Supplementary Information For

Supplementary Information for

Remoteness and fishing restrictions support fish biomass and trophic structure on

Indonesia’s coral reefs

Stuart J. Campbell*, Emily S. Darling, Shinta Pardede, Gabby Ahmadia, Sangeeta Mangubhai, Amkieltiela, Estradivari, and Eva Maire

*Corresponding author: Dr Stuart Campbell Email: [email protected]

This file includes: Supplementary Methods Figures S1 to S8 Tables S1 to S9 Supplementary References

Supplementary Methods

Coastal and oceanic productivity We attempted to characterize primary productivity at our sites with two metrics: coastal productivity and oceanic productivity. To characterize coastal productivity, we used estimates of net primary productivity developed by NOAA Coast

Watch (https://coastwatch.pfeg.noaa.gov) on a 2.5 arcmin grid (~4.5 km at the equator) derived from from the Moderate Resolution Imaging Spectroradiometer (MODIS; http://modis.gsfc.nasa.gov/). Estimates were processed from 8-day composite layers from

2003 to 2013 based on satellite measurements of photosynthetically available radiation, sea surface temperatures, and chlorophyll a concentrations; for each site we calculate a general mean of coastal productivity using the MSEC online platform (Yeager et al., 2017). We also assessed oceanic productivity, measured from the above MODIS estimates long-term satellite surface chlorophyll-a concentrations (mg/m3), but measured offshore of a 30 m bathymetric contour; this dataset of oceanic productivity was derived by Gove et al. (2013) and shown to be an important driver of Pacific reef fish assemblages (Gove et al., 2013; Williams et al.,

2015).

Population and market gravity To consider the influence of remote and populated areas on reef fish assemblages, we used established metrics of human population ‘gravity’, which defines a function of human population size and accessibility that can evaluate potential interactions between human population pressure and coral reefs (Cinner et al., 2018). We adopted two gravity metrics: (1) the gravity of the nearest human settlement, and (2) market gravity associated with provincial capitals, major population centres and ports within a 500 km radius of a site. Previous studies have identified market gravity as a main driver of reef fish biomass (Cinner et al., 2016), and total gravity (integrated across markets and settlements) has been associated with the reduced effectiveness of marine reserves at

S2 maintaining reef fish biomass and predators (Cinner et al., 2018). For both indicators, gravity was calculated as population size (of the nearest settlement or the cumulative population of all markets with a 500 km buffer) divided by travel time (hours) squared between the reef

(site) and each settlement, or the cumulative travel time between each market and the reef site

(Cinner et al., 2018). When no market was found within 500 km, the nearest market was defined using the shortest linear distance. These two metrics are weakly correlated (Pearson correlation coefficient, r = 0.10) and represent independent non-correlated indicators of reef accessibility by humans. From the same global data layers (Maire et al., 2016; Cinner et al.,

2018), we also estimated the travel time (hours) between each reef and the nearest human settlement and the nearest market to evaluate how we classified remote sites in our database

(Fig. S3).

Data analysis We first checked for collinearity among our covariates using pairwise correlations (Fig. S7). The age and size of MPAs were highly correlated and we removed MPA size from further analysis, which ensured that all remaining pairwise Pearson correlation coefficients were < 0.3 and variance inflation factor (VIF) estimates were less than 2 to indicate that multicollinearity was not a serious concern. We used Akaike’s information criteria to compare several model structures and their random effects before finalizing the mixed-effects models (Zuur et al., 2009). For MPA characteristics, surveys that occurred before implementation or outside of an MPA were given a ‘zero’ for MPA age and size.

All biomass response variables were log+1 transformed (total biomass and the biomass of each trophic group). Covariates were standardized by centering the mean on 0 and dividing by 2 standard deviations using the function ‘rescale’ in the package arm (Gelman & Su, 2018); we log-transformed one covariate (gravity of the nearest settlement) to account for right-skewed

S3 outliers. Due to low replication, we removed the reef flat (n = 34 transects) and lagoon (n =

108) habitat categories, which accounted for a minimal proportion of our data (140 out of 5,208 transects, or <3%). The remaining habitat classes were reef slope (n = 2,978 transects) and reef crest (n = 2090).

Models were evaluated using transect-level observations (where each transect was associated with a specific depth) fitted with normally distributed errors. The hierarchical structure of our data was modelled using random effects of survey (a site-year replicate) nested within site (to control for repeated surveys at the same site) nested within region, and a random effect of observer to control for any potential bias introduced by different reef fish data collectors. Model diagnostics were performed by visually assessing the normality of the residuals; p-values were calculated using the Wald-statistics approximation. All models were fit in the package ‘lme4’

(Bates et al., 2015), and p-values were estimated using the Wald-statistics approximation.

Supplementary Figures and Tables

Piscivore 3 40 62

Invertivore 1 35 135 59 5

c Planktivore 7 56 69 5 1

Omnivore 8 31 19

Herbivore−Detritivore 89 29 2

[2,2.5] (2.5,3] (3,3.5] (3.5,4] (4,4.5] Trophic level

Figure S1. Relationships between trophic groups and trophic levels. Heat map of the number of species from each trophic group within 0.5-level trophic level bins. Trophic groups are presented in the same order top to bottom as the trophic pyramids.

Figure S2. Change in relative % biomass by trophic level across a gradient in total (log) biomass. Mean trophic pyramid shape is based on the average relative biomass within each 1.0 log-unit interval. Lines show first-order polynomial trends lines with 95% confidence intervals and the blue shaded region indicates a proposed benchmark of 500 kg ha-1 ecosystem function and fisheries sustainability.

Figure S3. Map of coral reef study sites and their travel time (hours) to A) the nearest fishery market and B) the nearest human population. Colour and size indicates differences in travel time across our dataset. C) Comparison of travel time and gravity metrics across the four management categories used in our study. ‘Remoteness’ was assessed by surveyors based on their local knowledge of a reef’s accessibility by small-scale and commercial fisheries. In general, the remote categories reflect lower accessibility of reefs to markets, consistent with definitions used by Cinner et al., (2018) and McClanahan et al., (2019). There are some outliers, however, which we believe are related to a global-scale dataset that cannot reconcile all possible local knowledge at appropriate scales. Travel time and gravity estimates are derived from a previously published global dataset of coral reef accessibility to markets and populations

(Maire et al., 2016; Cinner et al., 2018).

