The data products described herein are part of the NOAA Coral Reef Conservation Program (CRCP) funded projects aimed at documenting the status and trends for benthic cover and composition on coral reef ecosystems across the U.S. Pacific States and Territories, conducted, by the Coral Reef Ecosystem Division (CRED) of the NOAA Pacific Islands Fisheries Science Center (PIFSC). Benthic habitat imagery collected as a part of Towed-diver Surveys (TDS) and Rapid Ecological Assessment (REA) surveys for corals and fish are quantitatively analyzed implementing the Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software, whereby 10 stratified random points are projected on each image and the benthic elements falling directly underneath each point will be identified to three functional groups levels: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae, etc.), Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g., Hard Coral = Astreopora sp, Favia sp, Pocillopora, etc.; Macroalgae = Caulerpa sp, Dictyosphaeria sp, Padina sp, etc.). Power analyses support the methodological approach outlined above, whereby statistically sound sub-jurisdictional (island) level, benthic cover estimates can be successfully derived from REA and TDS photos. Benthic percent cover at the island level can be determined from data derived from towed-diver survey images while benthic percent cover is calculated at the site level for data derived from stratified random sampling images. Benthic percent cover has been derived from imagery collected during TDS every other year in American Samoa from 2004 to 2010, Guam from 2005 to 2011, and the Main Hawaiian Islands from 2006 to 2010 as well as 2005, and during REA surveys in American Samoa in 2010, Guam and the Commonwealth of the Northern Mariana Islands (CNMI) in 2011, and the Main Hawaiian Islands in 2010 and 2013, survey imagery for Guam and the CNMI collected in 2014 is currently being analyzed (as of the publication date of this record).
These data are part of long-term monitoring or assessment data aimed at providing sound science to enable informed and effective ecosystem-based management of the coral reef ecosystems of the U.S. Pacific at approximately 40 primary islands and atolls in the Hawaiian Archipelago (Main Hawaiian Islands and Northwestern Hawaiian Islands), the Mariana Archipelago (Guam and the Commonwealth of the Northern Mariana Islands), American Samoa, and the Pacific Remote Island Areas, also known as the U.S. Minor Outlying Islands.
Information about the images collected during towed diver or Rapid Ecological Assessment (REA) surveys since 2004 at the islands listed below during CRED's Pacific Reef Assessment and Monitoring Program (RAMP) cruises can be found in the cruise reports for NOAA Ship Hi'ialakai or NOAA Ship Oscar Elton Sette, which are posted online on the PIFSC website at http://www.pifsc.noaa.gov/library/cruise.php. Occasionally, shore-based surveys are conducted around populated islands via NOAA small-boat operations, and these operations are not always associated with Pacific RAMP; see the reports for mission details. The reports for these missions are also listed herein; however access to them must be requested as the reports are not publicly available (URLs provided are internal to PIFSC). 2004 Mission: American Samoa Reef RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-04-02; Mission Dates: 03 February-26 February 2004 ; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0402-1.PSV.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, Swains, Tau, Tutuila 2005 Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-05-02; Mission Dates: 24 February-06 March 2005; Document: MHI RAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0502-PSV.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Hawaii, Maui Mission: Main Hawaiian Islands MHI RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-05-05; Mission Dates: 14 July-07 August 2005; Document: MHI RAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0505b-1.PSV.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Maui, Kauai Mission: Mariana Archipelago RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-05-12; Mission Dates: 03 October-09 October 2005; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0512-1.RES.pdf Survey Methods: Towed Diver Images analyzed for the following location: Guam 2006 Mission: American Samoa RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-06-02; Mission Dates: 09 February-10 March 2006; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0602-RS.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, Swains, Tau, Tutuila Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-06-10; Mission Dates: 27 July-20 August 2006 ; Document: MHIRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0610-REB.