The following supplement accompanies the article

Community-wide effects of protection reveal insights into effectiveness for reef

E. T. Heyns-Veale*, A. T. F. Bernard, A. Götz, B. Q. Mann, J. Q. Maggs, M. K. S. Smith

*Corresponding author: : [email protected]

Marine Ecology Progress Series 620: 99–117 (2019)

Table S1. List of target and non-target and their functional traits. Herb/Omni: herbivore/omnivore; IC: invertebrate carnivore; GC: general carnivore. Refer to Table S2 for a description of the trait categories. Fisheries Species Common name Size Feeding Level in Mobility Gregariousness Sum importance class guild water of column Max N Target Argyrops spinifer King Large IC Bentho- Within Small groups 1 soldierbream pelagic reef (3-20) Argyrosomus japonicus Dusky kob V.large GC Bentho- Between Small groups 1 pelagic reefs (3-20) Argyrozona argyrozona Carpenter Large GC Bentho- Within Small groups 508 pelagic reef (3-20) Atractoscion aequidens Geelbek V.large GC Bentho- Between Large groups 11 pelagic reefs (>50) Cheimerius nufar Santer Large GC Bentho- Within Small groups 242 pelagic reef (3-20) Chelidonichthys kumu Bluefin Medium IC Benthic Between Solitary 28 Gurnard reefs Chrysoblephus anglicus Englishman Large IC Bentho- Within Small groups 83 pelagic reef (3-20) Chrysoblephus Dageraad Large GC Bentho- Within Small groups 225 cristiceps pelagic reef (3-20) Chrysoblephus Red stumpnose Large IC Bentho- Within Small groups 156 gibbiceps pelagic reef (3-20) Chrysoblephus laticeps Roman Medium IC Bentho- Within Small groups 942 pelagic reef (3-20) Chrysoblephus lophus False Medium IC Bentho- Within Small groups 1 englishman pelagic reef (3-20) Chrysoblephus Slinger Medium IC Bentho- Within Small groups 584 puniceus pelagic reef (3-20) Cymatoceps nasutus Black Large IC Bentho- Within Solitary 78 musselcracker pelagic reef Diplodus capensis Blacktail Medium Herb/ Bentho- Within Small groups 211 Omni pelagic reef (3-20) Epinephelus White-edged Large GC Benthic Within Solitary 1 albomarginatus rockcod reef Epinephelus andersoni Catface Large GC Benthic Within Solitary 17 rockcod reef Epinephelus chabaudi Moustache V.large GC Benthic Within Solitary 19 rockcod reef Epinephelus marginatus Yellowbelly Large GC Benthic Within Solitary 29 rockcod reef Epinephelus rivulatus Halfmoon Medium GC Benthic Within Solitary 38 rockcod reef Galeorhinus galeus Soupfin shark V.large GC Bentho- Between Small groups 4 pelagic reefs (3-20) Lethrinus nebulosus Blue emperor Large GC Bentho- Within Small groups 195 pelagic reef (3-20) Mustelus mustelus Smooth-hound V.large GC Bentho- Between Solitary 94 pelagic reefs Mustelus spp. V.large GC Bentho- Between Solitary 2 pelagic reefs Pachymetopon aeneum Blue hottentot Medium IC Bentho- Within Small groups 876 pelagic reef (3-20) Pachymetopon blochii Hottentot Medium Herb/ Bentho- Within Small groups 130 Omni pelagic reef (3-20) Petrus rupestris Red steenbras V.large GC Bentho- Between Small groups 46

