Dataset and Code: Patch design principles for oyster reef restoration: Lessons from fish habitat use in natural remnant systems

README

Patch design principles for oyster reef restoration: Lessons from fish habitat use in natural remnant systems

Authors: Christopher Pine, Katherine Erickson, Ana Bugnot, Paul Gribben, & William Figueira

Journal: Ecological Applications

Overview

This repository contains the raw data and code required to replicate the statistical analyses and generate the figures for the above manuscript. The study examines how oyster reef characteristics (size, shape, complexity, and spatial arrangement) influence fish assemblage metrics (abundance, species richness, and diversity) across natural remnant oyster reef systems in southeastern Australia.

Repository Contents

Code and data

File
Description

Oyster_Reef_Data_Analysis.qmd
Quarto document containing all code to rerun statistical analyses and generate figures

species.data.csv
Species-level abundance and occurrence data for each fish species observed per survey deployment, with associated species trait metadata

MeanCount.NO.hyperabundants.dat.csv
Survey-level fish assemblage metrics (total abundance, species richness, Shannon's H) paired with reef morphological and spatial characteristics; hyperabundant species excluded

MeanCount.with.hyperabundants.dat.xlsx
Same structure as above but with hyperabundant species included; used for the species richness analysis

README.md
This metadata file

Pre-computed model objects

The multivariate analyses use manyglm models fitted via the mvabund R package, which are computationally intensive to run. Pre-computed model objects are provided as .rds files (R serialised data) so users can load results directly without re-running the full analysis.

File
Description

anova.mvPH.rds
manyglm model object (mvabund) for Port Hacking

anova.mvTP.rds
manyglm model object (mvabund) for Towra Point

anova.mvCR.rds
manyglm model object (mvabund) for Crookhaven River

Figures

File
Description

Figure1.png
Oyster reefs in NSW: satellite imagery of patch configuration, low-tide arrangement, and close-up views of centre and edge reef habitat

Figure2.png
Depiction of Remote Underwater Video (RUV) apparatus placement across the three reef zones (Centre, Edge, Off), with schematic diagram

Figure3.pdf
Comparison of mean assemblage metrics (abundance, species richness, Shannon's diversity) between seasons and reef zones for each estuary

Figure4_HeatmapPlot_A5_Size.pdf
Heatmap summarising the net trend of each patch characteristic on abundance, species richness, and diversity

Figure5.pdf
Net overall relationships between patch characteristics and fish abundance across estuaries, based on estimated marginal means

Figure6.pdf
Net overall relationships between patch characteristics and fish species richness across estuaries

Figure7.pdf
Net overall relationships between patch characteristics and Shannon's H diversity across estuaries

Figure8_NMDS_Plot_ggplot.pdf
nMDS ordination plots of fish assemblage composition (Bray-Curtis dissimilarity) by season and zone for each site

Figure9_ConceptualDiagram_High_res.png
Conceptual framework illustrating oyster reef design principles comparing a single large patch versus a system of smaller connected patches

Study Design

Surveys were conducted on natural remnant oyster reefs across three sites in southeastern Australia:

OP-CR – Crookhaven River

SY-PH – Port Hacking (Sydney)

SY-TP – Towra Point (Sydney)

At each reef, underwater video surveys were deployed in three zones:

Centre – On-reef, central area of the reef

Edge – On-reef, along the reef perimeter

Off – Off-reef, adjacent bare sediment or seagrass habitat

Surveys were conducted across seasons (Summer and Winter) and years (2019–2021). Fish assemblages were quantified from video footage using the MeanCount method.

Data File Descriptions

1. species.data.csv

This file contains one row per species per survey deployment. Each row records the abundance and occurrence of a single fish species at a specific reef, zone, season, and year, alongside taxonomic information and ecological trait classifications.

Survey identifiers and design

Column
Description
Example values

SpeciesCode
Abbreviated four-letter code for each species
abbe (Abudefduf bengalensis), acau (Acanthopagrus australis)

SurveyID
Unique identifier for each survey event, encoding site, reef number, zone (C/E/O), season (S/W), and year
CR-OP01_C_S2020

ReefID
Unique identifier for each oyster reef
CR01, TP15

Site
Study site code
OP-CR (Crookhaven River), SY-PH (Port Hacking), SY-TP (Towra Point)

ReefNo
Numeric reef identifier within a site
1, 15, 27

ReefZone
Zone of the reef where the survey was conducted
Centre, Edge, Off

Season
Season in which the survey was conducted
Summer, Winter

Year
Year of the survey
2019, 2020, 2021

TapeReader
Name or initials of the person who reviewed the video footage
Chris.P, Lydia.K, Katie.E

VideoLength
Duration of the video survey (minutes)
60, 61

AvgVis
Average underwater visibility during the survey, scored as the mean Secchi-equivalent visibility across sample periods (metres)
2.86, 4.0