Trophic group Herbivore−Detritivore Omnivore Planktivore Invertivore Piscivore

Selar crumenophthalmus a Naso caeruleacauda

Cheilinus undulatus Pterocaesio pisang

Odonus niger Caesio caerulaurea a

n Caesio teres o Caesio lunaris

Pterocaesio tile t Pterocaesio tile

Lethrinus olivaceus Cheilinus undulatus

f a

Caesio caerulaurea f Pterocaesio pisang

Selar crumenophthalmus Pterocaesio randalli o

1 Pterocaesio tile e Caesio lunaris

f Naso minor Pterocaesio tile

Pterocaesio chrysozona o Odonus niger

Chlorurus bleekeri Caesio teres L

Pterocaesio marri Lutjanus gibbus

Caesio caerulaurea u Pterocaesio tile

Caesio cuning 2 Caesio lunaris

Naso hexacanthus L Acanthurus mata

Caesio lunaris Macolor macularis a

B Lutjanus gibbus Caesio lunaris N

Caesio teres Cheilinus undulatus

3 Pterocaesio tile Pterocaesio tile

Cheilinus undulatus Naso vlamingii

e Macolor macularis K Naso hexacanthus

Naso hexacanthus r Pterocaesio randalli

Pterocaesio tile Lutjanus gibbus 1 Caesio teres Pterocaesio tile

Pterocaesio pisang Melichthys indicus a

u Naso hexacanthus Odonus niger n

N Melichthys indicus R Naso vlamingii

Melichthys niger Pterocaesio tile k

a Pterocaesio tile Caesio teres e

Pterocaesio chrysozona Caesio lunaris T

j Lutjanus gibbus g Selaroides leptolepis

Caesio teres Caesio caerulaurea

Pterocaesio tile Lutjanus gibbus t

Caesio lunaris n Pterocaesio tile

Scarus Chlorurus microrhinos T

u j

Naso vlamingii Macolor macularis u

Chlorurus microrhinos W Pterocaesio tile

Pterocaesio tile Gnathodentex aureolineatus t

r Caesio lunaris Odonus niger

Pterocaesio chrysozona Acanthurus auranticavus

Naso hexacanthus Lutjanus gibbus

Kyphosus vaigiensis Caesio lunaris

Pterocaesio tile r Selar crumenophthalmus Caesio lunaris Pterocaesio tile

Plectorhinchus albovittatus Scarus

W Cheilinus undulatus W Platax orbicularis

Naso minor r Selar crumenophthalmus

l Pterocaesio tile Caesio teres i Odonus niger Pterocaesio tile 0 5,000 10,000 0 5,000 10,000 Avg biomass, kg/ha Figure S4. Species composition at high-biomass sites. For the 20 sites with highest average site-level biomass, bars show the average biomass (kg ha-1) of the top five biomass- contributing species at each site. Colours indicate trophic groups, as per legend on top.

Planktivores of the family Caesionidae primarily drive high levels of biomass in our dataset.

Figure S5. Change in absolute (log) biomass of five coral reef fish trophic groups across a gradient in total (log) biomass. Mean trophic pyramid shape is based on the average relative biomass within each 1.0 log-unit interval. Lines show first-order polynomial trends lines with

95% confidence intervals and the blue shaded region indicates a proposed benchmark of 500 kg ha-1 ecosystem function and fisheries sustainability. Trophic groups within pyramids are ordered from lowest to highest mean TL (see Fig S1, S2).

Figure S6. Change in absolute (log) biomass by trophic level across a gradient in total (log) biomass. Mean trophic pyramid shape is based on the average relative biomass within each

1.0 log-unit interval. Lines show first-order polynomial trends lines with 95% confidence intervals and the blue shaded region indicates a proposed benchmark of 500 kg ha-1 ecosystem function and fisheries sustainability.

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● ● ● ● ● ●● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ●●● ●● ●●● ● ●● ● ● ●● ● ●● ●● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ● ● ● ●● ●● ● ● ●●●● ● ● ● ● A ● ● Gra● ● ● ● ● vP● ● ● ● ● ●●● ● ● ● ●●● ●● ● ● ● ● ●● ● ● ● ● ● ●● ●● ● ● ●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ●●● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●●● ●●● ● ● ● ● ●●●●● ●●●● ● ●● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ●● ●● ● ● ● ●●● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ●●● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ●● ● ● ● ●● ●●● ●●● ● ●● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ●● ●● ●●● ●● ● ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ● ●● ● ●● ● ● ●● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● D ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ●● ● ●● ●●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ●● ● ●● ● ● ●● 0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ●● ● ● ●●● ● ● ● ●●● ●● ●● ● ●●● ● ● ●● ● ● ●●● ● ●● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●●●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●● ● ●●● ● ● ●●● ● ● ● . ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● Plank ● ●● ● ● ● ● ● ●● ●● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ●● ● 0 ● ● ● ●●● ● ● ●● ●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●●● ● ● ● Herb ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●● ●● ● ●● ● ● ● ●●● ● ●● ●● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ●● ●●●● ●● R ● ● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ●● ● ● ● ● ●● ●● ● ● ● ●● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ●● ●● ● ● ● ●●●● ● ● 0 ● ● ● ● ●●● ● ● ●●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●● ● ● ●● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ●● ● ● ●●● ● ● ●● ●● ●● ● ●● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ●● ●● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ●● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ●●● ●●● ●● ● ● ● ●● ● ●● ● ●● ● ● ●● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●●● ● ● ●● ● ● ● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ●●● ● ● ●●● ● ● ●● ● ● ●●●●● ● ● ● ●● ● ● ● Pisc● ● ● ●●● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ● ●● ●●●● ● ● ● ●● ● ● ●● ●● ● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ●● ●● ●● ● ● GravM ● ● ● ● ● ● ● ● ● ●● ● ●● ●●● ●●● ● ● ●●● ●● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ●●● ● ●● ● ●● ● ● ●●● ●● ● ●● ● ● ● ●●● ● ●● ● ● ● ● ● ●● ●● ● ● ●● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ●● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ●●●● ● ● ● ● ●● ● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ●● ● ●●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●●● ● ●● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● Inv ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ●● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●●● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● Mana● ● ● ●●● ●● ● ● ● g_NTZ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 5 ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● . ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● OceanicP● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● 0 ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ● Depth ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● − ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Manag_OA ● ● ● ● ● ● ● ● ●● ●

