Photogrammetry-derived coral growth and structural complexity measurements from the Mo'orea Reef Back (MRB) Amount experiment. 54 Pocillopora spp. colonies were transplanted onto artificial reef patches at three coral density treatments (1, 3, or 6 colonies per 1 m2 patch). Colonies were photographed for 3D Structure-from-Motion reconstruction in December 2019 (baseline) and May 2021 (18 months post-transplant). Growth metrics include change in surface area, volume, and maximum height. Both unfiltered and quality-controlled growth datasets are provided. Supplemental files include raw mesh data, manual field measurements, and treatment assignments.

Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • Problem Description
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

See the "Related Datasets" section for other closely related data from the same project/study/experiments. Related Datasets also describes how datasets relate, for example, which share a common coral_id.
Study Description (describes this and related datasets):

Two field experiments and one observational survey were performed investigating how cryptic invertebrate communities (CAFI - Coral Associated Fauna and Invertebrates) interact with and influence coral reef ecosystems in Mo'orea, French Polynesia (2019-2021). The research addresses how spatial configuration of coral habitat affects CAFI community assembly and the reciprocal effects of CAFI on coral health and growth.

Study Experiments and Surveys:
(1) Maatea Size Experiment examining effects of coral colony size on CAFI communities using 60 Pocillopora colonies spanning a natural size gradient.
(2) MRB Amount Experiment testing effects of coral habitat density on CAFI colonization using 54 Pocillopora colonies in low, medium, and high density treatments arranged on a 9x6 experimental grid.
(3) Mo'orea Survey characterizing natural CAFI communities across 114 Pocillopora colonies at multiple reef sites.

Acronyms:

MRB = Maharepa Research Base
CAFI = Coral Associated Fauna and Invertebrates
AFDW = Ash-Free Dry Weight
WoRMS = World Register of Marine Species (marinespecies.org)
AphiaID = Aphia ID (ID for taxonomic names at WoRMS)
LSID = Life Sciences Identifier (ID for taxonomic names - ID includes what database it is for)

​Project location description:

Mo'orea Island, French Polynesia. Data were collected at three primary study sites on backreef habitats at 2-10 meter depth: (1) Maatea site on the south shore east of Atiha Pass (17.60°S, 149.81°W), (2) MRB (Maharepa Research Base) site on the north shore near Maharepa township (17.48°S, 149.81°W), and (3) multiple survey sites distributed around the island including northern and western shores. All sites were located 30-300 meters from the reef crest in sand and coral rubble habitats dominated by Pocillopora corals. Field work was conducted from the UC Berkeley Richard B. Gump South Pacific Research Station.

MRB AMOUNT EXPERIMENTAL DESIGN:
MRB Amount Experiment testing effects of coral habitat density on CAFI colonization using 54 Pocillopora colonies in low, medium, and high density treatments arranged on a 9x6 experimental grid.

CORAL COLLECTION AND DEPLOYMENT:
Pocillopora coral colonies were collected from natural reef sites and deployed at experimental sites on sand and rubble substrate at 2-10m depth. For experiments, colonies were attached to cement bases and arranged according to experimental design. Colonies were maintained in situ for 18 months (December 2019 to May 2021) with intermediate sampling in December 2019.

CAFI EXTRACTION AND IDENTIFICATION:
CAFI were extracted from coral colonies using clove oil anesthetic dissolved in seawater (concentration approximately 100 ppm). Colonies were placed in plastic bags underwater, anesthetic seawater was added, and bags were sealed and agitated for 5-10 minutes to narcotize cryptic fauna. Contents were emptied into collection buckets, and organisms were sorted, identified to lowest taxonomic level possible (typically family, genus, or species), counted, and measured for body size using digital calipers or microscope-mounted measuring tools. Organisms were identified using regional taxonomic guides and expert consultation. Taxonomic identifications were verified using the World Register of Marine Species (WoRMS) database, with WoRMS IDs recorded for all taxa.

SIZE MEASUREMENTS:
Body size measurements were organism-specific: fish measured as standard length (snout to caudal peduncle), crustaceans measured as carapace length, molluscs measured as shell length or width (species-dependent), polychaetes measured as body length, and other organisms measured as maximum body dimension. Measurements recorded in millimeters, with organisms smaller than 5mm recorded as "<5" and very small organisms (<1mm) recorded as "<1". Some organisms were categorized as Large (L), Medium (M), or Small (S) when precise measurement was not feasible.