1 pelagic reefs (3-20) Scotsman Large GC Bentho- Within Small groups 114 praeorbitalis pelagic reef (3-20) Polysteganus undulosus Seventy-four Large GC Bentho- Between Medium groups 76 pelagic reefs (20-50) Pterogymnus laniarius Panga Medium GC Bentho- Within Large groups 833 pelagic reef (>50) Rhabdosargus White Medium IC Bentho- Between Small groups 210 globiceps stumpnose pelagic reefs (3-20) Sarpa salpa Strepie Medium Herb/ Bentho- Between Large groups 270 Omni pelagic reefs (>50) Scomberomorus King mackerel V.large GC Pelagic Between Small groups 1 commerson reefs (3-20) Sparodon durbanensis Musselcracker Large IC Bentho- Between Small groups 5 pelagic reefs (3-20) Zeus faber John dory Large GC Bentho- Between Solitary 1 pelagic reefs Non-target Acanthurus dussumieri Eyestripe Medium Herb/ Bentho- Within Small groups 41 surgeonfish Omni pelagic reef (3-20) Amblyrhynchotes Evileye Medium GC Benthic Within Solitary 24 honckenii blaasop reef Aulacocephalus Goldribbon Medium GC Benthic Within Solitary 2 temminckii soapfish reef Bodianus bilunulatus Tarry hogfish Medium IC Bentho- Within Pairing 14 pelagic reef Bodianus perditio Golden-spot Large IC Bentho- Within Pairing 9 hogfish pelagic reef Caesio caerulaurea Blue and gold Medium IC Bentho- Between Large groups 1 fusilier pelagic reefs (>50) Cheilio inermis Cigar wrasse Medium IC Bentho- Within Pairing 2 pelagic reef Cheilodactylus pixi Barred Small IC Benthic Within Solitary 81 fingerfin reef Cheilodactylus spp. Small IC Benthic Within Solitary 1 reef Chromis dasygenys Bluespotted Small IC Bentho- Within Small groups 6 chromis pelagic reef (3-20) Chromis weberi Darkbar Small IC Bentho- Within Small groups 3 chromis pelagic reef (3-20) Coris caudimacula Spottail coris Small IC Bentho- Within Pairing 6 pelagic reef Ecsenius nalolo Nalolo Small IC Benthic Within Solitary 1 reef Eptatretus hexatrema Sixgill Large GC Benthic Between Small groups 9 reefs (3-20) Fistularia commersonii Smooth V.large GC Bentho- Within Pairing 2 flutemouth pelagic reef Gymnothorax Laced moray V.large GC Benthic Within Solitary 6 favagineus reef Gymnothorax Yellow-edged V.large GC Benthic Within Solitary 1 flavimarginatus moray reef Gymnothorax johnsoni Whitespotted V.large GC Benthic Within Solitary 4 moray reef Gymnothorax Yellowmouth V.large GC Benthic Within Solitary 1 nudivomer moray reef Gymnothorax spp. V.large GC Benthic Within Solitary 2 reef Gymnothorax undulatus Undulated V.large GC Benthic Within Solitary 4 moray reef Halaelurus lineatus Banded Medium GC Benthic Within Solitary 7 catshark reef Halaelurus natalensis Tiger catshark Medium GC Benthic Within Solitary 9 reef Haploblepharus Puffadder Medium GC Benthic Within Solitary 178 edwardsii shyshark reef Haploblepharus fuscus Brown Large GC Benthic Within Solitary 26 shyshark reef Haploblepharus pictus Dark shyshark Medium GC Benthic Within Solitary 13 reef Haploblepharus spp. Medium GC Benthic Within Solitary 4 reef Kyphosus bigibbus Grey cub Large Herb/ Bentho- Within Small groups 1 Omni pelagic reef (3-20) Parablennius pilicornis Ringneck Small Herb/ Benthic Within Small groups 2 blenny Omni reef (3-20) Parupeneus fraserorum Small IC Bentho- Within Pairing 6 pelagic reef

2 Parupeneus indicus Indian goatfish Medium GC Bentho- Within Small groups 2 pelagic reef (3-20) Parupeneus Long-barbel Medium IC Bentho- Within Small groups 3 macronemus goatfish pelagic reef (3-20) Parupeneus rubescens Rosy goatfish Medium IC Bentho- Within Small groups 70 pelagic reef (3-20) Parupeneus trifasciatus Doublebar Medium GC Bentho- Within Pairing 3 goatfish pelagic reef Plagiotremus Piano blenny Small GC Bentho- Within Small groups 7 tapeinosoma pelagic reef (3-20) Poroderma africanum Striped Large GC Benthic Within Solitary 363 catshark reef Poroderma Leopard Large GC Benthic Within Solitary 147 pantherinum catshark reef Scorpaena scrofa Red Medium GC Benthic Within Solitary 1 scorpionfish reef Serranus knysnaensis Comber Medium GC Benthic Within Solitary 40 reef Siganus sutor White spotted Medium Herb/ Bentho- Within Small groups 3 rabbitfish Omni pelagic reef (3-20) Sufflamen fraenatum Masked Medium GC Bentho- Within Solitary 18 triggerfish pelagic reef Synodus jaculum Blacktail Small GC Benthic Within Solitary 2 lizardfish reef Tetrosomus gibbosus Hunchback Medium IC Bentho- Within Solitary 1 boxfish pelagic reef