0 ● ● ● ● ● ● ● ● ● ● ●● ● . ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 1 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ● ● ● − ● ●

● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

●● ● ● ● ● ● ● ● ●

● ● ● CoastalP● ● ● ● ● ● ● ●● ●

● ● ●

●● ●

. ● ● ●

● ●

1 ● ● ●

●

−

●

−

−2 −1 0 1

RDA1

Figure S7. Redundancy analysis to explore relationships between the five trophic groups

(orange labels; Herbivore-Detritivore: Herb, Omnivore: Omn, Invertivore: Inv, Planktivore:

Plank, Piscivore: Pisc) and a set of the key environmental and socioeconomic variables expected to influence reef condition (blue labels; depth: Depth, habitat: Crest, gravity of the nearest market: GravM, gravity of the nearest population: GravP, coastal productivity:

CoastalP, oceanic productivity: OceanicP, fisheries management such as no-take zones:

Manag_NTZ, open access reefs: Manag-OA, MPA age: MPA_age, and remoteness: Remote).

Distances between reefs (grey dots) are not approximate Euclidean distances but angles between all vectors reflect linear correlation. The ordination explains 15.4% of variance.

S 11

Figure S8. Correlation matrix of variables considered in mixed-effects models of total reef fish biomass and the biomass of individual trophic groups. Bubble size shows the Pearson correlation coefficient between pairwise variables (blue, negative correlations; red, positive correlations). All variables are described in Methods and supplementary Methods. On account of the high collinearity (Pearson r = 0.95) between MPA age and MPA size, we removed MPA size from further analysis. After MPA size was removed, all variance inflation factors (VIFs) were <2 for all variables.

S 12

Table S1. Summary of biomass targets and reference points for, (A) ecological processes and diversity, and (B) fisheries management on coral reefs. References and data locations provided.

Total reef fish biomass, kg/ha Citation Data source

Mean biomass kg/ha <300 300-600 <500 <640 <850 >1130 >1200

Loss of ecosystem Biomass-based services including fish multispecies maximum species sustainable yield (B ). 9 countries in richness,proportion of MSY Increase in Decreases in the Above this B window, McClanahan the Western herbivorous fish in the MSY High cover (>30%) of Decline in predation rates on variance of the variance of macroalgal Description fish biomass values are Unfished biomass et al. 2011 Indian Ocean fishable biomass; sea macrolagae tethered sea urchins ratio of macroalgae cover at fishable often associated with (WIO) urchin to living hard coral biomass ecological stability created biomass; calcifying by high levels of benthic organisms; herbivory and predation and hard coral cover.

Mean biomass kg/ha >500 >1000

50% of B , MacNeil et MSY B , resident reef fish Global reference to maintain MSY al. 2015 Description biomass in the key functions like absence of fishing herbivory

Mean biomass kg/ha <300 300-450 450-600 >600 >1050

(A) Reef fish biomass targets: ecological McClanahan 13 countries Degradation of Low-range estimate for Mid-range estimate et al. 2016 WIO processes and High diversity sustainability Equilibrium Description ecological states, sustainable fisheries for sustainable diversity levels conservation target processes, and services production fisheries production

Mean biomass kg/ha >650

A concave trophic distribution emerges, suggesting that fisheries for upper trophic level Graham et al. 9 countries species will only be supported 2017 WIO Description under lightly fished scenarios; energetic efficiency may maximize channeling primary production from lower to higher trophic levels

Mean biomass kg/ha >360 >410 >470-480 >824 >1146 1306

Ratio of macroalgae Decreases in the Increase in Karr et al. 16 countries Proportion of herbivorous to coral cover; variance of macroalgal Description Increase in coral cover proportion of Unfished biomass 2015 Caribbean fishes Decrease in urchin cover at fishable invertivorous fish biomass biomass

Mean biomass kg/ha 269 390 489 957 1150 2180

Conservation target for recovered reef fish biomass. This target is expected to represent McClanahan 9 countries Management Low compliance new High compliance reefs with high et al. 2015 WIO Open access Destructive gears restricted Remote areas (B) Reef fish biomass category closure closures predation or herbivory targest: fisheries and ecological management stability, which are often the focus of conservation.

Mean biomass kg/ha 736.1 ± 464.2 1867.7 ± 1567.2 McClanahan Global Management High compliance et al. 2019 Remote areas category closures

S 13

Table S2. List of reef fish species and genera associated with each trophic group in 24 families

(Acanthuridae, Balistidae, Caesionidae, Carangidae, Chaetodontidae, Diodontidae,

Ephippidae, Haemulidae, Kyphosidae, Labridae, Lethrinidae, Lutjanidae, Monacanthidae,

Mullidae, Nemipteridae, Pinguipedidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae,

Siganidae, Sphyraenidae, Tetraodontidae, Zanclidae) included in surveys.