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Hawaii, Maui, Kauai 2007 Mission: Mariana Archipelago RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-07-02; Mission Dates: 12 May-22 May 2007; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0702-RS.pdf Survey Methods: Towed Diver Images analyzed for the following location: Guam 2008 Mission: American Samoa RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-08-02; Mission Dates: 18 February-19 March 2008; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0802-REB.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, Swains, Tau, Tutuila Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-08-10; Mission Dates: 16 October-14 November 2008 ; Document: MHI RAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0810-BVA.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Hawaii, Maui, Kauai 2009 Mission: Mariana Archipelago RAMP Cruise, Leg 2; Mission ID: Hi'ialakai, Cruise HA-09-02; Mission Dates: 02 April-14 April 2009; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA0902-RES.pdf Survey Methods: Towed Diver Images analyzed for the following location: Guam 2010 Mission: American Samoa RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-10-01, Leg 2; Mission Dates: 17 February-23 March 2010; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1001II-KD.pdf Survey Methods: REA and Towed-diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, South Bank, Swains, Tau, Tutuila Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-10-08; Mission Dates: 07 October-05 November 2010; Document: MHIRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1008-KD.pdf Survey Methods: REA and Towed-diver Images analyzed for the following locations: Hawaii, Maui, Kauai, Lanai, Molokai, Ni'ihau, Oahu Mission: Shore-based Fish Surveys; Mission ID: Small Boat Plan, SB-10-06; Mission Dates: 17 November-08 December 2010; Document: Contact CRED at nmfs.pic.credinfo@noaa.gov for more information. Survey Methods: REA Images analyzed for the following location: Oahu 2011 Mission: Mariana Archipelago RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-11-01, Legs II and III; Mission Dates: 07 April-09 May 2011; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1101II-KD.pdf Survey Methods: REA (all islands) Towed-diver (Guam only) Images analyzed for the following locations: Guam, Agrihan, Aguijan, Alamagan, Asuncion, Farallon de Pajaros, Guguan, Maug, Pagan, Rota, Saipan, Sarigan, Tinian Mission: Guam Shore-based Surveys; Mission ID: N/A (chartered vessel); Mission Dates: 06 June-17 June 2011; Document: A Report Based on Underwater Visual Surveys in Guam and the Mariana Archipelago, http://www.pifsc.noaa.gov/library/pubs/tech/NOAA_Tech_Memo_PIFSC_33.pdf Survey Methods: REA Images analyzed for the following locations: Guam 2013 Mission: Kauai Shore-based Surveys; Mission ID: Small Boat Plan, SB-13-09; Mission Dates: 29 April-07 May 2013; Document: Small Boat Mission Report: Coral disease surveys in the vicinity of Kauai Island, http://intra.pifsc.gov/sites/default/files/SBR1309-BVA.pdf Survey Methods: REA Images analyzed for the following location: Kauai Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-13-04, Legs I and II; Mission Dates: 1-23 August 2013; Document: MHIRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1304I.pdf Survey Methods: REA Images analyzed for the following locations: Hawaii, Maui, Kauai, Lanai, Molokai, Ni'ihau, Oahu. Mission: Main Hawaiian Islands RAMP Shore-based Surveys; Mission ID: Small Boat Plan, SB-13-20; Mission Dates: 30 September-23 October 2013; Document: Small Boat Mission Report: 2013 Pacific Reef Assessment and Monitoring Program (continued), Oahu Operations, http://intra.pifsc.gov/sites/default/files/SBR1320-BVA.pdf Survey Methods: REA Images analyzed for the following location: Oahu 2014 Mission: Mariana Archipelago RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-14-01, Legs I, II and III; Mission Dates: 25 March-07 May 2014; Document: MARAMP Cruise Report, Cruise report not yet published as of the publication date of this record. Contact CRED at nmfs.pic.credinfo@noaa.gov for a draft copy of the report. Survey Methods: REA Images analyzed for the following locations: Guam, Aguijan, Alamagan, Asuncion, Farallon de Pajaros, Guguan, Maug, Pagan, Rota, Saipan, Sarigan, Tinian
Ground Condition
Please cite CRED when using data. Coral Reef Ecosystem Division (CRED), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)
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Data sets derived from image analysis are highly reliable within the stipulated taxonomic context. Each time a production run is performed for a region a calibration exercise is conducted by all staff that will participate in that round of image analysis classification. Usually 100-150 photos are selected from the photos being processed as part of the production run series, or other region-relevant photo streams. Then, CPCE software has assigned 10 random fixed points per photo. Each photo analyst is asked to classify the same set of points in each of the photos used as part of the calibration exercise. The goal of the calibration exercise is to assess inter-observer variability. Inter-observer variability rates are available upon request for each production run.