CORAL PHOTOGRAMMETRY:
Three-dimensional coral morphometrics were quantified using Structure-from-Motion photogrammetry. Each coral colony was photographed underwater from multiple angles (50-100 images per colony) using a Canon EOS camera in underwater housing with two LED dive lights for consistent lighting. Scale bars (15cm PVC rulers) were included in each photo set for spatial calibration. Images were processed in Agisoft Metashape Professional (versions 1.6-1.7) using standard SfM workflows: photo alignment, dense point cloud generation, mesh construction (200,000 face count), and texture mapping. Measurements extracted included projected area, 3D surface area, volume, maximum height, and minimum height. Heights were measured relative to a horizontal reference plane; negative minimum heights indicate colony base below the reference plane and are valid measurements for colonies with irregular attachment surfaces.

CORAL PHYSIOLOGY:
Coral tissue samples were collected using a 10mL syringe to blast tissue from a standardized area of each colony. Samples were homogenized and divided for multiple analyses. Protein content was measured using Bradford assay with bovine serum albumin standards. Carbohydrate content was measured using phenol-sulfuric acid assay with glucose standards. Zooxanthellae density was quantified by taking subsamples of homogenate, counting cells using a hemocytometer, and normalizing to coral surface area. All physiological measurements were normalized to coral surface area (per cm²) determined from photogrammetry.

FISH SURVEYS:
Fish communities were surveyed using visual census methods. Observers conducted timed surveys of experimental arrays, recording all fish species present, abundance, estimated body size, and behavior (resident vs. transient). Surveys were conducted at multiple time points to assess temporal variation in fish community composition.

QUALITY CONTROL:
All CAFI identifications were reviewed by multiple researchers. Voucher specimens were photographed for reference. Photogrammetry models were quality-checked for reconstruction errors, and problematic models were flagged in the dataset. Physiological measurements included technical replicates, and outliers were investigated and verified or removed.

 

DATA CLEANING AND STANDARDIZATION:
Raw field data were transcribed from underwater data sheets and entered into digital spreadsheets. Taxonomic names were standardized using the World Register of Marine Species (WoRMS) database (accessed 2021-2023). WoRMS Aphia IDs were added for all taxa to ensure consistency and facilitate data integration. Size measurements recorded as text categories ("<5", "<1", "L", "M", "S") were retained in original field data columns, with separate numeric-only columns created for quantitative analyses (recorded as NA when non-numeric).

PHOTOGRAMMETRY PROCESSING:
Photogrammetry data were processed using Agisoft Metashape Professional (versions 1.6-1.7). Processing workflow: (1) photo alignment with high accuracy settings, (2) dense point cloud generation, (3) mesh construction at 200,000 face count for standardization, (4) texture mapping, (5) measurement extraction using polygon selection tools and volume measurement functions. Models were quality-checked for reconstruction artifacts, and problematic models were flagged in metadata. Scale bar measurements were used to verify spatial accuracy of reconstructions.

PHYSIOLOGICAL DATA PROCESSING:
Protein and carbohydrate concentrations were calculated from spectrophotometer absorbance values using standard curves generated from bovine serum albumin (protein) and glucose (carbohydrates) standards. Zooxanthellae densities were calculated from hemocytometer counts accounting for dilution factors and homogenate volumes. All measurements were normalized to coral surface area (determined from photogrammetry) and expressed per square centimeter.

STATISTICAL PROCESSING:
Data processing and quality control conducted in R (version 4.0+). Processing scripts documented data cleaning steps, outlier detection, and creation of derived variables. Missing data coded consistently as NA. Data files exported as CSV format with UTF-8 encoding.

VERSIONING:
* Note: The version number described here refers to the research group's internal versioning system used during data processing and quality control. It is independent of BCO-DMO's versioning system, which starts at version 1 and increments each time an updated version of this dataset is published at BCO-DMO.