Trophic Species group Acanthurus achilles, Acanthurus auranticavus, Acanthurus bariene, Acanthurus blochii, Acanthurus dussumieri, Acanthurus fowleri, Acanthurus gahhm, Acanthurus grammoptilus, Acanthurus guttatus, Acanthurus japonicus, Acanthurus leucocheilus, Acanthurus leucosternon, Acanthurus lineatus, Acanthurus maculiceps, Acanthurus nigricans, Acanthurus nigricauda, Acanthurus nigrofuscus, Acanthurus nigroris, Acanthurus olivaceus, Acanthurus pyroferus, Acanthurus tennentii, Acanthurus triostegus, Acanthurus tristis, Acanthurus xanthopterus, Calotomus carolinus, Centropyge bicolor, Centropyge bispinosa, Centropyge eibli, Centropyge fisheri, Centropyge multispinis, Centropyge nox, Centropyge tibicen, Centropyge vrolikii, Cetoscarus bicolor, Cetoscarus ocellatus, Chlorurus bleekeri, Chlorurus capistratoides, Chlorurus japanensis, Chlorurus microrhinos, Chlorurus perspicillatus, Chlorurus rhakoura, Chlorurus troschelii, Chrysiptera biocellata, Chrysiptera unimaculata, Dischistodus chrysopoecilus, Dischistodus fasciatus, Dischistodus melanotus, Dischistodus perspicillatus, Dischistodus prosopotaenia, Hemiglyphidodon plagiometopon, Kyphosus bigibbus, Kyphosus Herbivore- cinerascens, Kyphosus vaigiensis, Melichthys vidua, Naso brachycentron, Naso elegans, Naso Detritivore lituratus, Naso tonganus, Naso tuberosus, Naso unicornis, Plectroglyphidodon johnstonianus, Plectroglyphidodon lacrymatus, Plectroglyphidodon leucozonus, Plectroglyphidodon phoenixensis, Pomacentrus adelus, Pomacentrus alexanderae, Pomacentrus bankanensis, Pomacentrus brachialis, Pomacentrus burroughi, Pomacentrus taeniometopon, Pomacentrus tripunctatus, Prionurus chrysurus, Scarus altipinnis, Scarus chameleon, Scarus dimidiatus, Scarus flavipectoralis, Scarus forsteni, Scarus frenatus, Scarus ghobban, Scarus globiceps, Scarus hypselopterus, Scarus niger, Scarus oviceps, Scarus prasiognathos, Scarus psittacus, Scarus quoyi, Scarus rubroviolaceus, Scarus russelii, Scarus schlegeli, Scarus spinus, Scarus tricolor, Scarus viridifucatus, Scarus xanthopleura, Siganus argenteus, Siganus canaliculatus, Siganus corallinus, Siganus doliatus, Siganus fuscescens, Siganus guttatus, Siganus javus, Siganus lineatus, Siganus magnificus, Siganus punctatissimus, Siganus punctatus, Siganus rivulatus, Siganus spinus, Siganus stellatus, Siganus vermiculatus, Siganus virgatus, Siganus vulpinus, Stegastes albifasciatus, Stegastes fasciolatus, Stegastes lividus, Stegastes obreptus, Zebrasoma desjardinii, Zebrasoma flavescens, Zebrasoma rostratum, Zebrasoma scopas Abudefduf lorenzi, Abudefduf notatus, Abudefduf septemfasciatus, Abudefduf sordidus, Abudefduf vaigiensis, Acanthochromis polyacanthus, Amblyglyphidodon curacao, Amphiprion frenatus, Amphiprion perideraion, Apolemichthys trimaculatus, Arothron hispidus, Arothron mappa, Bolbometopon muricatum, Canthigaster coronata, Canthigaster ocellicincta, Canthigaster papua, Canthigaster rivulata, Canthigaster solandri, Canthigaster valentini, Chaetodon adiergastos, Chaetodon auriga, Chaetodon auripes, Chaetodon kleinii, Chaetodon punctatofasciatus, Chaetodon selene, Chaetodon xanthurus, Chaetodontoplus melanosoma, Omnivore Chaetodontoplus mesoleucus, Chlorurus bowersi, Chlorurus sordidus, Chlorurus spilurus, Chlorurus strongylocephalus, Chromis amboinensis, Chromis atripes, Chromis margaritifer, Chrysiptera bleekeri, Chrysiptera brownriggii, Chrysiptera cyanea, Chrysiptera flavipinnis, Chrysiptera oxycephala, Chrysiptera rex, Chrysiptera springeri, Chrysiptera talboti, Ctenochaetus binotatus, Ctenochaetus cyanocheilus, Ctenochaetus marginatus, Ctenochaetus striatus, Ctenochaetus strigosus, Ctenochaetus tominiensis, Dascyllus aruanus, Dascyllus melanurus, Dascyllus reticulatus, Hipposcarus harid, Hipposcarus longiceps, Platax boersii, Platax orbicularis, Platax pinnatus, Stegastes nigricans