Quality control is enforced by means of point-to-point, inter-observer calibration exercises that are conducted before each image analysis production series. Training modules and standard operating procedures have also been developed and documented to ensure improved performance and consistent imagery analysis results produced by multiple analysts.
The data set derived from the image analysis is as good as the images themselves; poor images with low contrast, inappropriate white balance, or out of focus may have to be discarded. Therefore, percent cover estimates for some sites may derive from differing number of points between sites. Although the analysis process is statistically robust to allow for differing n (points) between sites the users should be aware of this limitation. For REA survey imagery analyzed or collected since 2013, classification is completed to the functional group/genus level (Tier 3); prior to 2013 classification is done to the functional group level (Tier 2). All TDS survey imagery is analyzed to the functional group level (Tier 2). Benthic percent cover has been derived from imagery collected during TDS every other year in American Samoa from 2004 to 2010, Guam from 2005 to 2011, and the Main Hawaiian Islands from 2006 to 2010 as well as 2005, and during REA surveys in American Samoa in 2010, Guam and the Commonwealth of the Northern Mariana Islands (CNMI) in 2011, and the Main Hawaiian Islands in 2010 and 2013. Survey imagery for Guam and the CNMI collected in 2014 is currently being analyzed (as of the publication date of this record). There are several missions in which the benthic images collected by the program are in the process of or have not yet been analyzed. In some cases, the benthic imagery sets are not planned to be analyzed due to funding and resource constraints. Contact CRED at nmfs.pic.credinfo@noaa.gov for more information.
Benthic habitat imagery are collected as a part of Towed-diver Surveys (TDS) and Rapid Ecological Assessment (REA) surveys for corals and fish according to procedures documented in the metadata for these data collections. Alternatively, see the "Methods" sections of the following reports (RAMP = Reef Assessment and Monitoring Program): 2004 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0402-1.PSV.pdf. 2005 "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0502-PSV.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0505b-1.PSV.pdf. "Mariana Archipelago Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0512-1.RES.pdf. 2006 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0602-RS.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0610-REB.pdf. 2007 "Mariana Archipelago RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0702-RS.pdf. 2008 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0802-REB.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0810-BVA.pdf. 2009 "Mariana Archipelago RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA0902-RES.pdf. 2010 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1001II-KD.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1008-KD.pdf. 2011 "Mariana Archipelago RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1101II-KD.pdf. "A Report Based on Underwater Visual Surveys in Guam and the Mariana Archipelago", http://www.pifsc.noaa.gov/library/pubs/tech/NOAA_Tech_Memo_PIFSC_33.pdf. 2013 "Small Boat Mission Report: Coral disease surveys in the vicinity of Kauai Island", http://intra.pifsc.gov/sites/default/files/SBR1309-BVA.pdf. "MHIRAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1304I.pdf. "Small Boat Mission Report: 2013 Pacific Reef Assessment and Monitoring Program (continued), Oahu Operations", http://intra.pifsc.gov/sites/default/files/SBR1320-BVA.pdf. "Pacific Reef Assessment and Monitoring Program. Fish monitoring brief: main Hawaiian Islands 2013", http://www.pifsc.noaa.gov/library/pubs/DR-13-016.pdf. 2014 "Mariana Archipelago RAMP Cruise Report", Cruise report not yet published as of the publication date of this record. Contact CRED at nmfs.pic.credinfo@noaa.gov for a draft copy of the report. "Pacific Reef Assessment and Monitoring Program. Fish monitoring brief: southern Mariana Archipelago 2014.", http://www.pifsc.noaa.gov/library/pubs/DR-14-009.pdf. "Pacific Reef Assessment and Monitoring Program. Fish monitoring brief: northern Mariana Archipelago 2014.", http://www.pifsc.noaa.gov/library/pubs/DR-14-010.pdf. "Coral Reef Ecosystem Division standard operating procedures: data collection for Rapid Ecological Assessment fish surveys", http://www.pifsc.noaa.gov/library/pubs/admin/PIFSC_Admin_Rep_11-08.pdf. It is assumed that images have already undergone appropriate post-collection processing in the field to catalog and rename the images using standard naming conventions prior to the beginning of the benthic image analysis. If