Table S2. Functional traits modified from Mouillot et al. (2014). Functional trait Description / biological relevance Trait Categories Body size Defines ecological niche: energy Small: 0 – 25 cm needs; predator-prey relationships; Medium: 26 – 65 cm growth rate; mortality Large: 66 – 120 cm V. Large: > 121 cm Diet Diet impacts trophic interactions; Herb/Omni: mixed diet of plant nutrient cycling; habitat and material requirements IC: Benthic and pelagic invertebrates GC: Fish and invertebrate prey Mobility Energy needs; spatial extent to Within reefs: Sedentary, which fish control their resources territorial and mobile within reefs and transfer nutrients Between reefs: Mobile between reefs Level in the water column Influences prey available; nutrient Benthic: Closely associated with transfer benthos Bentho-pelagic: In the water column above benthos Pelagic: Not associated with benthos Gregariousness Escaping predation; impacts local Solitary processes, e.g. schooling fish Pairing massive nutrient cycling and Small groups (3 – 20) resource depletion Medium groups (20 – 50) Large groups (>50) Life stage Indication of the size class; Juveniles important in determining fishing Adults effects Used size at 50% maturity *Herb/Omni: herbivore/omnivore; IC: invertebrate carnivore; GC: general carnivore

3 Table S3. Summary (a) and analysis of variance (ANOVA; b) of the generalised additive model [tweedie distribution with a log link function and the basis dimension set to 3 (Lm ~ s(L.oo, bs = "tp", by = Family, k = 3) + Family] to determine the predicted relationship between maximum attainable size and size at maturity for the fish families. a) Summary Parametric coefficients: Std. Estimate Error t value Pr (>|t|) (Intercept) 3.761 0.2159 17.422 < 2e-16 *** Family Blenniidae 1.447 1.3357 1.083 0.279063 Family Carangidae -0.4234 0.2194 -1.93 0.054087 . Family Carcharhinidae 0.2539 0.2299 1.104 0.269854 Family Dasyatidae -0.2119 0.2265 -0.936 0.349775 Family Gobidae 1.4307 0.3676 3.892 0.000109 *** Family Haemulidae -0.3112 0.2361 -1.318 0.187935 Family Labridae -0.736 0.2242 -3.283 0.001081 ** Family Lethrinidae -0.3465 0.2357 -1.47 0.14195 Family Lutjanidae -0.4064 0.2206 -1.843 0.065834 . Family Mullidae -0.8375 0.2832 -2.957 0.003218 ** Family Muraenidae -0.2834 0.2422 -1.17 0.242273 Family Rajidae 0.1764 0.2228 0.792 0.42893 Family Rhinobatidae 0.2179 0.2423 0.899 0.368796 Family Sciaenidae -0.5222 0.2192 -2.382 0.017503 * Family Scombridae -0.1564 0.2246 -0.696 0.486403 Family Scyliorhinidae 0.1112 0.2193 0.507 0.612187 Family Sebastidae -0.3392 0.2192 -1.547 0.122326 Family Serranidae -0.3469 0.2184 -1.589 0.11262 Family -0.5917 0.2186 -2.707 0.006971 ** Family Triakidae 0.1838 0.2396 0.767 0.443468 Family Triglidae -0.4573 0.2461 -1.858 0.063595 .

Approximate significance of smooth terms:

edf Ref.df F p-value s(L.oo):Family Acanthuridae 0.9512 2 9.898 5.99E-06 *** s(L.oo):Family Blenniidae 0.8893 2 4.047 0.00265 ** s(L.oo):Family Carangidae 0.9926 2 64.191 < 2e-16 *** s(L.oo):Family Carcharhinidae 1.9047 2 114.7 < 2e-16 *** s(L.oo):Family Dasyatidae 1.9549 2 60.054 < 2e-16 *** s(L.oo):Family Gobidae 0.9943 2 87.758 < 2e-16 *** s(L.oo):Family Haemulidae 0.9643 2 13.377 1.83E-07 *** s(L.oo):Family Labridae 0.9947 2 89.343 < 2e-16 *** s(L.oo):Family Lethrinidae 0.7478 2 1.504 0.04532 * s(L.oo):Family Lutjanidae 0.9836 2 29.328 3.74E-14 *** s(L.oo):Family Mullidae 0.5315 2 0.561 0.14665 s(L.oo):Family Muraenidae 0.9763 2 20.01 2.73E-10 *** s(L.oo):Family Rajidae 1.8286 2 40.766 < 2e-16 *** s(L.oo):Family Rhinobatidae 1.7472 2 28.683 4.39E-14 *** s(L.oo):Family Sciaenidae 0.9971 2 109.274 < 2e-16 *** s(L.oo):Family Scombridae 1.9345 2 51.591 < 2e-16 ***

4 s(L.oo):Family Scyliorhinidae 0.9838 2 30.351 1.43E-14 *** s(L.oo):Family Sebastidae 0.9887 2 43.845 < 2e-16 *** s(L.oo):Family Serranidae 1.9213 2 197.905 < 2e-16 *** s(L.oo):Family Sparidae 0.9894 2 45.756 < 2e-16 *** s(L.oo):Family Triakidae 0.959 2 11.669 1.01E-06 *** s(L.oo):Family Triglidae 0.8888 2 4.012 0.00276 ** b) ANOVA Parametric Terms:

df F p-value Family 21 24.23 <2e-16

Approximate significance of smooth terms:

edf Ref.df F p-value s(L.oo):Family Acanthuridae 0.9512 2 9.898 5.99E-06 s(L.oo):Family Blenniidae 0.8893 2 4.047 0.00265 s(L.oo):Family Carangidae 0.9926 2 64.191 < 2e-16 s(L.oo):Family Carcharhinidae 1.9047 2 114.7 < 2e-16 s(L.oo):Family Dasyatidae 1.9549 2 60.054 < 2e-16 s(L.oo):Family Gobidae 0.9943 2 87.758 < 2e-16 s(L.oo):Family Haemulidae 0.9643 2 13.377 1.83E-07 s(L.oo):Family Labridae 0.9947 2 89.343 < 2e-16 s(L.oo):Family Lethrinidae 0.7478 2 1.504 0.04532 s(L.oo):Family Lutjanidae 0.9836 2 29.328 3.74E-14 s(L.oo):Family Mullidae 0.5315 2 0.561 0.14665 s(L.oo):Family Muraenidae 0.9763 2 20.01 2.73E-10 s(L.oo):Family Rajidae 1.8286 2 40.766 < 2e-16 s(L.oo):Family Rhinobatidae 1.7472 2 28.683 4.39E-14 s(L.oo):Family Sciaenidae 0.9971 2 109.274 < 2e-16 s(L.oo):Family Scombridae 1.9345 2 51.591 < 2e-16 s(L.oo):Family Scyliorhinidae 0.9838 2 30.351 1.43E-14 s(L.oo):Family Sebastidae 0.9887 2 43.845 < 2e-16 s(L.oo):Family Serranidae 1.9213 2 197.905 < 2e-16 s(L.oo):Family Sparidae 0.9894 2 45.756 < 2e-16 s(L.oo):Family Triakidae 0.959 2 11.669 1.01E-06 s(L.oo):Family Triglidae 0.8888 2 4.012 0.00276 Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 R-sq.(adj) = 0.915, Deviance explained = 91.8%; -REML = 2564.7, Scale est. = 0.1915, n = 721

5 Table S4. Full model output of the sequential PERMANOVAs of the multivariate trait data based on adjusted Bray-Curtis resemblance to test for significant effects of protection (model 1) for the species level functional entities (SFEs; abundance) of the target (a) and non-target (b) species. Visibility and per cent water column were fitted first and second to account for differences in the field of view between stereo-BRUVs samples and water temperature, depth and bottom type were fitted last to account for environmental effects. Values indicated in bold represent significant effect. df degrees of freedom, SS sum of squares, MS mean square, Pseudo-F F-ratios, P (perm) probability density. a) Target b) Non-target