S 14

Abudefduf bengalensis, Abudefduf sexfasciatus, Acanthurus albipectoralis, Acanthurus mata, Acanthurus nubilus, Acanthurus thompsoni, Amblyglyphidodon aureus, Amblyglyphidodon batunai, Amblyglyphidodon indicus, Amblyglyphidodon leucogaster, Amblyglyphidodon ternatensis, Amphiprion akallopisos, Amphiprion chrysopterus, Amphiprion clarkii, Amphiprion ephippium, Amphiprion melanopus, Amphiprion ocellaris, Amphiprion percula, Amphiprion polymnus, Amphiprion sandaracinos, Amphiprion sebae, Caesio caerulaurea, Caesio cuning, Caesio lunaris, Caesio teres, Caesio varilineata, Caesio xanthonota, Chromis alpha, Chromis analis, Chromis atripectoralis, Chromis caudalis, Chromis cinerascens, Chromis delta, Chromis dimidiata, Chromis elerae, Chromis fumea, Chromis iomelas, Chromis lepidolepis, Chromis lineata, Chromis opercularis, Chromis retrofasciata, Chromis scotochiloptera, Chromis ternatensis, Chromis viridis, Chromis weberi, Chromis xanthochira, Chromis xanthura, Chrysiptera hemicyanea, Chrysiptera parasema, Chrysiptera rollandi, Chrysiptera starcki, Cirrhilabrus aurantidorsalis, Cirrhilabrus cyanopleura, Cirrhilabrus exquisitus, Cirrhilabrus filamentosus, Cirrhilabrus lubbocki, Cirrhilabrus solorensis, Dascyllus carneus, Dascyllus trimaculatus, Decapterus macarellus, Genicanthus lamarck, Gymnocaesio gymnoptera, Hemitaurichthys polylepis, Hemitaurichthys zoster, Lepidozygus tapeinosoma, Macolor macularis, Macolor niger, Melichthys niger, Naso annulatus, Naso brevirostris, Naso Planktivore caeruleacauda, Naso caesius, Naso hexacanthus, Naso lopezi, Naso minor, Naso thynnoides, Naso vlamingii, Neoglyphidodon oxyodon, Neoglyphidodon thoracotaeniatus, Neopomacentrus anabatoides, Neopomacentrus azysron, Neopomacentrus cyanomos, Neopomacentrus filamentosus, Neopomacentrus violascens, Odonus niger, Paracanthurus hepatus, Paracheilinus filamentosus, Paracheilinus flavianalis, Paracheilinus nursalim, Pentapodus caninus, Pinjalo lewisi, Pomacentrus alleni, Pomacentrus amboinensis, Pomacentrus auriventris, Pomacentrus caeruleus, Pomacentrus coelestis, Pomacentrus grammorhynchus, Pomacentrus imitator, Pomacentrus lepidogenys, Pomacentrus littoralis, Pomacentrus melanochir, Pomacentrus moluccensis, Pomacentrus nagasakiensis, Pomacentrus nigromanus, Pomacentrus nigromarginatus, Pomacentrus pavo, Pomacentrus philippinus, Pomacentrus polyspinus, Pomacentrus reidi, Pomacentrus similis, Pomacentrus simsiang, Pomacentrus smithi, Pomacentrus vaiuli, Premnas biaculeatus, Pseudanthias dispar, Pseudanthias evansi, Pseudanthias huchtii, Pseudanthias hypselosoma, Pseudanthias lori, Pseudanthias luzonensis, Pseudanthias pascalus, Pseudanthias pleurotaenia, Pseudanthias squamipinnis, Pseudanthias tuka, Pseudocoris heteroptera, Pseudocoris yamashiroi, Pterocaesio chrysozona, Pterocaesio digramma, Pterocaesio lativittata, Pterocaesio marri, Pterocaesio pisang, Pterocaesio randalli, Pterocaesio tessellata, Pterocaesio tile, Pterocaesio trilineata, Selar crumenophthalmus, Thalassoma amblycephalum, Xanthichthys auromarginatus Anampses caeruleopunctatus, Anampses chrysocephalus, Anampses elegans, Anampses geographicus, Anampses lineatus, Anampses melanurus, Anampses meleagrides, Anampses twistii, Arothron meleagris, Arothron nigropunctatus, Arothron stellatus, Atule mate, Balistapus undulatus, Balistoides conspicillum, Balistoides viridescens, Bodianus anthioides, Bodianus axillaris, Bodianus bilunulatus, Bodianus diana, Bodianus mesothorax, Canthigaster compressa, Chaetodon andamanensis, Chaetodon baronessa, Chaetodon bennetti, Chaetodon citrinellus, Chaetodon collare, Chaetodon decussatus, Chaetodon ephippium, Chaetodon falcula, Chaetodon guentheri, Chaetodon guttatissimus, Chaetodon interruptus, Chaetodon lineolatus, Chaetodon lunula, Chaetodon melannotus, Chaetodon mertensii, Chaetodon meyeri, Chaetodon ocellicaudus, Chaetodon octofasciatus, Chaetodon ornatissimus, Chaetodon oxycephalus, Chaetodon pelewensis, Chaetodon rafflesii, Chaetodon semeion, Chaetodon speculum, Chaetodon triangulum, Chaetodon trifascialis, Chaetodon trifasciatus, Chaetodon ulietensis, Invertivore Chaetodon unimaculatus, Chaetodon vagabundus, Chaetodon wiebeli, Chaetodontoplus dimidiatus, Cheilinus chlorourus, Cheilinus fasciatus, Cheilinus oxycephalus, Cheilinus trilobatus, Cheilinus undulatus, Cheiloprion labiatus, Chelmon rostratus, Chilomycterus reticulatus, Choerodon anchorago, Choerodon oligacanthus, Choerodon zosterophorus, Coradion altivelis, Coradion chrysozonus, Coradion melanopus, Coris batuensis, Coris gaimard, Coris pictoides, Diagramma melanacrum, Diagramma pictum, Diodon holocanthus, Diodon hystrix, Diodon liturosus, Diproctacanthus xanthurus, Epinephelus bontoides, Epinephelus corallicola, Epinephelus fasciatus, Epinephelus rivulatus, Forcipiger flavissimus, Forcipiger longirostris, Gnathodentex aureolineatus, Gomphosus caeruleus, Gomphosus varius, Halichoeres argus, Halichoeres biocellatus, Halichoeres chloropterus, Halichoeres chrysus, Halichoeres cosmetus, Halichoeres hartzfeldii, Halichoeres hortulanus, Halichoeres leucoxanthus, Halichoeres leucurus, Halichoeres margaritaceus, Halichoeres marginatus, Halichoeres