images need to be corrected for photo analysis run series or calibration exercises, a copy of the original image is preserved. Generally, for stratified random coral and fish site survey photos, if the cameras were properly white-balanced in the field, no color-correction is required. TDS all photos analyzed have undergone color correction implementing Picasa. Corrections may include brightness/contrast adjustments, color adjustments, sharpening, etc. In general, the software's auto-adjustment capabilities are sufficient for the majority of images. Some additional manual adjustments may still be required. If color-correction doesn't improve the image, this image may be excluded from the analysis for that location or transect. Images are quantitatively analyzed implementing the Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software. Images are opened up in the CPCe program and the area for image analysis is set. Due to how the images are collected the area for image analysis may vary. Due to image distortion that occurs along the edges of the majority of images, all towed-diver survey imagery and REA survey imagery from 2014 and beyond are analyzed with a pixel buffer around the entire perimeter of the image; pixel offset (228,192) and (60,42) for TDS and REA respectively. Prior to that the entire image was used for stratified random fish and benthic REA site survey photos. Ten stratified random points are calculated and projected on each image by the CPCe software. The benthic elements falling directly underneath each point are identified to two (TSD) or three (REA surveys) functional groups levels: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae, etc.) and Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g., Hard Coral = Acropora, Montipora, Pocillopora, etc.; Macroalgae = Padina, Dictyota, Dictosphaeria, etc.). In cases where a coral colony exhibits more than one growth form, it is the morphology directly under the point that is classified, rather than the morphology of the colony overall. If a point falls precisely between two coral growth morphologies, or on the border between two benthic categories (e.g., coral-algae), the benthic category occupying the greatest area within symbol (circle wrapping the cross-hairs) is classified. Additionally, if the two benthic categories occupy equal space within the symbol, the benthos falling on the top left quadrant within the point symbol is classified. The category Shadow is used when the point falls on an area that is dark and the nature of the benthos cannot be assessed due to diminished light. The category Unclassified is used when the nature of the benthos cannot be determined due to image quality or unfamiliarity with the type of benthos. The category Wand is used when the point falls on a transect line/tape measure, or photo quadrat frame/spacing wand. If any photo has more than 5 combined points classified as Shadow or Unclassified, or if a stratified random site photo has more than 1 point classified as Wand these data are not saved. Instead a new set of points to analyze is generated by using the Point Overlay menu and selecting Recalculate point coordinates. This step of regenerating points for analysis will be repeated up to three times before the image is removed from the production series. For tows with several photographs whose quality is insufficient for use, ~35% (40 images) of the total number of images to be analyzed is the minimum acceptable number that need to be analyzed to grant retention of those data in the production series. Power analyses support the methodological approach outlined above, whereby statistically sound sub-jurisdictional (island) level, benthic cover estimates can be successfully derived from REA and TDS photos processed at: 300 points/survey (i.e., 10 points/photo x 30 photos) and 600-700 points/survey (i.e., 10 points/image x 60-70 photos), respectively. Percent cover at the island level can be determined from data derived from towed-diver survey images while percent cover is calculated at the site level for data derived from stratified random sampling images. The complete Benthic Image Analysis Standard Operating Procedure (SOP) is available on the NOAA Wiki at https://www.st.nmfs.noaa.gov/confluence/display/CRED/Benthic+Image+Analysis. Non-NOAA users can contact CRED at nmfs.pic.credinfo@noaa.gov to request a copy of the SOP.
For the purposes of this image analysis, hard corals are defined as those that are responsible for the persistent, hard, three-dimensional structure of a coral reef. In general, this classification will include all members of Order Scleractinia, as well as some other small groups of non-scleractinian corals with hard skeletons, including fire corals (Family Milleporidea), blue coral (Order Helioporacea), and Stylasterid hydrocorals (Family Stylasteridae).