Pseudo- Pseudo- Source df SS MS P(perm) SS MS P(perm) F F Visibility 1 31355 31355 5.2159 0.0028 30428 30428 3.3196 0.046 Water column 1 2021.6 2021.6 2.1367 0.0725 5557.2 5557.2 4.9419 0.004 Temperature 1 26556 26556 7.2208 0.0002 17506 17506 3.2454 0.0301 Depth 1 35242 35242 22.359 0.0001 11674 11674 5.7766 0.0009 Bottom type 4 14197 3549.2 3.3764 0.0001 15347 3836.7 2.924 0.0016 Location 4 34370 8592.6 14.263 0.0001 53145 13286 22.157 0.0001 Status 1 6305.5 6305.5 1.1069 0.4044 18605 18605 12.15 0.0137 Location x Status 4 20013 5003.3 8.3052 0.0001 5327.5 1331.9 2.2211 0.0123 Res 295 177720 602.43 176900 599.64 Total 312 347780 334480

Table S5. Sequential pairwise analyses based on adjusted Bray-Curtis resemblances to investigate the significant interaction between ‘location’ (random) and ‘status’ (fixed; model 1) of the species level functional entities (SFEs; abundance) of the target (a) and non-target (b) species and individual and species level functional entities (ISFEs; length) of the target (c) and non-target (d) species. Values indicated in bold represent significant effect. t t statisic, P (perm) probability density. a) Target b) Non-target c) Target d)Non-target t P(perm) t P(perm) t P(perm) t P(perm) De Hoop 3.5923 0.0001 4.2671 0.0001 3.1095 0.0001 2.7074 0.0028 Tsitsikamma 2.8586 0.0002 3.8006 0.0001 3.403 0.0001 1.8899 0.0307 Bird Island 1.8626 0.011 1.5237 0.1061 1.6949 0.0132 0.4184 0.8067 Amathole 1.7241 0.027 1.9501 0.0341 1.6144 0.0466 1.4569 0.105 Pondoland 1.786 0.0228 1.6349 0.03 2.624 0.0001 1.5382 0.0487

6 Table S6. Results from the similarity percentages of the species level functional entities (SFEs; abundance) of target species (a) and non-target species (b) calculated from the fourth root transformed Bray-Curtis resemblance. Av.Diss: Average dissimilarity, Diss/SD: Dissimilarity/Standard deviation, Contrib%: percentage contribution, Cum%: Cumulative percentage contribution. Refer to Table S2 for a description of the trait categories.

a) Target Protected Exploited Av.Diss Diss/SD Contrib% Cum.% Species

Average dissimilarity = 65.27

IC/Medium/Bentho- pelagic/Between reefs/Small groups (3-20) 0.14 1.17 10.47 1.66 16.04 16.04 Rhabdosargus globiceps IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Pachymetopon groups (3-20) 0.72 1.26 8.42 1.1 12.89 28.93 aeneum

GC/Large/Bentho- pelagic/Within reef/Small Argyrozona argyrozona, Cheimerius nufar, groups (3-20) 0.75 1.04 8.14 1.14 12.47 41.4 Chrysoblephus cristiceps

De Hoop Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20) 0.16 0.87 8.07 1.22 12.36 53.77 Pachymetopon blochii GC/Medium/Bentho- pelagic/Within reef/Large groups (>50) 0.31 0.82 7.62 1.08 11.67 65.43 Pterogymnus laniarius GC/V.large/Bentho- pelagic/Between reefs/Solitary 0.76 0.33 7.1 0.95 10.88 76.32 Mustelus mustelus

Average dissimilarity = 54.62

GC/Medium/Bentho- pelagic/Within reef/Large groups (>50) 0.67 1.18 11.57 1.17 21.19 21.19 Pterogymnus laniarius IC/Medium/Bentho-

pelagic/Within reef/Small Chrysoblephus laticeps, Pachymetopon groups (3-20) 1.6 0.98 9.34 0.84 17.1 38.28 aeneum GC/Large/Bentho- pelagic/Within reef/Small Argyrozona argyrozona, Cheimerius nufar,

Tsitsikamma groups (3-20) 0.94 1.06 7.74 0.95 14.17 52.46 Chrysoblephus cristiceps Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20) 0.53 0.08 5.43 0.79 9.94 62.4 Diplodus capensis, Pachymetopon blochii IC/Medium/Bentho- pelagic/Between reefs/Small groups (3-20) 0.13 0.34 4.49 0.65 8.22 70.61 Rhabdosargus globiceps

