DOI: 10.5061/dryad.fxpnvx12r
title: Code and data for: Habitat and local factors influence fish biomass recovery in marine protected areas

description: Well-designed and managed marine protected areas (MPAs) can have positive
 outcomes for reef biodiversity, but their effectiveness for conservation
 outcomes is also influenced by local environmental and anthropogenic
 factors. To assess the importance of local factors on MPA effectiveness,
 we compared field-collected data on total reef fish biomass from 922 sites
 inside and outside a network of 49 MPAs across temperate Australia using
 modelled predictions of biomass based on local biogenic habitat, physical
 environment, and anthropogenic factors. We found fish biomass was 34%
 greater in fully protected MPAs in temperate Australia than predicted if
 they were openly fished, whereas biomass in partially protected MPAs was
 equivalent to fished sites. Local biogenic habitat and physical
 environmental features significantly shaped shallow reef biomass across
 large spatial scales but their effects did not differ between fished and
 fully protected MPA sites, providing reassurance that regional habitat
 change inside and outside MPAs will not greatly affect relative effect
 sizes. These findings affirm the role of fishing in shaping fish biomass
 on shallow reefs across broad spatial scales and underscore the importance
 of strict protection from fishing. Strategic MPA design and management
 should consider local conditions to refine expectations, optimize fish
 biomass recovery, and enhance conservation outcomes.
description: Data include total reef fish biomass in kilograms for
 globally-distributed shallow reef sites surveyed between 2008 and 2023.
 Environmental, anthropogenic, and ecological variables characterizing the
 conditions for each site-year combination are also provided. 
description: Code and data for: Habitat and local factors influence fish biomass
 recovery in marine protected areas --- Total reef fish biomass and
 associated environmental, anthropogenic, and ecological variables for
 reproducing the analysis in the manuscript "Habitat and local factors
 influence fish biomass recovery in marine protected areas." A
 comprehensive description of the data included in this analysis can be
 found in the corresponding manuscript. Code for processing the data and
 reproducing the analysis in the corresponding manuscript are described
 under Code/Software below. --- ## Description of the data and file
 structure GENERAL INFORMATION 1. Title of Dataset: Environmental,
 anthropogenic, and ecological data for globally-distributed shallow reef
 sites. 2. Author Information: withheld in this addition to maintain
 anonymity of data 3. Date of data collection: 2008-2024 4. Geographic
 location of data collection: Global DATA & FILE OVERVIEW 1.
 Description of dataset 2. File List: File 1 Name:
 global_RLS_biomass_environmental_data_new.csv File 1 Description: Total
 reef fish biomass & Bio-Oracle broadscale environmental data for 700+
 openly fished Australian Reef Life Survey shallow reef sites. File 2 Name:
 Temperate_AUS_RLS_local_factors_data_new.csv File 2 Description: Total
 reef fish biomass, broadscale environmental information, and local
 anthropogenic, physical environment, and biogenic habitat data for 922
 Reef Life Survey shallow reef sites inside and outside MPAs. 
 METHODOLOGICAL INFORMATION In summary: ``` Fish Biomass and Biogenic
 Habitat: collected via underwater visual census using a 50m transect.
 Detailed methods are available on the Reef Life Survey methods page:
 https://reeflifesurvey.com/methods/ and described in *Reef Life Survey:
 Establishing the Ecological Basis for Conservation of Shallow Marine Life*
 (Edgar et al., 2020, Biological Conservation). Environmental Variables:
 broad-scale, remotely sensed environmental covariates were obtained from
 Bio-Oracle (https://www.bio-oracle.org/index.php), representing surface
 mean values at each site (2000–2020), extracted from rasters with a native
 resolution of 5-arcmins. Biogenic Habitat data: biogenic habitat was
 assessed using photo quadrats and in-situ quadrats. Data was standardized
 across methods to aggregate into five categories: turfing algae, sessile
 invertebrates, sand, canopy-forming macroalgae, and understory-forming
 algae. Physical Environmental Conditions: Wave exposure, currents, slope,
 and relief were scored on a scale of 1–4 by divers familiar with each
 site. Human Gravity: calculated using the gravity of human impact model
 described in *Gravity of Human Impacts Mediates Coral Reef Conservation
 Gains* (Cinner et al., 2018, PNAS). ``` DATA-SPECIFIC INFORMATION FOR:
 global_RLS_biomass_environmental_data_new.csv 1. Number of variables: 14
 2. Number of cases/rows: 724 3. Variable List: total_biomass_log: total
 reef fish biomass recorded using Underwater Visual Census methods at a
 given Reef Life Survey site on the last available survey (log10
 transformed).\ latitude: latitude in decimal degrees of reef site
 longitude: longitude in decimal degrees of reef site sst_mean: Mean sea
 surface temperature (SST) at the site over the two years preceding the
 date of survey\ KDPAR_mean_mean: diffuse attenuation at the surface in
 meters. PAR_mean_mean: photosynthetically available radiation (Em2/day).