NOAA/NMFS/CRED
Coral colonies with distinct and boulder-like; small ones have more of a dome or cushion-shape silhouette. It is not unusual for massive colonies to exhibit a bumpy or knobby surface, but for the most part all possess a solid thick shape.
Coral colonies with tabulate growth morphology are those that have the appearance of a table or bench, supported on a short, stout base that is attached to the substrate. The horizontal plate or plates have numerous fused and interlocking branches, forming a roughly circular or oblong plate sometimes several feet in diameter.
Coral colonies with encrusting morphology are those with flattened, thick or thin sheets/plates that adhere to, and follow the contour of the substrate. Colony surfaces often range from smooth to rough, bumpy, knobby, or crinkled, with some specimens exhibiting raised colony edges, giving colonies a platy/foliose appearance. Some corals like Montipora spp. have colonies exhibiting mixed morphologies, such as encrusting bases with vertical, columnar or branching up-growths. If up-growths are low-profile bumps or knob-like protrusions and most of the colony is still encrusting, then the colony should be classified as encrusting. Conversely, if the encrusting base is covered with sizable, vertical, dichotomous branching projections, then the colony should be classified as having a branching morphology.
Corals forming large, arborescent (tree-like) colonies exhibiting elongated branched projections, to smaller, stubby and compact branches with finger-like (digitate) protrusions should be classified as branching morphology.
Some coral colonies, generally massive- and encrusting-looking, can exhibit club-like or column-like up-growths; these colonies should be classified as having a columnar morphology. Columns can be smooth, knobby, or bumpy, and nearly cylindrical or tapered, but not branched. Columns typically protrude several inches from the base of the colony; this should not include stubby digitate protrusions or incipient branchlets. Corals including Porites rus, P. cyllindrica, P. evermanni, Coscinaraea exesa, Pavona maldivensis, and Favia stelligera, can grow colonies exhibiting columnar morphology.
Use the free-living morphology for coral colonies that live unattached from the substrate. This excludes broken-off colony branches or other products of fragmentation. Free-living corals are conspicuous; most develop as flattened, dome-shaped disks, with a central mouth and apparent, radiating ridge-like structures known as septa..
Coral colonies with foliose morphology are those that grow in flattened sheets or plates where a substantial portion of the colony is detached and elevated from the substrate forming shingle-like rows or tiers of overlapping plates, fused or convoluted whorls, vases, or leafy/lettuce-like stands.
This classification category is to be used for other groups of non-scleractinian corals with hard skeletons, including fire corals (Family Milleporidae, e.g., Millepora sp), blue coral (Order Helioporacea, e.g. Heliopora coerulea), and Stylasterid hydrocorals (Family Stylasteridae), regardless of growth form.
For the purposes of this image analysis, this category groups a collection of fairly related organisms that do not produce a substantial, rigid calcium carbonate skeleton and therefore are neither reef-builders nor do they lay new foundations for future corals. This classification will include members of Subclass Alcyonaria (octocorals), except blue coral and the organ pipe coral, which includes true soft corals, sea fans, sea whips, sea pens, and also members of the Order Antipatheria (black corals).
Use this Tier 2 classification for gorgonian corals, sea fans, sea whips, sea pens, and other members of Subclass Alcyonaria (octocorals), except blue coral (Order Helioporacea), which should be classified as Non-scleractinian hard coral. All members of this classification category produce skeletal elements made of protein and calcium carbonate that and give the colony sufficient soft support and the flexibility to sway with the ocean waves and currents.
These corals resemble gorgonians forming tree-like colonies. They possess a hard axial protein skeleton and non-retractable polyps, including black coral and wire coral (Order Antipatheria).
For the purpose of these image analyses, CCA is defined as any calcified, hard, non-segmented, encrusting or branched, red (or pink) alga.
CCA commonly grow on rubble, which is defined as hard fragments (e.g. rocks, pebbles, pieces of dead coral) typically of gravel (> 5 mm) and cobble (baseball) size with finer and coarser sediments mixed in, in patches. A piece of rubble completely encased in CCA is termed a rhodolith.