Average dissimilarity = 33.86

GC/Medium/Bentho- pelagic/Within reef/Large groups (>50) 0.62 0.66 5.88 1.11 17.37 17.37 Pterogymnus laniarius Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20) 0.12 0.64 4.77 1.06 14.08 31.45 Diplodus capensis GC/Large/Bentho- pelagic/Between reefs/Medium groups (20- 50) 0.51 0.4 4.46 1 13.18 44.63 Polysteganus undulosus IC/Large/Bentho-

Bird Island pelagic/Within reef/Small Chrysoblephus anglicus, Chrysoblephus groups (3-20) 1.02 1.02 2.65 0.76 7.82 52.45 gibbiceps Herb-Omni/Medium/Bentho- pelagic/Between reefs/Large groups (>50) 0.14 0.29 2.56 0.49 7.55 59.99 Sarpa salpa GC/V.large/Bentho- pelagic/etween reefs/Small groups (3-20) 0.34 0.03 2.52 0.71 7.44 67.43 Petrus rupestris GC/V.large/Bentho- pelagic/Between reefs/Solitary 0.22 0.24 2.49 0.73 7.34 74.78 Mustelus mustelus

e Average dissimilarity = 54.39 thol Ama

7 IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Chrysoblephus groups (3-20) 1.39 1.49 10.85 0.82 19.94 19.94 puniceus, Pachymetopon aeneum GC/Large/Bentho- Argyrozona argyrozona, Cheimerius nufar, pelagic/Within reef/Small Chrysoblephus cristiceps, Polysteganus groups (3-20) 1.26 0.87 10.71 0.88 19.69 39.63 praeorbitalis GC/Medium/Bentho- pelagic/Within reef/Large groups (>50) 0.68 0.9 10.39 1.05 19.1 58.73 Pterogymnus laniarius GC/Large/Bentho- pelagic/Between reefs/Medium groups (20- 50) 0.3 0.28 4.49 0.75 8.25 66.98 Polysteganus undulosus Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20) 0.22 0.18 3.74 0.59 6.88 73.86 Diplodus capensis

Average dissimilarity = 37.12

IC/Medium/Bentho- pelagic/Within reef/Small , Pachymetopon groups (3-20) 1.84 1.22 8.08 1.14 21.77 21.77 aeneum IC/Large/Bentho- pelagic/Within reef/Solitary 0.79 0.42 5.45 1.16 14.67 36.44 Cymatoceps nasutus GC/Medium/Benthic/Within

Pondoland reef/Solitary 0.42 0.71 5.13 1.06 13.82 50.25 Epinephelus rivulatus GC/Large/Benthic/Within Epinephelus marginatus, Epinephelus reef/Solitary 0.7 0.47 4.85 1.08 13.06 63.31 albomarginatus Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20) 0.36 0.53 4.82 0.93 12.98 76.29 Diplodus capensis, Pachymetopon blochii

b) Non-target Protected Exploited Av.Diss Diss/SD Contrib% Cum.% Species

Average dissimilarity = 63.90

GC/Large/Benthic/Within Haploblepharus fuscus, Poroderma reef/Solitary 0.69 1.3 29.33 1.02 45.9 45.9 africanum, Poroderma pantherinum Hoop Haploblepharus pictus, Scorpaena scrofa, De GC/Medium/Benthic/Within Serranus knysnaensis, Haploblepharus reef/Solitary 0.14 0.93 25.36 1.41 39.69 85.59 edwardsii

Average dissimilarity = 46.84

GC/Large/Benthic/Within Haploblepharus fuscus, Poroderma reef/Solitary 0.97 1.02 18.1 0.85 38.63 38.63 africanum, Poroderma pantherinum

Tsitsikamma GC/Medium/Benthic/Within Haploblepharus pictus, Serranus reef/Solitary 0.57 0.96 17.64 0.94 37.66 76.29 knysnaensis, Haploblepharus edwardsii

Average dissimilarity = 43.00 GC/Medium/Benthic/Within Serranus knysnaensis, Haploblepharus reef/Solitary 0.28 0.64 15.7 1.06 36.52 36.52 edwardsii

Bird Island GC/Large/Benthic/Within Haploblepharus fuscus, Poroderma reef/Solitary 1.13 1.12 14.26 0.59 33.16 69.69 africanum, Poroderma pantherinum

