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 4Aquarium-based 4Autonomous Underwater Vehicle (AUV) 16Baited Remote Underwater Video (BRUV) 9Coring / drilling 4Diving (unspecified) 63Diving - Regular Open-Circuit 88Diving - Technical Open-Circuit 60Diving - Technical Rebreather 72Dredging / trawling 13Fishing 9Land-based 2Manned Submersible 88Remotely Operated Vehicle (ROV) 78Snorkeling 6Sonar / Multibeam 23Surface-deployed sensors and samplers 7Towed Video 9 .
  • Research field: categorical. Indicates the research field(s) the publication can be categorized under. show categories

    Behavior 6Biodiversity 177Biomedicine 4Climate Change 4Community structure 167Connectivity 58Disturbances 18Ecology 148Evolution 9Fisheries 26Geomorphology 31Long-term monitoring 23Management and Conservation 54Methods and Technology 5Molecular ecology 70Oceanography 15Paleoecology 13Physiology 62Reproduction 23Taxonomy 33 .
  • Focus taxon/taxa: categorical. Indicates the focal taxon/taxa of the publication. show categories

    Actiniaria and Ceriantharia (Sea anemones) 4Algae (Macro, Turf and Crustose Coralline) 52Antipatharia (Black Corals) 19Bacteria and Archaea 11Crustacea 17Fishes 115Hydrozoa 5Octocorallia (Soft Corals) 49Other endosymbionts (non-Symbiodinium) 2Other invertebrates 15Overall benthic (groups) 83Porifera (Sponges) 22Scleractinia (Hard Corals) 161Symbiodinium (zooxanthellae) 56Viruses 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 24Australia - Northern Australia 5Australia - Scott Reef 3Australia - Southeastern Australia 4Australia - Western Australia 5Bahamas 29Barbados 5Belize 3Bermuda 11Bonaire 6Brazil - Eastern Brazil 12Brazil - Fernando Noronha 1Brazil - St Peter and St Paul Archipelago 3Brazil - Trindade and Martin Vaz 5British Virgin Islands 2Brunei 0Cayman Islands 9Chagos Archipelago 1Colombia - Caribbean Sea 1Colombia - Pacific Ocean 0Cook Islands 2Costa Rica - Pacific Ocean 1Cuba 4Curaçao 32Denmark 1Dominica 2Dominican Republic 2Ecuador - Galápagos Islands 1El Salvador 1Fiji 1French Polynesia 2Grenada 1Guadeloupe 1Honduras - Bay Islands 10Israel - Mediterranean Sea 0Israel - Red Sea 38Italy - Ligurian Sea 2Italy - Tyrrhenian Sea 16Jamaica 11Japan - Okinawa 9Malaysia 1Martinique 1Micronesia - Caroline Islands 6Micronesia - Chuuk atoll 1Micronesia - Guam 5Micronesia - Mariana Islands 4Micronesia - Marshall Islands 6Norway 0Panama - Caribbean Sea 1Panama - Pacific Ocean 2Papua New Guinea 1Philippines 1Poland 1Puerto Rico 40Republic of Maldives 1Saint Kitts and Nevis 1Saint Lucia 2Saudi Arabia - Red Sea 1Solomon Islands 0South Africa 1Spain - Mediterranean Sea 13St Vincent 2Sudan - Red Sea 1São Tomé and Príncipe 0Trinidad and Tobago 1Turks and Caicos 1US Virgin Islands 43USA - Continental Atlantic 8USA - Continental Pacific 4USA - Gulf of Mexico 11USA - Hawaii 52USA - Johnston Atoll 8USA - Pulley Ridge 20Vanuatu 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