DOI: 10.5061/dryad.ns1rn8q4n
title: Protection of coral reef fish delivers ecosystem-critical biocontrol of coral-eating starfish across the Great Barrier Reef

description: Crown-of-thorns starfish (CoTS, Acanthaster ssp.) are regarded as
 a pest species across the Indo-Pacific, where they are voracious predators
 of corals and represent one of the largest causes of coral mortality on
 the Great Barrier Reef (GBR). We have incorporated reef fish into a
 metacommunity model known as the Coral Community Network (CoCoNet) model
 for the GBR to demonstrate the critical role that marine reserves and
 other fisheries regulations have played in limiting the prevalence of CoTS
 outbreaks and maintaining the resilience of the GBR ecosystem. This
 submission includes the CoCoNet model user-guide, the CoCoNet code
 (developed in NetLogo), coastline and reef definition files needed to run
 the model, and model output files (.csv) generated by the study. Each
 output file includes variables for each reef, in each year (annual
 timestep), for each run within an ensemble (runs within an ensemble vary
 stochastically to capture uncertainty).
description: # Protection of coral reef fish delivers ecosystem-critical biocontrol of
 coral-eating starfish across the Great Barrier Reef Dataset DOI:
 [10.5061/dryad.ns1rn8q4n](10.5061/dryad.ns1rn8q4n) ## Description of the
 data and file structure The data consists the CoCoNet model, supporting
 data files, documentation files, and model output files run for a range of
 interventions on the Great Barrier Reef related to biocontrol strategies
 such as conservation of predatory fish and manual control of coral-eating
 crown-of-thorns starfish.  ### Files and variables #### File:
 CoCoNet-user-guide-and-technical-summary-v3.4.docx **Description:** User
 guide for setting up and running the CoCoNet model. This includes links
 for downloading NetLogo multi-agent programmable modelling environment.
 #### File: CoCoNet_V3_biocontrol.nlogo **Description:** Code and graphical
 user interface for the CoCoNet model. #### File: coastline.csv
 **Description:** Low resolution coastline file used by the CoCoNet model.
 ##### Variables * LON: Longitude of coastline * LAT: Latitude of coastline
 #### File: reefs2024.csv **Description:** File defining key
 characteristics of the 3806 reefs that together form the Great Barrier
 Reef   ##### Variables * RM_ID: Run ensemble number * ReefID: Reef
 identification number * LAT: Latitude of reef * LON: Longitude of reef *
 GBR_NAME: Name of reef * OldReefName: Original name of reef *
 GBRMPARegion: Geographical region of reef * Shelf_position: Offshore
 position of reef (inner, mid, or offshore) * AIMS_sector: Geographical
 sector of reef * GreenZone: Conservation zoning status of reef * Priority:
 Priority level of reef for the crown-of-thorns starfish control program *
 Reference_Area_km2: Area of reef in square kilometres *
 Geom_total_km2: Alternative measure of area of reef in square kilometres *
 Geom_CH_km2: Alternative measure of area of reef in square kilometres *
 GeomCH_2D_Area_km2: Alternative measure of area of reef in square
 kilometres * GeomCH_3D_Area_km2: Alternative measure of area of reef in
 square kilometres * CullSites: Number of crown-of-thorns starfish control
 sites on reef * C_oct15: Month of coral spawning * C_con1: Estimated
 strength of primary coral larvae dispersal (from October 2015) *
 C_dir1: Estimated direction of primary coral larvae dispersal (from
 October 2015) * C_ang1: Estimated spread of primary coral larvae dispersal
 (from October 2015) * C_dis1: Estimated distance of primary coral larvae
 dispersal (from October 2015) * C_con2: Estimated strength of secondary
 coral larvae dispersal (from October 2015) * C_dir2: Estimated direction
 of secondary coral larvae dispersal (from October 2015) *
 C_ang2: Estimated spread of secondary coral larvae dispersal (from October
 2015) * C_dis2: Estimated distance of secondary coral larvae dispersal
 (from October 2015) Repeated for other spawning months. * S_dec15a: Month
 of crown-of-thorns (CoTS) spawning (a = 1st half, b = 2nd half) *
 S_con1: Estimated strength of primary CoTS larvae dispersal (from December
 2015) * S_dir1: Estimated direction of primary CoTS larvae dispersal (from