Average dissimilarity = 85.91 GC/Large/Benthic/Within Poroderma africanum, Poroderma reef/Solitary 0.12 0.51 35.01 0.88 40.75 40.75 pantherinum

Amathole GC/Medium/Benthic/Within reef/Solitary 0.28 0.44 29.46 0.85 34.29 75.04 Serranus knysnaensis

Average dissimilarity = 75.89

IC/Medium/Bentho- pelagic/Within reef/Small Parupeneus macronemus, Parupeneus groups (3-20) 0.64 0.91 14.05 0.93 18.52 18.52 rubescens GC/Medium/Benthic/Within Pondoland reef/Solitary 0.1 0.52 11.44 0.7 15.08 33.6 Serranus knysnaensis GC/Medium/Bentho- pelagic/Within reef/Solitary 0.36 0.3 7.9 0.77 10.41 44.01 Sufflamen fraenatum

8 GC/V.large/Benthic/Within Gymnothorax favagineus, Gymnothorax reef/Solitary 0.25 0.25 7.86 0.57 10.35 54.36 johnsoni, Gymnothorax undulatus Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20) 0.12 0.31 6.99 0.47 9.21 63.57 Acanthurus dussumieri IC/Medium/Bentho- pelagic/Within reef/Pairing 0.32 0.29 6.71 0.8 8.84 72.41 Bodianus bilunulatus, Cheilio inermis

Table S7. Full model output of the sequential PERMANOVAs of the multivariate trait data based on adjusted Bray-Curtis resemblance to test for significant effects of protection (model 1) for the individual and species level functional entities (ISFEs; length) of target (a) and non-target (b) species. Visibility and per cent water column were fitted first and second to account for differences in the field of view between stereo-BRUVs samples and water temperature, depth and bottom type were fitted last to account for environmental effects. Values indicated in bold represent significant effect. df degrees of freedom, SS sum of squares, MS mean square, Pseudo-F F-ratios, P (perm) probability density. a) Target b) Non-target

Pseudo P(perm Pseudo P(perm Source df SS MS SS MS -F ) -F ) Visibility 1 25727 25727 3.5978 0.0051 18719 18719 2.432 0.0659 7130. Water column 1 4077.3 4077.3 2.5649 0.0233 7130.7 7 5.3194 0.0011 9818. Temperature 1 22142 22142 4.4569 0.0007 9818.6 6 1.9365 0.1173 2431. Depth 1 28656 28656 12.962 0.0001 2431.4 4 1.3074 0.2755 2453. Bottom type 4 20243 5060.8 3.2436 0.0001 9814 4 1.8102 0.0323 Location 4 45100 11275 11.395 0.0001 49808 12452 17.702 0.0001 7040. Status 1 22763 22763 4.1925 0.0269 7040.6 6 4.4788 0.0623 Location x Status 4 19149 4787.4 4.8382 0.0001 5588.2 1397 1.9861 0.0179 26 18641 703.4 Res 5 262220 989.5 0 2 28 29676 Total 2 450070 0

9 Table S8. Results from the similarity percentages of the individual and species level functional entities (ISFEs; lengths) of target species (a) and non-target species (b) calculated from the fourth root transformed Bray-Curtis resemblance. Av.Diss: Average dissimilarity, Diss/SD: Dissimilarity/Standard deviation, Contrib%: percentage contribution, Cum%: Cumulative percentage contribution a) Target Protected Exploited Av.Diss Diss/SD Contrib% Cum.% Species

Average dissimilarity = 79.77 IC/Medium/Bentho- pelagic/Between reefs/Small groups (3-20)/Adult 0.11 1.04 9.98 1.32 12.51 12.51 Rhabdosargus globiceps GC/Large/Bentho- pelagic/Within reef/Small Argyrozona argyrozona, Cheimerius groups (3-20)/Juvenile 0.37 0.92 8.43 1.14 10.57 23.07 nufar, Chrysoblephus cristiceps IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Pachymetopon groups (3-20)/Adult 0.57 0.89 7.07 1.11 8.86 31.94 aeneum IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Pachymetopon groups (3-20)/Juvenile 0.18 0.72 7.01 1.13 8.79 40.73 aeneum Herb-Omni/Medium/Bentho-