Dataset version 2.2 reflects final quality control and BCO-DMO submission preparation. All processing steps were documented in repository README files. Original raw data files were preserved alongside processed versions.  Raw data are not provided as part of this dataset but were used for internal verification, and provenance tracking  (see Github repository https://github.com/stier-lab/moorea-cafi-data).

SOFTWARE:
- Agisoft Metashape Professional (v1.6+) for 3D reconstruction
- CloudCompare (v2.11+) for mesh cleaning and metric extraction
- R v4.3+ (tidyverse, lme4) for data processing and analysis

 

This dataset shares the same experimental colonies (linked by coral_id) as "MRB Amount Experiment - CAFI Community (2021)" — CAFI taxonomy from the same 54 colonies sampled destructively in May 2021.
Some coral colonies had incomplete photogrammetry models due to complex branching geometry or poor visibility during underwater photography. These were flagged during quality control. The filtered growth dataset (44 colonies) excludes extreme outliers caused by photogrammetry reconstruction errors, while the unfiltered dataset (54 colonies) retains all measurements.
Negative minimum height values are valid and indicate the coral base extends below the reference plane.

Coverage: Mo’orea, French Polynesia (17° 29.433'S, 149° 49.579'W)

NSF Award Abstract:
Nearshore habitats such as coral reefs, seagrass beds, and oyster reefs perform a number of services including reducing storm protection, nutrient cycling, and water purification. Many of these habitats have experienced widespread loss and fragmentation due to human activities. This loss threatens the services these ecosystems provide to humans as well as the extraordinary biodiversity of fishes and invertebrates that live within them. However, there is still a lot that is unknown about these habitats which makes it difficult to understand the likely impacts of habitat loss or the benefits of habitat restoration. This research focuses on habitat loss and fragmentation in coral reef ecosystems. The focus of the research is to understand how habitat loss and fragmentation affect the biodiversity of fish and crustaceans on coral reefs in the South Pacific. Because many creatures living within the coral offer important benefits to the coral such as defense from coral predators and removal of sediment, this research also seeks to better understand how changes in the biodiversity and abundance of fish and invertebrates associated with corals, affect the capacity of corals to withstand future impacts, such as sedimentation and outbreaks of coral-eating seastars. Understanding whether habitat loss alters the capacity of corals to withstand stress in an increasingly stressful world is critical to devise effective strategies to manage and protect coral reefs and the many services they provide to society. Furthermore, this research facilitates restoration efforts, enhance the scientific workforce through mentorship of a diverse group of undergraduates, graduate students and a postdoctoral fellow, and engage the public in both French Polynesia and the United States in scientific research and knowledge.

Many marine systems are characterized by habitat-forming foundation species, which harbor a diversity of occupants, and whose dynamics are thought to drive resilience of entire ecosystems As a result, there is widespread concern over the ongoing loss and fragmentation of biogenic habitats such as seagrass beds, oyster reefs, kelp forests, and coral reefs. Yet, without a more complete understanding of marine landscape ecology, we struggle to predict how the degradation or restoration of habitat alters ecosystem dynamics, function, and resilience. Most research in marine landscape ecology has focused on spatial patterns of occupant abundance and biodiversity; however, the causes and consequences of these patterns are rarely explored. An important but understudied consequence of variation in occupant density is that it may alter how occupants interact with their biogenic habitat. Because occupants can benefit biogenic habitat or harm biogenic habitat, changes in occupant density can affect habitat growth and survival. Consequently, habitat-driven variation in occupant density should feed back to alter habitat dynamics and the spatial patterning of the habitat. In summary, we are limited in our understanding of why patterns in landscape ecology exist, how these patterns alter the population dynamics and spatial patterns of the occupants as well as their habitat, and the implications of habitat degradation or restoration. The central objective of this proposal is to examine the causes and consequences of the nonlinear relationship between occupant abundance and the amount of biogenic habitat. Specifically, the investigators: (i) examine the habitat-based mechanisms that produce spatial variation in occupant density; (ii) quantify how habitat-driven occupant density feeds back to alter habitat growth and survival; and (iii) apply this knowledge to understand how bidirectional habitat-occupant interactions affect the long-term dynamics, create novel spatial patterns, and drive variation in how systems respond to and recover from disturbances.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.