Pseagrass
Percentage cover of seagrass within the survey area (%)
0, 4.3

Taxonomic and trait information

Column
Description
Example values

Family
Taxonomic family
Pomacentridae, Sparidae

Genus
Taxonomic genus
Abudefduf, Acanthopagrus

Species
Specific epithet
bengalensis, australis

ScientificName
Full binomial scientific name
Abudefduf bengalensis, Acanthopagrus australis

CrRelevent
Whether the species is of commercial or recreational relevance
Yes, No

Range
Biogeographic range classification
Tropical, Temperate

HabitatAssociation
Degree of habitat association with reef structures: HHA = Highly Habitat Associated (species closely tied to reef structure); LHA = Low Habitat Association (more transient species)
HHA, LHA

Generallised.Feeding.Level
Broad trophic category
Omnivore, Carnivore, Detritivore, Herbivorous

Functional.Group
Specific functional feeding group
Zooplanktivore, Macro-Carnivore, Micro-Carnivore, Piscivore, Detritivore, Grazer, Herbivorous, Omnivore, Omnivorous Grazer

Species abundance and occurrence metrics

All metrics below are derived from the MeanCount video analysis method. In this method, the video is divided into equal sample periods, and within each sample period the maximum number (MaxN) of each species visible in any single frame is recorded. The MeanCount is the average of these MaxN values across all sample periods.

Column
Description
Units

AverageMeanCount
Mean count of the species per sample period across the survey (i.e., the MeanCount value)
count per sample period

FramesPresent
Number of sample periods in which the species was detected
count

AverageOccupancy
Average number of individuals observed per sample period when the species was present (i.e., conditional abundance: mean count given detection)
individuals per sample period

PercentageSamplePeriodsPresent
Percentage of sample periods in which the species was observed; a measure of temporal occurrence
%

sum_MeanCount
Sum of the MeanCount values across all sample periods; effectively a total abundance estimate for that species in that survey
count

Community-level metrics (repeated per survey)

These values are repeated for all species rows sharing the same SurveyID.

Column
Description
Units

Species_Richness_Zone
Total number of fish species recorded in that survey zone
count

ShannonsH
Shannon-Wiener diversity index (H') for the full fish assemblage in that survey
dimensionless (nats)

Derived grouping variable

Column
Description
Example values

SeasonReefZone
Concatenation of Season and ReefZone, used as an interaction term in statistical analyses
Summer.Centre, Winter.Off

2. MeanCount.NO.hyperabundants.dat.csv

This file contains one row per survey deployment. Each row summarises the fish assemblage at a specific reef, zone, season, and year, and includes the morphological and spatial characteristics of the associated reef. Hyperabundant species have been excluded from the assemblage metrics in this dataset.

Survey identifiers and design

Column
Description
Example values

ReefID
Unique identifier for each oyster reef
CR01, TP15

SurveyID
Unique identifier for each survey event
CR-OP01_C_S2020

Site
Study site code
OP-CR, SY-PH, SY-TP

ReefNo
Numeric reef identifier within a site
1, 15

ReefZone
Zone of the reef where the survey was conducted
Centre, Edge, Off

Season
Season in which the survey was conducted
Summer, Winter

Year
Year of the survey
2019, 2020, 2021

TapeReader
Name or initials of the person who reviewed the video footage
Chris.P, Lydia.K

VideoLength
Duration of the video survey (minutes)
60, 61

AvgVis
Average underwater visibility during the survey, scored as the mean Secchi-equivalent visibility across sample periods (metres)
3.0, 4.0

Pseagrass
Percentage cover of seagrass within the survey area (%)
0, 4.3

Fish assemblage metrics

Column
Description
Units

Species_Richness_Zone
Number of fish species recorded in the survey zone
count

ShannonsH
Shannon-Wiener diversity index (H') for the fish assemblage
dimensionless (nats)

TotalAbundance
Total count of individual fish observed (sum of MeanCount values across all species, excluding hyperabundant species)
count

Reef spatial and morphological characteristics

Landscape metrics (shape, iso.index, circle, frac, para, perimeter, perimeterarea.ratio) were derived using FRAGSTATS or equivalent landscape ecology software from georeferenced reef outlines. These values are constant across all survey deployments from the same reef.