S 15

melanochir, Halichoeres melanurus, Halichoeres nebulosus, Halichoeres nigrescens, Halichoeres ornatissimus, Halichoeres pallidus, Halichoeres papilionaceus, Halichoeres podostigma, Halichoeres prosopeion, Halichoeres richmondi, Halichoeres scapularis, Halichoeres solorensis, Halichoeres trimaculatus, Halichoeres vrolikii, Halichoeres zeylonicus, Hemigymnus fasciatus, Hemigymnus melapterus, Heniochus acuminatus, Heniochus chrysostomus, Heniochus monoceros, Heniochus pleurotaenia, Heniochus singularius, Heniochus varius, Hologymnosus doliatus, Labrichthys unilineatus, Labroides bicolor, Labroides dimidiatus, Labroides pectoralis, Labropsis alleni, Labropsis manabei, Lethrinus erythracanthus, Lethrinus erythropterus, Lethrinus harak, Lethrinus obsoletus, Lethrinus ornatus, Lethrinus variegatus, Lutjanus bengalensis, Lutjanus biguttatus, Lutjanus ehrenbergii, Lutjanus fulviflamma, Lutjanus fulvus, Lutjanus gibbus, Lutjanus kasmira, Lutjanus lemniscatus, Lutjanus lunulatus, Lutjanus lutjanus, Lutjanus quinquelineatus, Lutjanus vitta, Macropharyngodon meleagris, Macropharyngodon negrosensis, Macropharyngodon ornatus, Melichthys indicus, Monotaxis grandoculis, Mulloidichthys vanicolensis, Neoglyphidodon bonang, Neoglyphidodon crossi, Neoglyphidodon melas, Neoglyphidodon nigroris, Novaculichthys taeniourus, Paracentropyge multifasciata, Parachaetodon ocellatus, Parapercis clathrata, Parapercis hexophtalma, Parapercis lineopunctata, Parapercis millepunctata, Parupeneus barberinoides, Parupeneus barberinus, Parupeneus ciliatus, Parupeneus crassilabris, Parupeneus indicus, Parupeneus macronemus, Parupeneus multifasciatus, Parupeneus pleurostigma, Parupeneus spilurus, Parupeneus trifasciatus, Pentapodus aureofasciatus, Pentapodus bifasciatus, Pentapodus emeryii, Pentapodus paradiseus, Pentapodus trivittatus, Pinjalo pinjalo, Plectorhinchus chrysotaenia, Plectorhinchus lessonii, Plectorhinchus lineatus, Plectorhinchus picus, Plectroglyphidodon dickii, Pomacanthus annularis, Pomacanthus imperator, Pomacanthus navarchus, Pomacanthus semicirculatus, Pomacanthus sexstriatus, Pomacanthus xanthometopon, Pomacentrus chrysurus, Pomacentrus cuneatus, Pseudobalistes flavimarginatus, Pseudobalistes fuscus, Pseudocheilinus evanidus, Pseudocheilinus hexataenia, Pseudocheilinus octotaenia, Pseudodax moluccanus, Pteragogus cryptus, Pteragogus enneacanthus, Pygoplites diacanthus, Rhinecanthus aculeatus, Rhinecanthus rectangulus, Rhinecanthus verrucosus, Scolopsis affinis, Scolopsis aurata, Scolopsis bilineata, Scolopsis ciliata, Scolopsis lineata, Scolopsis margaritifera, Scolopsis monogramma, Scolopsis temporalis, Scolopsis trilineata, Scolopsis xenochroa, Selaroides leptolepis, Siganus puelloides, Siganus puellus, Stethojulis balteata, Stethojulis bandanensis, Stethojulis interrupta, Stethojulis strigiventer, Stethojulis trilineata, Sufflamen bursa, Sufflamen chrysopterum, Sufflamen fraenatum, Thalassoma hardwicke, Thalassoma jansenii, Thalassoma lunare, Thalassoma lutescens, Thalassoma purpureum, Thalassoma quinquevittatum, Trachinotus baillonii, Upeneus tragula, Uraspis helvola, Zanclus cornutus Aethaloperca rogaa, Anyperodon leucogrammicus, Aphareus furca, Aprion virescens, Belonoperca chabanaudi, Carangoides bajad, Carangoides ferdau, Carangoides gymnostethus, Carangoides oblongus, Carangoides orthogrammus, Carangoides plagiotaenia, Caranx ignobilis, Caranx melampygus, Caranx sexfasciatus, Cephalopholis argus, Cephalopholis boenak, Cephalopholis cyanostigma, Cephalopholis formosa, Cephalopholis leopardus, Cephalopholis microprion, Cephalopholis miniata, Cephalopholis sexmaculata, Cephalopholis sonnerati, Cephalopholis spiloparaea, Cephalopholis urodeta, Cheilio inermis, Cromileptes altivelis, Diploprion bifasciatum, Elagatis bipinnulata, Epibulus insidiator, Epinephelus areolatus, Epinephelus coeruleopunctatus, Epinephelus coioides, Epinephelus diacanthus, Epinephelus fuscoguttatus, Epinephelus hexagonatus, Epinephelus lanceolatus, Epinephelus longispinis, Epinephelus macrospilos, Epinephelus malabaricus, Epinephelus melanostigma, Piscivore Epinephelus merra, Epinephelus ongus, Epinephelus polyphekadion, Epinephelus quoyanus, Epinephelus spilotoceps, Epinephelus tauvina, Gnathanodon speciosus, Gracila albomarginata, Grammistes sexlineatus, Gymnocranius grandoculis, Hologymnosus annulatus, Lethrinus lentjan, Lethrinus microdon, Lethrinus olivaceus, Lutjanus argentimaculatus, Lutjanus bohar, Lutjanus boutton, Lutjanus carponotatus, Lutjanus decussatus, Lutjanus monostigma, Lutjanus peru, Lutjanus rivulatus, Lutjanus russellii, Lutjanus sebae, Lutjanus semicinctus, Mulloidichthys flavolineatus, Oxycheilinus arenatus, Oxycheilinus bimaculatus, Oxycheilinus celebicus, Oxycheilinus digramma, Oxycheilinus orientalis, Oxycheilinus unifasciatus, Parupeneus cyclostomus, Platax teira, Plectorhinchus albovittatus, Plectorhinchus chaetodonoides, Plectorhinchus flavomaculatus, Plectorhinchus gibbosus, Plectorhinchus polytaenia, Plectorhinchus vittatus, Plectropomus areolatus, Plectropomus laevis, Plectropomus leopardus, Plectropomus maculatus, Plectropomus oligacanthus, Pogonoperca punctata,

S 16

Pseudocaranx dentex, Scomberoides commersonnianus, Seriola dumerili, Seriola lalandi, Seriola rivoliana, Sphyraena barracuda, Sphyraena flavicauda, Sphyraena forsteri, Sphyraena jello, Sphyraena qenie, Symphorichthys spilurus, Symphorus nematophorus, Variola albimarginata, Variola louti

S 17

Table S3. Province, management authority, location (see Figure 1), formal name, size and year of declaration for Indonesia marine protected areas (MPAs) included in this study.

