About


 You are currently looking at a beta release of the new website. Apologies for the inconvenience, but for now expect some (= lots of) bugs & mistakes!

Mission

  • Collate available research focusing on the mesophotic depth zone, and make it accessible through a single webportal.
  • Allow for the identification of knowledge gaps around particular taxa and geographic areas at mesophotic depths
  • Provide a central place on the web for the exchange of scientific information and ongoing research efforts
  • Act as an independent platform and shared resource for and by the mesophotic research community.

Metadata

The primary entities in the database are scientific publications, for which standard citation data and the full-text contents are indexed. In addition, the following metadata are manually curated (and validated by at least 3 editorial members):

  • Mesophotic: true / false. Indicates whether the publications presents data from, or presents a discussion on, the mesophotic depth range (true), or whether it is focused on another depth range (e.g. shallow or deep-sea) but relevant to mesophotic studies (false), and therefore included in the database. The mesophotic depth range is defined to be from 30-150 m.
  • Mesophotic Coral Ecosystem (tropical & subtropical) : true / false. Indicates whether the publications presents data from, or presents a discussion on, a “mesophotic coral reef ecosystem (MCE)” as characterized by the following definition (altered from the Hinderstein et al. 2010 definition): “characterized by the presence of photosynthetically active corals, algae and associated communities at depths ranging from 30 to 150 m in tropical and subtropical regions” (true), or whether it is focused on an ecosystem that does not fall under this definition (false). The altered definition is to reflect the fact despite the “presence of light-dependent corals”, they are often a very small component of the overall ecosystem (particularly at lower mesophotic depths); additionally, while photosynthetically-active, the “dependence” on light may be debatable at lower mesophotic depths. Ecosystems that do not fall under this definition are those in Mediterranean and temperate systems (not subtropical/tropical), or azooxanthellate systems such as subtropical Oculina reefs (not a photosynthetically-active community).
  • Original data: true / false. Indicates whether the publication presents novel data (true) or instead represents a review or meta-analysis (false).
  • Reports new species: true / false. Indicates whether the publication includes the establishment of one or more new scientific names of species (true). Publications reporting on new species without establishing new scientific names for them are not included (e.g. undescribed, cryptic lineages discovered in a phylogenetic study) (false).
  • Minimum depth: integer (in meters). “The lesser depth of a range of depth below the local surface, in meters” (sensu DarwinCore). More specifically, this indicates the depth (in meters) of the shallowest data record (e.g. specimen or transect) in the presented dataset or meta-analysis (using normal rounding to obtain integer). Only given for publications that present "Original data". Personal observations mentioned in the publication are not included.
  • Maximum depth: integer (in meters). “The greater depth of a range of depth below the local surface, in meters” (sensu DarwinCore). More specifically, this indicates the depth (in meters) of the deepest data record (e.g. specimen or transect) in the presented dataset or meta-analysis (using normal rounding to obtain integer). Only given for publications that present "Original data". Personal observations mentioned in the publication are not included.
  • Latitude: integer (in meters). “The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive” (sensu DarwinCore).
  • Longitude: integer (in meters). “The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.” (sensu DarwinCore).
  • Publication type: Scientific / Technical / Popular. Indicates whether the publication is scientific (peer-reviewed), technical (which can be either peer-reviewed or non-peer-reviewed) and popular.
  • Publication format: Article / Review / Chapter / Book / Report / Thesis. Indicates the format of the publication.
  • Platform: categorical. Indicates the platform(s) used to collect the presented data. Only given for publications that present `Original data`. show categories

    Acoustic Telemetry 7Aquarium-based 5Autonomous Underwater Vehicle (AUV) 17Baited Remote Underwater Video (BRUV) 10Coring / drilling 6Diving (unspecified) 82Diving - Regular Open-Circuit 97Diving - Technical Open-Circuit 67Diving - Technical Rebreather 77Dredging / trawling 21Fishing 12In-situ instrumentation 1Land-based 5Manned Submersible 96Remotely Operated Vehicle (ROV) 87Snorkeling 7Sonar / Multibeam 27Surface-deployed sensors and samplers 19Towed Video 15 .
  • Research field: categorical. Indicates the research field(s) the publication can be categorized under. show categories

    Acoustics 2Behavior 12Biodiversity 196Biomedicine 5Climate Change 5Community structure 177Connectivity 57Disturbances 26Ecology 170Evolution 12Fisheries 33Geomorphology 37Long-term monitoring 31Management and Conservation 54Methods and Technology 7Molecular ecology 68Oceanography 25Paleoecology 13Physiology 73Reproduction 29Taxonomy 48Vision 0 .
  • Focus taxon/taxa: categorical. Indicates the focal taxon/taxa of the publication. show categories

    Actiniaria and Ceriantharia (Sea anemones) 5Algae (Macro, Turf and Crustose Coralline) 59Antipatharia (Black Corals) 22Bacteria and Archaea 12Crustacea 17Fishes 133Hydrozoa 7Octocorallia (Soft Corals) 52Other endosymbionts (non-Symbiodinium) 2Other invertebrates 16Overall benthic (groups) 92Plankton 2Porifera (Sponges) 29Scleractinia (Hard Corals) 177Seagrass 1Symbiodinium (zooxanthellae) 60Viruses 1Zoantharia (Zoanthids) 0 .
  • Geographic location: categorical. Indicates the geographic location the publication focuses on. show categories