 December 2015) * S_ang1: Estimated spread of primary CoTS larvae dispersal
 (from December 2015) * S_dis1: Estimated distance of primary CoTS larvae
 dispersal (from December 2015) * S_con2: Estimated strength of secondary
 CoTS larvae dispersal (from December 2015) * S_dir2: Estimated direction
 of secondary CoTS larvae dispersal (from December 2015) *
 S_ang2: Estimated spread of secondary CoTS larvae dispersal (from December
 2015) * S_dis2: Estimated distance of secondary CoTS larvae dispersal
 (from December 2015) Repeated for other spawning periods. #### File:
 Model_runs.xlsx **Description:**  List of model runs, each corresponding
 to a biocontrol intervention scenario. ##### Variables * No.: Run number *
 Name: Run name * Description: Extended description of run. * Type of
 management: Classification of management approach used for that run. ####
 File: M4.csv **Description:** Fixed parameters and output variables from
 run M4 (10 control vessels operating in green zones) ##### Fixed
 parameters * Ensemble runs: Number of runs in ensemble * Start year: First
 year of model run (1956) * Save year: Year from which outputs were saved
 (1986) * Projection year: First year that future (projected) environmental
 conditions were applied (2025) * End year: Last year of model run (2075) *
 Search year: Not used * CoTS control start year: First year that CoTS
 control was applied * CoTS control ecological threshold (CoTS per ha):
 Minimum CoTS density to deploy control on a site * CoTS control CoTS
 threshold (CoTS per ha): Maximum CoTS density to deploy control on a reef
 * CoTS control coral threshold (CoTS per ha): Minimum coral cover to
 deploy control on a reef * CoTS vessels across GBR: Number of control
 vessels deployed across the GBR * CoTS vessels in Far-northern
 Region: Number of control vessels deployed only in the far north region *
 CoTS vessels in Northern Region: Number of control vessels deployed only
 in the north region * CoTS vessels in Central Region: Number of control
 vessels deployed only in the central region * CoTS vessels in Southern
 Region: Number of control vessels deployed only in the south region *
 Catchment restoration start year: First year that catchment restoration
 began * Catchment restoration timescale (years): Time for catchment
 restoration to be complete * Future zoning start year: First year that
 additional reefs were protected from fishing * Number of reefs included in
 future rezoning: Number of additional reefs protected from fishing *
 Reduction in fisheries catch start year: First year that fisheries catches
 were reduced * Fractional reduction in fisheries catches: Fractional
 reduction in catches * Upper fish size limit start year: First year that
 upper size limits on catches were applied * Lower fish size limit start
 year: First year that lower size limits on catches were applied * Exclude
 fishing from active outbreak reefs start year: First year that fishing was
 excluded from reefs with CoTS outbreaks * Emperor release start
 year: First year of emperor fish release program * Number of release
 reefs: Number of reefs where emperor fish were released each year *
 Maximum adult emperors (per ha) for release: Maximum adult emperor density
 on reef for a release * Number of juvenile emperors released per
 reef: Number of juvenile emperor fish released each year * Regional
 shading start year: First year of regional shading of reefs * Absolute DHW
 reduction due to regional shading (DHW): Reduction in Degree Heating Weeks
 by shading * Minimum longitude of interventions: Geographical extent of
 interventions * Maximum longitude of interventions: Geographical extent of
 interventions * Minimum latitude of interventions: Geographical extent of
 interventions * Maximum latitude of interventions: Geographical extent of
 interventions * Rubble consolidation start year: First year of
 consolidating rubble * Annual number of consolidated reefs. Number of
 reefs where rubble is consolidated * Minimum rubble cover threshold for
 consolidation: Minimum rubble cover to deploy consolidation * Total annual
 consolidated area (ha): Total area of rubble that can be consolidated per
 year * Thermally tolerant coral seeding start year: First year that
 thermally tolerant coral were outplanted * Annual number of reefs seeded