MPAs are listed from the east to west of Indonesia. Management Authorities include:

Ministry of Marine Affairs and Fisheries (MMAF), Ministry of Environment and Forestry

(MoEF), Community based are managed by various community institutions.

Province and Yr Location MPA Size, ha Declaration policy Management Authority declared

Sumatra Taman Wisata Alam Laut Panglima Laot community Aceh 2,600 2008 Community based Pulau Weh Sabang based zoning agreement Sumatra Kawasan Konservasi Keputusan Walikota Sabang MMAF Aceh Perairan Pesisir Timur 3,208 2010 No. 729/2010 Pulau Weh Kota Sabang Sumatra Kawasan Konservasi Keputusan Bupati NAD Besar MMAF Aceh Daerah Kawasan Bina 200 2010 No.43/ 2010 Bahari Sumatra Taman Wisata Alam Laut Menteri Kehutanan No. Simuelue 227,500 1996 MoEF Kepulauan Banyak 596/Kpts-II/1996 Kawasan Konservasi Laut Sumatra Daerah Perairan Pulau SK Bupati Simeulue No. Simuelue 50,000 2006 MoEF Pinang, Siumat dan 523.1/104/2006 Simanaha (Pisisi) Central Java Taman Nasional Laut SK Dirjen PHKA No. Karimunjawa 111,625 2005 MoEF Karimunjawa 79/IV/Set-3/2005 Bali SK Dirjen PHKA No.433/Kpts- Bali Taman Nasional Bali Barat 19,002 1999 MoEF II/1999 West Nusa Tenggara Taman Wisata Perairan Gili Menteri Kelautan dan MoEF Lombok Ayer, Gili Meno, Gili 2,954 2009 Perikanan No. 67/MEN/2009 Trawangan West Nusa Tenggara Perairan Gili Tangkong, Keputusan Bupati Lombok MMAF Lombok Gili Nanggu dan Gili 21,556 2014 Barat No. 23/ 2014 Sundak West Nusa Tenggara Taman Wisata Perairan Peraturan Bupati Lombok Lombok 6,310 2013 MMAF Teluk Bumbang Tengah 2013 West Nusa Tenggara Keputusan Bupati Lombok Taman Wisata Perairan Gili MMAF Lombok 10,000 2014 Timur No. Sulat dan Lawang 188.45/332/KP/2014

S 18

West Nusa Tenggara Taman Pulau Kecil Gili Keputusan Bupati Sumbawa MMAF Sumbawa Balu dan Taman Pesisir 6,728 2014 Barat No. 9/2014 Penyu Tatar Sepang West Nusa Tenggara Taman Pulau Kecil Pulau Keputusan Bupati Sumbawa MMAF Sumbawa Keramat, Bedil dan 2,000 2014 No.1198/2014 Temudong West Nusa Tenggara Taman Pesisir Penyu Keputusan Bupati Sumbawa Sumbawa 70,000 2014 MMAF Lunyuk No.1212/2014 West Nusa Tenggara Suaka Alam Perairan Teluk Keputusan Bupati Dompu No. Sumbawa 39,000 2014 MMAF Cempi 23/2014 West Nusa Tenggara Taman Wisata Perairan Keputusan Bupati Sumbawa MMAF Sumbawa Pulau Liang dan Pulau 33,461 2015 No. 1441/2015 Ngali Kalimantan Kawasan Konservasi MMAF Taman Pesisir dan Taman Keputusan Bupati No. 70/2003 Derawan Pulau Kecil Kepulauan 285,549 2003 (Wiryawan et al. 2005) Derawan dan Perairan sekitarnya

Keputusan Bupati 2001 East Nusa Tenggara Komodo Taman Nasional Komodo 173,308 2001 (Mous et al. 2004) MoEF South Sulawesi Taka Bone Taman Nasional Laut Taka Surat Keputusan Menteri 530,765 2001 MoEF Rate Bone Rate Kehutanan No.92/2001 East Nusa Tenggara East Flores, Kawasan Konservasi Laut 276,693 2009 Surat Keputusan No. 6/2009 MMAF Alor Solor Daerah Selat Pantar North Sulawesi North Peraturan Desa from 2000- Daerah Perlindungan Laut 546 2003 Community based Sulawesi 2003 Kawasan Konservasi North North Sulawesi Wilayah Pesisir dan Pulau- 9,647 2014 No.188.45/HKM/SK/121/2014 Sulawesi MMAF pulau Kecil Kota Bitung Kawasan Konservasi Keputusan Bupati Maluku Maluku Pesisir dan Pulau-Pulau Tanimbar 783,806 2016 Tenggara Barat No. 523- MMAF Kecil (KKP3K) Kabupaten 246/2016 Maluku Tenggara Barat Kawasan Konservasi North Maluku Perairan Daerah Kepulauan Keputusan Bupati Halmahera MMAF Halmahera Guraici dan Laut 6,386 2012 Selatan No.99/2012 Sekitarnya di Kab. Halmahera Selatan West Papua Kawasan Konservasi Laut Peraturan Bupati Raja Ampat Raja Ampat 170,000 2009 MMAF Kofiau, Raja Ampat No. 05/2009

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Table S4. Summaries of average and standard deviation (SD) of total reef fish biomass by management type, including the number and per cent of surveys above a previously reported global biomass target of 500 kg/ha, and a proposed conservation target of 1150 kg/ha. Red and blue colours correspond to biomass targets in Figure 4.