CCA commonly grows in patches on hard substrates, forming hard pink crusts. Hard substrates range from pavement flats to basalt formations to bare carbonate (i.e. coral skeleton) structures.
Turf algae is a category that includes numerous species from multiple evolutionary groups (red algae, green algae, brown algae, and cyanobacteria). These types of mixed algal assemblages are typically short in stature (< 2 cm in height), and often contain filamentous algae (hair-like morphologies) as opposed to fleshy algae (thick branched or sheet-like morphologies).
Turf algae often cover rubble, which is defined as hard fragments (e.g. rocks, pebbles, pieces of dead coral) typically of gravel (> 5 mm) and cobble (baseball) size with finer and coarser sediments mixed in, giving the fragments a fuzzy appearance.
Turf algae often appear as fuzzy carpets growing across hard substrates. Hard substrates range from pavement flats to basalt formations to bare carbonate (i.e. coral skeleton) structures. NOTE that turf algae will tend to trap a fine layer of sediment and this still constitutes a turf covered surface and should NOT be classified as Sand.
All hard surfaces are colonized by turf algae within days of being placed in the water. All rubble, which is defined as hard fragments (e.g. rocks, pebbles, pieces of dead coral) typically of gravel (> 5 mm) and cobble (baseball) size with finer and coarser sediments mixed in, are covered by turf algae even though these small organisms might not be visible in a photograph. Sometimes they're even difficult to discern by a diver in the field.
All hard surfaces are colonized by turf algae within days of being placed in the water. All hard substrates are covered by turf algae even though these small organisms might not be visible in a photograph. Hard substrates range from pavement flats to basalt formations to bare carbonate (i.e. coral skeleton) structures.
Any alga whose structure can be seen in the photograph should be labeled as a macroalga rather than turf. Macroalgae possess numerous different types of morphologies that resemble leaves, blades, umbrellas, ferns, grapes, balls, feathers, branched shrubs, etc. Some macroalgae do possess calcification; however, for the purpose of image analyses here, calcified and fleshy representatives (with the exception of Halimeda sp., below) will be lumped together.
Macroalgae that do not form crusts adherent to rubble or the substrate should be termed as upright.
Encrusting macroalgae may resemble CCA by forming crusts across rubble or hard bottom communities. For the purpose of image analyses, if the encrusting alga is not red or pink, it should be considered an encrusting macroalga rather than CCA. It's important to note that EMA can also be pink and red in addition to all other options. Color can usually NOT be the sole distinguishing factor. Other features used to distinguish EMA include growth pattern, texture, and striations in color pattern.
Blue-green algae (more correctly termed cyanobacteria) are rare in the majority of photographs examined. However, when they are recorded, they often form gregarious assemblages that look different from macroalgae or turf algae. When observed, cyanobacteria often form deep purple to black filamentous tufts or mats that may stretch for multiple centimeters in length, and therefore look different from turf algae. They may also form mucilaginous masses that are white or pale yellow in color.
The calcified green algal genus Halimeda is easily discernible by it's plate-like discs that form "chains" of segments. Living plants appear green, although dead segments may be white.
Seagrasses are flowering plants from one of four plant families (Posidoniaceae, Zosteraceae, Hydrocharitaceae, or Cymodoceaceae), which grow in marine, fully-saline environments.
Many organisms besides corals and algae are found in coral reef ecosystems. This Tier 1 classification is to be used for animals that are permanently affixed to the substrate. Animals with ability to move about the substrate or swim are classified as Mobile Fauna.
Classification points that land on giant clams (Family Tridacnidae) should be classified in this Tier 2 category. While their shell may be drab in color and/or colonized by algae or other sessile organisms, the mantle can colorful and they can grow from .25 m to more than 1 m in diameter. The Bivalve category is used for all other bivalves (clams, oysters, and mussels) in Class Bivalvia.
Clams, oysters, and mussels are common examples of bivalves (Class Bivalvia). Giant clams (Family Tridacnidae) are a special case, and have their own Tier 2 classification category.
