30 to June 12, 2021 by NOAA National Marine Fisheries on the NOAA Ship Pisces with the UNCW Mohawk ROV with a pre-cruise Shelter in Place (SIP. Other collaborators involved include: the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) at Harbor Branch Oceanographic Institute, Florida Atlantic University (HBOI-FAU), and University of North Carolina at Wilmington (UNCW). Harbor Branch Oceanographic Institute Technical Report Number 199.
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Date Issued: 2021
PURL: http://purl.flvc.org/fau/fd/FAUIR000421
Format: Document (PDF)

Title: South Atlantic MPAs and Oculina HAPC: Characterization of benthic habitat and biota. NOAA Ship Pisces Cruise 15-02. NOAA CIOERT Cruise Report.
Creator: Harter, Stacey, Reed, John K., Farrington, Stephanie, David, Andrew, Harbor Branch Oceanographic Institute
Date Issued: 2016
PURL: http://purl.flvc.org/fau/fd/FA00007524
Subject Headings: Marine parks and reserves, Oculinidae, Benthos, NOAA Ship Pisces, Mohawk, Ship
Format: Document (PDF)

Title: South Atlantic MPAs and Oculina HAPC: Characterization of Fish Communities, Benthic Habitat, and Benthic Macrobiota: Final Report for 2015-2017 NOAA Ship Pisces Cruises (15-02, 16-20, 17-02).
Creator: Reed, John K., Harter, Stacey, Farrington, Stephanie, David, Andrew
Date Issued: 2018-06-27
PURL: http://purl.flvc.org/fau/fd/FAUIR000240
Format: Citation

Title: SOUTH ATLANTIC MPAS AND OCULINA HAPC: Characterization of Fish Communities, Benthic Habitat, and Benthic Macrobiota Final Report for 2018-2019 NOAA Ship Pisces Cruises (18-02, 19-02).
Creator: Harter, Stacey, Reed, John K., Farrington, Stephanie
Abstract/Description: The South Atlantic Fishery Management Council (SAFMC) and Department of Commerce through the Magnuson-Stevens Fishery Management Act have established eight deepwater Marine Protected Areas (MPAs), five deepwater Coral Habitat Areas of Particular Concern (CHAPCs), and the Oculina Coral HAPC along the outer continental shelf off the southeastern U.S. This project proposed to document and characterize the benthic habitat, benthic sessile biota, and fish populations within some of these protected...
Show moreThe South Atlantic Fishery Management Council (SAFMC) and Department of Commerce through the Magnuson-Stevens Fishery Management Act have established eight deepwater Marine Protected Areas (MPAs), five deepwater Coral Habitat Areas of Particular Concern (CHAPCs), and the Oculina Coral HAPC along the outer continental shelf off the southeastern U.S. This project proposed to document and characterize the benthic habitat, benthic sessile biota, and fish populations within some of these protected areas and within the jurisdiction of the SAFMC. In February 2009, the SAFMC implemented eight Type II MPAs between Cape Hatteras, NC and the Florida Keys to protect seven species of the deepwater snapper-grouper complex. The closures, however, will provide ecosystem-level benefits to the entire complex as well as protect the shelfedge reef habitat they utilize. These consist of five species of grouper: snowy grouper (Hyporthodus niveatus), yellowedge grouper (H. flavolimbatus), warsaw grouper (H. nigritus), misty grouper (H. mystacinus) and speckled hind (Epinephelus. drummondhayi), and two species of tilefish: golden tilefish (Lopholatilus chamaeleonticeps) and blueline tilefish (Caulolatilus microps). The shelf-edge MPAs are known to contain reef habitat exploited by these five species of grouper as well as deepwater soft bottom habitat used by the two tilefish species. These species are considered to be at risk due to currently low stock densities and to life history characteristics which subject them to substantial fishing mortality. This monitoring program for the MPAs will ensure the Council remains well informed of changes within reef fish populations and coral habitats associated with these MPAs. NOAA NMFS conducted preliminary examinations of five of these potential MPA sites in 2004, 2006, 2007 and 2008. Post-closure data were also collected in 2009, 2010, and 2012 – 2019. The MPAs afforded the opportunity to obviate the criticisms of comparing MPAs with adjacent open-to fishing areas by examining the MPAs for four years prior to the closures. Since monitoring began in 2004, this project has produced population density estimates of targeted reef fish species within the boundaries of five of the eight MPAs and adjacent control areas, before and after closure.
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Date Issued: 2020
PURL: http://purl.flvc.org/fau/fd/FAUIR000409
Format: Document (PDF)

Title: Spawning aggregation of beardfish Polymixia lowei, in adeep-water sinkhole off the Florida Keys.
Creator: Baumberger, Rex E., Jr., Brown-Peterson, N. J., Reed, John K., Gilmore, R. G.
Date Issued: 2010
PURL: http://purl.flvc.org/fau/fd/FA00007111
Subject Headings: Florida Keys (Fla.), Beardfishes, Polymixiidae, Spawning, Sinkholes, Johnson-Sea-Link II (Submarine)
Format: Document (PDF)

Title: Submersible and scuba collections in the coastal waters of the Bahama Islands and Florida's oculina coral banks: Biomedical and biodiversity research of the benthic communities with emphasis on porifera and gorgonacea.
Creator: Pomponi, Shirley A., Reed, John K., Wright, Amy E., Janda, Kathleen E., Willoughby, Robin, Sennett, Susan H., Kelly-Borges, M., McInerney, James O., Adams, Christi L., Kelly-Borges, Klaus, Myles, David
Date Issued: 1997-01-23
PURL: http://purl.flvc.org/fcla/dt/3359258
Subject Headings: Biomedical research, Sponges--Research, Biodiversity--Research, Gorgonacea, Benthos
Format: Document (PDF)

Title: Submersible studies of deepwaterOculina and Lophelia coral banks off southeastern U.S.A.
Creator: Reed, John K., Harbor Branch Oceanographic Institute
Date Issued: 1992
PURL: http://purl.flvc.org/fau/fd/FA00007304
Subject Headings: Southeastern United States, Deep sea corals, Lophelia, Oculinidae, Submersibles
Format: Document (PDF)

Title: Summary of seafloor mapping and benthic sampling in 200-2000m, from North Carolina through Florida.
Creator: Arendt, M. D., Barans, C. A., Sedberry, G. R., Van Dolah, R. F., Reed, John K., Ross, S. W.
Date Issued: 2003
PURL: http://purl.flvc.org/FCLA/DT/3318904
Subject Headings: Submarine topography--Atlantic Coast (U.S.)--Maps, Ocean bottom--Maps, Benthos--Habitat--Maps, Benthos--Sampling
Format: Document (PDF)

HBOI Faculty Contributions (64)	+ -
HBOI Technical Reports (38)	+ -
Mesophotic Coral Reefs of Cuba (4)	+ -
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Deep sea corals (17)	+ -
Oculinidae (16)	+ -
Benthos Habitat (10)	+ -
Marine natural products (10)	+ -
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Sponges (7)	+ -
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Pulley Ridge (6)	+ -
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Biomedical research (3)	+ -
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