 with coral: Number of reefs outplanted per year * Maximum coral cover
 threshold for coral seeding: Maximum existing coral cover to outplant a
 reef * Total annual area of seeded corals (ha): Total area of coral
 outplanting per year * Fraction of staghorn acropora corals able to
 hybridise with thermally tolerant corals: level of hybridisation *
 Dominance of thermally tolerant corals in setting thermal tolerance of
 hybrids: thermal tolerance of hybrid corals * Coral slicks start year:
 First year of releasing coral slicks * Annual number of reefs with coral
 slicks released: Number of reefs where coral slicks were released *
 Maximum coral cover threshold for coral slicks: Maximum existing coral
 cover to release a coral slick * Total annual area of slick corals
 (ha): Total area coral from settling of coral slicks per year * Reef
 shading start year: First year of shading individual reefs * Annual number
 of reefs locally shaded: Number of individual reefs shaded each year *
 Fractional DHW reduction due to local shading: Fractional reduction in
 Degree Heating Weeks by shading individual reefs * Ocean acidification
 treatment start year: First year of reducing ocean acidification on
 individual reefs * Annual number of reefs treated for ocean acidification:
 Number of reefs where ocean acidification was reduced each year *
 Fractional protection from ocean acidification: Level of ocean
 acidification protection applied ##### Output variables * Ensemble: Run
 ensemble number - Year: Year * Reef_ID: Reef ID number * Region_name:
 S=south, C=central, N=north, FN= far-north * Shelf_position:
 I=inner-shelf, M=mid-shelf, O=outer-shelf - Rezone_year: Year that zoning
 changes from blue (fishing allowed) to green (fishing excluded) -
 Priority: Priority for control of CoTS (N=non-priority, P=priority,
 T=target) - Longitude: Longitude of reef - Latitude: Latitude of reef -
 km_offshore: Distance offshore in kilometres - Reef_sites: Number of
 standard CoTS control sites (~ 10 ha of coral habitat) on reef - C_sa:
 Coral cover – staghorn Acropora species - C_ta: Coral cover – tabular
 Acropora species - C_mo: Coral cover – Montipora species - C_po: Coral
 cover – Poritidae species - C_fa: Coral cover – Favids species - C_tt:
 Coral cover – thermally tolerant species (intervention) - C_out_degree:
 Weighted out-degree (recruits dispersed to other reefs) - Rubble: Rubble
 cover - DHW: Degree heating weeks - bleach_sa: Bleaching mortality –
 staghorn Acropora species - bleach_ta: Bleaching mortality – tabular
 Acropora species - bleach_mo: Bleaching mortality – Montipora species -
 bleach_po: Bleaching mortality – Poritidae species - bleach_fa: Bleaching
 mortality – Favids species - bleach_tt: Bleaching mortality – thermally
 tolerant species - Maximum_cyclone_category: Highest cyclone category in
 year - cyclone_sa: Cyclone mortality – staghorn Acropora species -
 cyclone_ta: Cyclone mortality – tabular Acropora species - cyclone_mo:
 Cyclone mortality – Montipora species - cyclone_po: Cyclone mortality –
 Poritidae species - cyclone_fa: Cyclone mortality – Favids species -
 cyclone_tt: Cyclone mortality – thermally tolerant species - predate_sa:
 CoTS predation mortality – staghorn Acropora species - predate_ta: CoTS
 predation mortality – tabular Acropora species - predate_mo: CoTS
 predation mortality – Montipora species - predate_po: CoTS predation
 mortality – Poritidae species - predate_fa: CoTS predation mortality –
 Favids species - predate_tt: CoTS predation mortality – thermally tolerant
 species - S_1: Starfish per hectare - juveniles - S_2: Starfish per
 hectare – age 2 years - S_3: Starfish per hectare – age 3 years - S_4:
 Starfish per hectare – age 4 years - S_5: Starfish per hectare – age 5
 years - S_6: Starfish per hectare – age 6+ years - Control_dives: Control
 dives on reef - Benthic_invert: Benthic invertebrates (preying on juvenile
 CoTS) per hectare - Triggerfish: Triggerfish per hectare - E_1: Emperor
 fish per hectare – juveniles - E_2: Emperor fish per hectare – age 2 years
 - E_3: Emperor fish per hectare – age 3 years - E_4: Emperor fish per
 hectare – age 4 years - E_5: Emperor fish per hectare – age 5 years -
 E_catch_kg: Emperor fish catch – age 3-5 years - G_1: Grouper fish per