Sponges (Phylum Porifera) have numerous species and growth morphologies, many of which can be confused with other benthic organisms. Sponges have porous tissue for filter feeding and many have large openings through which expelled water flows (excurrent openings). To help identify sponges, zoom-in with the photograph and examine the surrounding tissue. In general, sponges are more colorful than tunicates. In general, sponges are not as smooth as a tunicate, rather they are "rougher" around the edges due to a lack of a "tunic" and being composed of spicules. In general, most sponges, unlike tunicates, are not able to close their excurrent openings. In general sponges can protrude/extend upwards off the benthos from their encrusting state whereas tunicates tend to grow along the contours of the substrate underneath them.
Tunicates (Class Ascidiacea) have numerous species and growth morphologies, many of which can be confused with other benthic organisms (particularly sponges). They can grow as solitary individuals or in colonies. Their soft body is surrounded by a thick test, or tunic, often transparent or translucent and varying in consistency from gelatinous to leathery. In solitary tunicates, there are two siphons that project from the animal's body; water enters the incurrent siphon at the top of the body and leaves the excurrent siphon at the side. They appear heart shaped. Colonial tunicates share excurrent siphons but zooids (individuals) have their own incurrent siphon. The following is a generalization however, more often than not, if the organism has multiple holes (which represents the individual incurrent siphons of the zooid) with a few larger holes (the shared excurrent siphons) spread out, it is probably a tunicate. Tunicates will be able to close their siphons rather quickly whereas sponges are for the most part unable. Thus if some of the openings of the sessile organism appear to be closed in the photograph, it is likely a tunicate. Another generalization that helps separate tunicates from sponges is that tunicates don't usually have visible "channels," whereas certain sponges do. One final generalization is that tunicates tend to grow with the contours of the substrate whereas sponges can grow upwards from the encrusting state.
These colonial animals are early colonizers of bare surfaces in coral reefs. Most attach to solid surfaces but some live in sand. Each "member" lives in a zooid, or house, and has lophophores which are "tentacles" that extend out of the house to filter feed. The lophophores are ciliated and very "regular" in appearance. However, unless the image is really clear, it will be hard to detect the lophophores and use them to distinguish between a tunicate or sponge. The individual zoids join to neighboring ones forming bushy, branching, fanlike, or encrusting colonies that may be rigid or flexible. Most bryozoans have a lace-like appearance and can be confused with algae or sponges. However, unlike sponges and tunicates, you will not see incurrent and excurrent openings. This is because the lophophores in bryozoans are used for feeding. In general, bryozoans will not appear smooth like a tunicate and their upright structure will appear to be "flower" and "plant"- like.
Corallimorphs (Order Corallimorpharia) are anemone-like animals that are found either solitary or in colonies. Their tentacles are generally much shorter than those of true anemones. They can be invasive and at this stage resemble a fuzzy carpet.
Anemones have many tentacles, the number of which varies by species, surrounding a single mouth opening on top of a tubular body. However, you will probably never see the mouth opening, just the tentacles. Anemones usually attach themselves to the hard substrate with a pedal disc, which is found at the base of the body. Members of Order Actiniaria (anemones) and Order Ceriantheria (tube-dwelling anemones) are classified with this Tier 2 category.
Zoanthids (Order Zoanthidea) are colonial anemone-like animals having smooth, flat, broad oral disks with tentacles that radiate outward from their margins. Tentacles are found in two nearby rows, and always are in a number that is a multiple of six. The polyp's mouth has a ciliated groove at one or both ends of the mouth. Zoanthids are connected by runners (called stolons) and they lack the hard skeletons of scleractinian corals.
This Tier 2 category is used when the classification point falls on a sessile invertebrate that doesn't fall within one of the other Tier 2 categories, or in situations when a sessile invertebrate can't be distinguished, for example, differentiating between an encrusting sponge or tunicate.
Photographs capture a solitary instant in time. As a result, creatures that are not permanently affixed to a single location on the sea floor (e.g. sea cucumbers, sea stars, sea urchins, fish) sometimes also appear in photographs intended for benthic analysis. While every effort should be made to discern what the benthic classification is underneath the mobile fauna, if that is not possible, this classification category should be used. This is both a Tier 1 and Tier 2 classification category.