    American Samoa 2Aruba 1Australia - Coral Sea 7Australia - Great Barrier Reef 28Australia - Northern Australia 5Australia - Scott Reef 3Australia - Southeastern Australia 5Australia - Western Australia 5Bahamas 31Barbados 5Belize 4Bermuda 13Bonaire 6Brazil - Eastern Brazil 14Brazil - Fernando Noronha 2Brazil - St Peter and St Paul Archipelago 3Brazil - Trindade and Martin Vaz 5British Virgin Islands 2Brunei 1Cayman Islands 9Chagos Archipelago 1Colombia - Caribbean Sea 3Colombia - Pacific Ocean 0Cook Islands 2Costa Rica - Pacific Ocean 3Cuba 4Curaçao 33Denmark 1Djibouti 1Dominica 2Dominican Republic 2Ecuador - Galápagos Islands 1Egypt - Red Sea 1El Salvador 1Fiji 1French Polynesia 3Grenada 1Guadeloupe 1Honduras - Bay Islands 10Indonesia 1Israel - Mediterranean Sea 0Israel - Red Sea 43Italy - Ligurian Sea 2Italy - Tyrrhenian Sea 18Jamaica 13Japan - Okinawa 14Malaysia 1Martinique 1Mexico - Baja California 1Micronesia - Caroline Islands 7Micronesia - Chuuk atoll 1Micronesia - Guam 5Micronesia - Mariana Islands 4Micronesia - Marshall Islands 6Montserrat 0Netherlands Antilles - Saba Bank 1Norway 0Panama - Caribbean Sea 1Panama - Pacific Ocean 2Papua New Guinea 2Philippines 3Pitcairn Islands 1Poland 1Puerto Rico 42Republic of Maldives 1Saint Kitts and Nevis 1Saint Lucia 2Saudi Arabia - Red Sea 1Solomon Islands 0South Africa 1Spain - Mediterranean Sea 13St Vincent 2Sudan - Red Sea 2São Tomé and Príncipe 0Trinidad and Tobago 1Turks and Caicos 1US Guam 0US Virgin Islands 45USA - Continental Atlantic 11USA - Continental Pacific 4USA - Gulf of Mexico 18USA - Hawaii 54USA - Johnston Atoll 8USA - Pulley Ridge 24Vanuatu 1Venezuela - Islas Los Hermanos 1 .

Release history

  • 2016-now: The second (latest) release: A beta version of the new mesophotic.org went on-line in June 2016, coinciding with the 13th International Coral Reef Symposium in Hawai'i (USA). This new version is backed by a relational database that contains extensive metadata on all of the listed publications, and offers searching across the full contents of the indexed publications.

  • 2012-2016: Wordpress & social media: Over the past several years, a simplified semi-static (Wordpress) version with just news items and a list of publications/abstracts replaced the original (databases-backed) website. Admittedly only as a temporary solution, however due to a lack of time a new back-end was not developed until 2016. Instead, there was an increased focus on using social media (Facebook and Twitter) to communicate news around mesophotic coral ecosystems.

  • 2008-2011: The original release: The mesophotic.org website officially went on-line in 2008 when it was first announced at the 11th International Coral Reef Symposium in Ft. Lauderdale (Florida / USA) and the International Collaborative Workshop to Prioritize Research and Management Needs for Mesophotic Coral Ecosystems in Jupiter (Florida / USA). The original website was started by Pim Bongaerts (The University of Queensland), with support from Felix Martinez and Lara Hinderstein (National Oceanic Atmospheric Administration - Center for Sponsored Coastal Ocean Research). Over these initial years, the website received small grants from the Center for Sponsored Coastal Ocean Research (CSCOR/NOAA), the Perry Institute for Marine Science (PIMS), the University of Puerto Rico at Mayagüez (UPR) and the Pacific Blue Foundation. The website eventually went down due to being hacked (and admittedly not the most secure PHP coding practises).

 
Current contributors
Pimbongaerts sm
Pim Bongaerts
The University of Queensland
Website development

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Ryan Booker
Global Underwater Explorers
Website development

Dab high res
Dominic Andradi-Brown
World Wildlife Fund
Content Editor

Gal eyal
Gal Eyal
Interuniversity Institute for Marine Sciences at Eilat
Content Editor

Andrea gori2
Andrea Gori

Content Editor

Alejandra hernandez agreda 200x200
Alejandra Hernandez-Agreda
James Cook University
Content Editor

Hudson
Hudson Pinheiro
California Academy of Sciences
Content Editor

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Richard Pyle
Bishop Museum
Content Editor

Gon
Gonzalo Perez-Rosales
École Pratique des Hautes Études
Content Editor

Veronica chagos small cropped
Veronica Radice
The University of Queensland
Content Editor

  Are you interested in helping out? Let us know!

Past contributors
Felix
Felix Martinez
National Oceanic and Atmospheric Administration
Editorial board

Norbert
Norbert Englebert
The University of Queensland
Data curation

Source code
The website source code was written in Ruby (2.2.1) on Rails (4.2.0) and is (for now privately) hosted on GitHub. Original set-up was done using RailsBricks, layout was formatted using Bootstrap, and authentication done with Devise. Charts and maps are generated with Highcharts.
Contact
For any questions, please contact us at: info[at]mesophotic.org