 hectare – juveniles - G_2: Grouper fish per hectare – age 2 years - G_3:
 Grouper fish per hectare – age 3 years - G_4: Grouper fish per hectare –
 age 4 years - G_5: Grouper fish per hectare – age 5 years - G_catch_kg:
 Grouper fish catch – age 3-5 years #### File: M3.csv
 **Description:** Fixed parameters and output variables from run M3 (10
 control vessels operating in blue zones) **Variables:** As above ####
 File: H1.csv **Description:** Fixed parameters and output variables from
 run H1 (Historical management restrictions to 2025 and then discontinued
 from 2026) **Variables:** As above #### File: C2.csv
 **Description:** Fixed parameters and output variables from run C2
 (Extreme combination of additional zoning and manual CoTS control)
 **Variables:** As above #### File: C1.csv **Description:** Fixed
 parameters and output variables from run C1 (Plausible combination of
 additional zoning and manual CoTS control) **Variables:** As above ####
 File: F4.csv **Description:** Fixed parameters and output variables from
 run F4 (Catch of small size class fish (&lt;= 3 yo) set to zero from 2026)
 **Variables:** As above #### File: F3.csv **Description:** Fixed
 parameters and output variables from run F3 (Catch of large size class
 fish (&gt;= 5 yo) set to zero from 2026) **Variables:** As above ####
 File: F2.csv **Description:** Fixed parameters and output variables from
 run F2 (Fishing closures on reefs with CoTS outbreaks from 2026)
 **Variables:** As above #### File: A1.csv **Description:** Fixed
 parameters and output variables from run A1 (Annual release of 2000
 juvenile emperors on each of the 500 GBRMP priority reefs from 2026)
 **Variables:** As above #### File: F1.csv **Description:** Fixed
 parameters and output variables from run F1 (Total catch of emperors and
 groupers reduced to 50% of historical levels from 2026) **Variables:** As
 above #### File: H2.csv **Description:** Fixed parameters and output
 variables from run H2 (No management restrictions applied within the
 historical or projection periods (1956-2050)) **Variables:** As above ####
 File: Z2.csv **Description:** Fixed parameters and output variables from
 run Z2 (No-take zones increased to 60% of all reefs from 2026)
 **Variables:** As above #### File: Z1.csv **Description:** Fixed
 parameters and output variables from run Z1 (No-take zones increased to
 40% of all reefs from 2026) **Variables:** As above #### File: M2.csv
 **Description:** Fixed parameters and output variables from run M2 (10
 CoTS control vessels operating on reefs following GBRMP prioritisation
 from 2026) **Variables:** As above #### File: Z3.csv
 **Description:** Fixed parameters and output variables from run Z3
 (No-take zones increased to 100% of all reefs from 2026) **Variables:** As
 above #### File: M1.csv **Description:** Fixed parameters and output
 variables from run M1 (5 CoTS control vessels operating on reefs following
 GBRMP prioritisation from 2026) **Variables:** As above #### File: H0.csv
 **Description:** Fixed parameters and output variables from run H0
 (Historical management restrictions (excluding manual CoTS control):
 approximately 4% of reefs in 1987; increasing to 30% in 2004 with
 reductions in fishing effort; assuming no further changes to 2050)
 **Variables:** As above ## Code/software The Coral Community Network
 (CoCoNet) model has been developed within the NetLogo environment (v.
 6.4.0). NetLogo is an agent based programmable modelling environment
 ([https://ccl.northwestern.edu/netlogo/](https://ccl.northwestern.edu/netlogo/)) used widely across many science disciplines. All models developed within NetLogo are packaged within a single file with tabs for a user interface, model documentation, and model code. Install and run CoCoNet with the following steps: (i) Install Netlogo free of charge at [https://ccl.northwestern.edu/netlogo/6.4.0/](https://ccl.northwestern.edu/netlogo/6.4.0/) (ii) Upload the CoCoNet model, the coastline file, and the reef file to one folder. (iii) Open CoCoNet and select the interface tab. (iv) Specify run parameters within the interface including the output filename; climate scenario; size of ensemble; run period; and all the intervention parameters. (v) Click on the “setup” button. (vi) Click on the “go” button to run the ensemble of runs.