Photographs capture a solitary instant in time. As a result, creatures that are not permanently affixed to a single location on the sea floor (e.g. sea cucumbers, sea stars, sea urchins, fish, marine mammals) sometimes also appear in photographs intended for benthic analysis. While every effort should be made to discern what the benthic classification is underneath the mobile fauna, if that is not possible, this classification category should be used. This is both a Tier 1 and Tier 2 classification category.
Sediment describes a "soft" benthos smaller than rubble (i.e. < 5 mm) which due to it's unsettled nature generally, but not always, is devoid of organisms growing on the individual gains comprising the sediment. However, sea grasses, macroalgae including Halimeda spp., and blue-green algae (a.k.a. cyanobacteria) can be found in soft sediment areas. If a classification point falls on an identifiable organism growing in sediment, that's what should be used for the point classification. The sediment classification should only be used if point falls on the sediment itself.
Sand is defined as sediment with a grain size between 1/16 mm and 5 mm. This can include silica sand, fine calcium carbonate sand, lava sand, and/or Halimeda spp. blade sand. A thin dusting of sand over a turf covered surface is not sufficient to be called Sand habitat.
Fine sediment is defined as sediment with a grain size of < 1/16 mm.
A particular analysis point may be unclassified because image quality was poor, because not enough of the surrounding area is visible to definitively classify the organism underneath the point, because the benthos is obstructed by something other than mobile fauna, tape, wand, or shadow (e.g. bubble or smear on the camera lens, high turbidity in the water column).
This classification is required by the Coral Point Count with Excel Extensions (CPCe) software. It is to be used whenever a classification point lands on a transect line/tape measure, photo quadrat frame/spacing wand, or a shadow cast by natural or anthropogenic features which prevents organism classification.
Unclassified
Image analysis classification scheme overview: Tier 1: Hard Coral Tier 2: Massive; Encrusting; Branching; Columnar; Free-living; Foliose; Tabulate; Non-scleractinian Tier 3: branching Acropora sp, tabulate Acropora sp, Acanthastrea sp, Astreopora sp, Coscinaraea sp, Cyphastrea sp, Echinophyllia sp, Echinopora sp, Favia sp, Favites sp, Galaxea sp, Goniopora/Alveopora sp, Goniastrea sp, Hydnophora sp, Isopora sp, Leptastrea sp, Leptoseris sp, Lobophyllia/Symphyllia sp, encrusting Montipora sp, non-encrusting Montipora sp, Pavona sp, Platygyra/Leptoria sp, Pocillopora sp, massive Porites sp, non-massive Porites sp, Psammocora sp, Stylophora sp, Turbinaria sp, --- Tier 1 Soft coral Tier 2: Octocoral; Unclassified --- Tier 1: Crustose coralline red algae (CCA) Tier 2: CCA on rubble; CCA on hardbottom --- Tier 1: Turf Alga Tier 2: Visible turf on rubble; Visible turf on hardbottom; Invisible turf on rubble; Invisible turf on hardbottom --- Tier 1: Macroalgae or seagrass Tier 2: Upright macroalgae; Encrusting macroalgae; Blue-green macroalgae; Halimeda; Seagrass Tier 3: Avrainvillea sp, Boodlea sp, Caulerpa sp, Chlorodesmis sp, Dictyosphaeria sp, Halimeda sp, Microdictyon sp, Neomeris sp, Dictyopteris/Dictyota, Lobophora sp, Padina sp, Acanthophora sp, Amansia sp, Asparagopsis sp, Galaxaura sp, Ganonema/Liagora, Peyssonnelia sp --- Tier 1: Sessile Invertebrate Tier 2: Giant clam; Bivalve; Sponge; Tunicate; Bryozoan; Corallimorph; Anemone; Zoanthid; Unclassified --- Tier 1: Mobile Fauna Tier 2: Mobile fauna --- Tier 1: Sediment Tier 2: Sand; Fine sediment --- Tier 1: Unclassified Tier 2: Tape, wand, shadow; Unclassified
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