N N surveys Percent surveys Percent Median total SD total above above above above biomass, biomass, N 500 500 1150 1150 Management kg/ha kg/ha surveys kg/ha kg/ha kg/ha kg/ha Open 309.76 346.78 359 92 25.63 13 3.62 Gear Restriction 427.08 634.85 503 209 41.55 55 10.93 No Take Zone 445.35 553.47 289 126 43.60 23 7.96 Remote 1432.09 3258.78 117 84 71.79 62 52.99

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Table S5. Mixed-effect model results of herbivore biomass (kg ha-1) evaluated for the effects of depth (m), habitat, human gravity, productivity, fisheries management and remoteness.

Management type and habitat are categorical variables; categorical coefficients are relative to the intercept of slope (habitat) and open access fished sites (no management).

Herbivore-detritivore biomass Predictors Estimates 95% CI p-value Intercept 3.89 3.20 – 4.57 <0.001

Depth -0.16 -0.38 – 0.07 0.173

Habitat, crest 0.07 -0.13 – 0.27 0.501

Market gravity -0.36 -0.55 – -0.17 <0.001

Gravity of nearest settlement -0.19 -0.33 – -0.05 0.008

Net primary productivity -0.29 -0.43 – -0.14 <0.001

Oceanic productivity 0.35 0.03 – 0.66 0.033

Management, gear restriction 0.29 0.10 – 0.48 0.003

Management, no take 0.23 0.01 – 0.44 0.041

Management, remote 1.39 -0.20 – 2.97 0.086

MPA age 1.26 0.96 – 1.55 <0.001 Marginal R2 / Conditional R2 0.219 / 0.725

S 21

Table S6. Mixed-effect model results of omnivore biomass (kg ha-1) evaluated for the effects of depth (m), habitat, human gravity, productivity, fisheries management and remoteness.

Management type and habitat are categorical variables; categorical coefficients are relative to the intercept of slope (habitat) and open access fished sites (no management).

Omnivore biomass Predictors Estimates 95% CI p-value Intercept 3.20 2.58 – 3.82 <0.001

Depth 0.14 -0.08 – 0.35 0.217

Habitat, crest 0.35 0.15 – 0.54 <0.001

Market gravity -0.26 -0.42 – -0.10 0.001

Gravity of nearest settlement -0.07 -0.19 – 0.05 0.259

Net primary productivity -0.24 -0.37 – -0.12 <0.001

Oceanic productivity 0.18 -0.09 – 0.45 0.198

Management, gear restriction 0.19 0.03 – 0.35 0.022

Management, no take 0.10 -0.09 – 0.28 0.301

Management, remote 1.29 -0.05 – 2.63 0.059

MPA age 1.02 0.76 – 1.29 <0.001 Marginal R2 / Conditional R2 0.176 / 0.647

S 22

Table S7. Mixed-effect model results of planktivore biomass (kg ha-1) evaluated for the effects of depth (m), habitat, human gravity, productivity, fisheries management and remoteness.

Management type and habitat are categorical variables; categorical coefficients are relative to the intercept of slope (habitat) and open access fished sites (no management).

Planktivore biomass Predictors Estimates 95% CI p-value Intercept 3.61 2.94 – 4.28 <0.001

Depth 1.21 0.90 – 1.52 <0.001

Habitat, crest -0.45 -0.72 – -0.17 0.002

Market gravity -0.21 -0.49 – 0.06 0.125

Gravity of nearest settlement 0.05 -0.16 – 0.25 0.658

Net primary productivity -0.01 -0.22 – 0.20 0.917

Oceanic productivity -0.15 -0.58 – 0.27 0.473

Management, gear restriction 0.81 0.52 – 1.10 <0.001

Management, no take 0.65 0.33 – 0.97 <0.001

Management, remote 2.15 0.69 – 3.61 0.004

MPA age 0.40 0.01 – 0.80 0.044 Marginal R2 / Conditional R2 0.270 / 0.678

S 23

Table S8. Mixed-effect model results of invertivore biomass (kg ha-1) evaluated for the effects of depth (m), habitat, human gravity, productivity, fisheries management and remoteness.

Management type and habitat are categorical variables; categorical coefficients are relative to the intercept of slope (habitat) and open access fished sites (no management).

Invertivore biomass Predictors Estimates 95% CI p-value Intercept 3.93 3.49 – 4.36 <0.001

Depth 0.55 0.38 – 0.73 <0.001

Habitat, crest 0.30 0.14 – 0.46 <0.001

Market gravity -0.31 -0.45 – -0.16 <0.001

Gravity of nearest settlement -0.03 -0.13 – 0.08 0.643

Net primary productivity 0.00 -0.10 – 0.11 0.948

Oceanic productivity 0.01 -0.21 – 0.23 0.924

Management, gear restriction 0.04 -0.11 – 0.19 0.614

Management, no take -0.01 -0.18 – 0.15 0.870

Management, remote 0.84 0.05 – 1.64 0.037

MPA age 0.44 0.24 – 0.64 <0.001 Marginal R2 / Conditional R2 0.143 / 0.610

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Table S9. Mixed-effect model results of piscivore biomass (kg ha-1) evaluated for the effects of depth (m), habitat, human gravity, productivity, fisheries management and remoteness.

Management type and habitat are categorical variables; categorical coefficients are relative to the intercept of slope (habitat) and open access fished sites (no management).

Piscivore biomass Predictors Estimates 95% CI p-value Intercept 2.49 1.85 – 3.13 <0.001

Depth 0.80 0.53 – 1.07 <0.001

Habitat, crest 0.18 -0.06 – 0.43 0.145

Market gravity -0.31 -0.50 – -0.12 0.002

Gravity of nearest settlement -0.06 -0.20 – 0.08 0.423

Net primary productivity 0.08 -0.07 – 0.22 0.316

Oceanic productivity -0.27 -0.59 – 0.04 0.091

Management, gear restriction 0.02 -0.18 – 0.21 0.879

Management, no take 0.07 -0.15 – 0.30 0.532

Management, remote 0.96 -0.41 – 2.33 0.168

MPA age 0.59 0.29 – 0.89 <0.001 Marginal R2 / Conditional R2 0.116 / 0.512

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