 chl_mean: chlorophyll-a (mmol / m3) sws_mean: sea water velocity (m/2)
 dfe_mean: iron (mmol / m3) no3_mean: nitrate (mmol / m3 po4_mean:
 phosphate (mmol / m3) phyc_mean: phytoplankton (mmol / m3) so_mean:
 salinity si_mean: silicate (mmol / m3) DATA-SPECIFIC INFORMATION FOR:
 Temperate_AUS_RLS_local_factors_data_new.csv 1. Number of variables: 35 2.
 Number of cases/rows: 922 3. Variable List: site_code: unique Reef Life
 Survey shallow reef site identifier survey_id: unique survey identifier
 survey_date: date of survey (dd/m/yyyy) survey_governance: level of
 protection against fishing at a given site at the time of survey: fished
 (openly fished, no restrictions on fishing); restricted (some restrictions
 on fishing present); no-take (no extractive/ fishing activities
 permitted). total_biomass_kg: total reef fish biomass in kilograms
 recorded using Underwater Visual Census methods at a given Reef Life
 Survey site on the last available survey. depth: mean depth in meters of
 survey transect canopy: percent coverage of canopy forming-macroalgae
 along the survey transect understorey: percent coverage of
 understorey-forming algae along the survey transect sand: percent coverage
 of sand along the survey transect sessile_invertebrates: percent cover of
 sessile invertebrates along the transect turf: percent cover of turfing
 alga along the transect wave_exposure: degree of oceanic swell a site
 receives on average: 1, sheltered; 2, maximum wave height 1-3 m; 3, ocean
 swell maximum &gt;3 m; 4, open swell from prevailing direction. relief:
 mean vertical relief along the transect line: 1, &lt;0.5 m; 2, 0.5 – 1 m;
 3, 1 – 2 m; 4, &gt;2 m. slope: mean gradient along the transect line: 1,
 &lt;1:10 gradient; 2, 1:10 - 1:4; 3, 1:4 - 1:2; 4, &gt;1:2. currents: mean
 relative strength of the currents at a given site: 1, none; 2, weak; 3,
 moderate; 4, strong. latitude: latitude in decimal degrees of reef site
 longitude: longitude in decimal degrees of reef site sst_mean: Mean sea
 surface temperature (SST) at the site over the two years preceding the
 date of survey KDPAR_mean_mean: diffuse attenuation at the surface in
 meters. PAR_mean_mean: photosynthetically available radiation (Em2/day).
 chl_mean: chlorophyll-a (mmol / m3) sws_mean: sea water velocity (m/2)
 dfe_mean: iron (mmol / m3) no3_mean: nitrate (mmol / m3 po4_mean:
 phosphate (mmol / m3) phyc_mean: phytoplankton (mmol / m3) so_mean:
 salinity si_mean: silicate (mmol / m3)\ distance: distance from the
 nearest shoreline to each site in meters distance_from_shore_m: distance
 from the nearest shoreline to each site in meters - log10 transformed 
 total gravity: a measure of how large and far away a human population is
 to a given reef site, as detailed in Cinner et al., 2018. grid_cell: 100km
 by 100km grid cell each site falls inside year: year of survey (yyyy) ##
 CODE/ Software Two R script files are provided to reproduce the analysis
 in the corresponding manuscript. All provided R files are described below.
 "1. Random Forest model.R": R source code predicting total reef
 fish biomass across shallow temperate Australian reef sites of interest
 using a global random forest (RF) model of total reef fish biomass and
 broadscale environmental conditions. "2. Multimodel
 inference.R": R source code estimating the relative importance of
 local anthropogenic, biogenic habitat, and physical environmental factors
 for differences in reef fish biomass using Generalized Linear Mixed Models
 (GLMMs) in a multi-model inferences framework.