Column
Description
Units

TwoDArea
Two-dimensional (planar) area of the reef
m²

shape
Shape index of the reef, quantifying deviation from a simple geometric form; higher values indicate greater shape complexity
dimensionless

iso.index
Isolation index, a measure of how isolated the reef is from surrounding reefs
dimensionless

circle
Related circumscribing circle index, indicating how close the reef shape is to a perfect circle; a value of 1 indicates a perfect circle
dimensionless (0–1)

frac
Fractal dimension index, capturing the complexity of the reef perimeter; values range from 1 (simple shape) to 2 (highly complex perimeter)
dimensionless (1–2)

para
Perimeter-to-area ratio, an alternative measure of shape complexity
m/m²

perimeter
Total perimeter length of the reef
m

perimeterarea.ratio
Perimeter divided by area
m⁻¹

avg_dist.to.all.nearest.reefs
Mean distance from the focal reef to all other reefs in the study area
m

nearest.neighbour
Distance to the nearest neighbouring reef (Euclidean, edge-to-edge)
m

Rugosity
Surface rugosity, calculated as the ratio of three-dimensional surface area to two-dimensional planar area; values >1 indicate greater structural complexity
dimensionless

ThreeDArea
Three-dimensional surface area of the reef
m²

3. MeanCount.with.hyperabundants.dat.xlsx

This file has the same structure and columns as MeanCount.NO.hyperabundants.dat.csv (see above), but retains hyperabundant species in the assemblage metrics. This version of the dataset is used for the species richness analysis, where excluding hyperabundant species is not appropriate. See Section 2 above for full column descriptions.

Figure Descriptions

Figure 1 – Oyster reefs in various locations throughout NSW. (A) Satellite image of Port Hacking oyster reef showing patch configuration (NearMaps). (B) Port Hacking oyster reef at low tide showing the arrangement and height of patches. (C) Centre of an oyster reef during high tide at Port Hacking showing the three-dimensional complexity of the interior patch habitat. (D) Edge of an oyster reef patch illustrating the complexity and diversity of refuge spaces along the edge and the interface between the patch and the sand matrix, highlighting the vertical relief of the reef structure. Photo credits (B, C, D): Christopher Pine.

Figure 2 – Depiction of how Remote Underwater Video (RUV) apparatuses were placed on the three zones of the oyster reef. (A) Centre of the reef. (B) Edge of the reef. (C) Off the reef (from the camera's perspective). (D) Schematic diagram illustrating the placement of the apparatuses on an oyster patch. Photo credits (A, B, C) and illustration credit (D): Christopher Pine.

Figure 3 – Comparison of the mean of each key assemblage metric between seasons (yellow = summer, blue = winter) and reef zones (Centre, Edge, Off) for each study estuary. Panels show: (A–C) Abundance (MeanCount, sampling every minute for 60 minutes); (D–F) Species Richness (per 60 minutes of video); (G–I) Shannon's Diversity.

Figure 4 – Net trend of each patch characteristic on abundance (A), species richness (B), and diversity (C) of fish assemblages. Blue up arrows represent significant net positive trends; red down arrows represent net negative trends. Blank cells indicate non-significant effects or variables removed during model selection. "N.I" indicates variables excluded due to collinearity. Asterisks (*) denote marginally significant effects (0.05 < p < 0.08). Net trends were determined by averaging significant trends across reef zones, seasons, and—where present—season × reef zone pairwise combinations. Detailed tables are available in Appendix 4.

Figure 5 – Net overall relationships between patch characteristics and fish abundance across estuaries (Port Hacking, Towra Point, Crookhaven River), based on estimated marginal means from the generalised linear model. Panels show relationships with: (A) patch area, (B) shape index, (C) circle index, (D) fractal dimension, (E) isolation index, (F) nearest neighbour distance, (G) perimeter-area ratio, (H) rugosity. Colours correspond to site; shaded areas indicate 95% confidence intervals; points represent raw data.

Figure 6 – Net overall relationships between patch characteristics and fish species richness across estuaries, based on estimated marginal means. Panels show relationships with: (A) circle index, (B) fractal dimension. Colours correspond to site; shaded areas indicate 95% confidence intervals; points represent raw data.

Figure 7 – Net overall relationships between patch characteristics and Shannon's H diversity across estuaries, based on estimated marginal means. Panels show relationships with: (A) circle index, (B) fractal dimension, (C) isolation index. Symbols denote season × reef zone combinations; colours correspond to site; shaded areas indicate 95% confidence intervals; points represent raw data.

Figure 8 – nMDS ordination plots of fish abundance data (Bray-Curtis dissimilarity) showing differences in fish assemblage composition by season and zone at each site: (A/B) Port Hacking (stress = 0.2), (C/D) Towra Point (stress = 0.18), (E/F) Crookhaven River (stress = 0.17).

Figure 9 – Conceptual framework illustrating oyster reef design principles in two hypothetical systems. System 1 represents one large continuous reef patch totalling 100 m². System 2 represents a system of smaller connected patches with the same total area budget (100 m²) incorporating the design principles developed in this study, illustrating how ecological understanding can maximise ecological outcomes per unit area restored. Illustration credit: Christopher Pine.

Software and Dependencies

The analysis code (Oyster_Reef_Data_Analysis.qmd) was written in R and rendered using Quarto. Please refer to the Quarto document for specific package dependencies and version information.

Contact

For questions regarding this dataset, please contact Christopher Pine (corresponding author).