De Hoop De pelagic/Within reef/Small groups (3-20)/Adult 0.12 0.69 6.56 1.11 8.22 48.95 Pachymetopon blochii Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20)/Juvenile 0.11 0.56 5.33 0.94 6.68 55.63 Pachymetopon blochii GC/Medium/Bentho- pelagic/Within reef/Large groups (>50)/Adult 0.16 0.49 5.1 0.78 6.4 62.03 Pterogymnus laniarius IC/Medium/Benthic/Between reefs/Solitary/Juvenile 0.41 0 4.68 0.71 5.87 67.9 Chelidonichthys kumu IC/Large/Bentho- pelagic/Within reef/Small groups (3-20)/Adult 0.16 0.45 4.3 0.91 5.39 73.29 Average dissimilarity = 71.47 IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Pachymetopon groups (3-20)/Adult 1.38 0.6 10.86 1.09 15.2 15.2 aeneum GC/Large/Bentho- pelagic/Within reef/Small Argyrozona argyrozona, Cheimerius groups (3-20)/Juvenile 0.52 0.91 8.52 1.1 11.92 27.12 nufar, Chrysoblephus cristiceps IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Pachymetopon

groups (3-20)/Juvenile 0.68 0.47 7.37 0.96 10.32 37.43 aeneum GC/Medium/Bentho- pelagic/Within reef/Large groups (>50)/Juvenile 0.22 0.58 7.03 0.83 9.84 47.27 Pterogymnus laniarius GC/Medium/Bentho- Tsitsikamma pelagic/Within reef/Large groups (>50)/Adult 0.48 0.49 6.89 0.9 9.64 56.92 Pterogymnus laniarius GC/Large/Bentho- pelagic/Within reef/mall Argyrozona argyrozona, Cheimerius groups (3-20)/Adult 0.46 0.08 4.79 0.78 6.71 63.62 nufar, Chrysoblephus cristiceps Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20)/Adult 0.44 0.03 4.02 0.72 5.63 69.25 Diplodus capensis, Pachymetopon blochii GC/V.Large/Bentho- pelagic/Between reefs/Small groups (3-20)/Juvenile 0.4 0.05 3.97 0.74 5.55 74.8 Petrus rupestris

Average dissimilarity = 41.74 GC/Large/Bentho- Argyrozona argyrozona, Cheimerius pelagic/Within reef/Small nufar, Chrysoblephus cristiceps,

groups (3-20)/Adult 1.2 0.63 5.08 1.23 12.17 12.17 Polysteganus praeorbitalis IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Chrysoblephus groups (3-20)/Juvenile 1.1 1.14 4.7 1.11 11.26 23.43 puniceus, Pachymetopon aeneum Bird Island Bird GC/Medium/Bentho- pelagic/Within reef/Large groups (>50)/Adult 0.32 0.56 4.44 0.92 10.63 34.06 Pterogymnus laniarius GC/Large/Bentho- Argyrozona argyrozona, Cheimerius pelagic/Within reef/Small 0.98 1.24 3.98 1 9.53 43.59 nufar, Chrysoblephus cristiceps,

10 groups (3-20)/Juvenile Polysteganus praeorbitalis Herb/Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20)/Adult 0.12 0.49 3.54 0.85 8.47 52.06 Diplodus capensis IC/Large/Bentho- pelagic/Within reef/Small Chrysoblephus anglicus, Chrysoblephus groups (3-20)/Adult 0.84 0.84 3.32 0.9 7.95 60.02 gibbiceps GC/Large/Bentho- pelagic/Between reefs/Medium groups (20- 50)/Juvenile 0.33 0.33 3.24 0.79 7.76 67.78 Polysteganus undulosus GC/V.Large/Benthic/Within reef/Solitary/Juvenile 0.28 0.07 2.22 0.65 5.31 73.09 Epinephelus chabaudi

Average dissimilarity = 59.60 GC/Large/Bentho- Argyrozona argyrozona, Cheimerius pelagic/Within reef/Small nufar, Chrysoblephus cristiceps, groups (3-20)/Adult 1.11 0.57 9.77 0.94 16.4 16.4 Polysteganus praeorbitalis IC/Medium/Bentho-

pelagic/Within reef/Small Chrysoblephus laticeps, Chrysoblephus groups (3-20/)Juvenile 0.96 0.94 8.98 0.96 15.07 31.47 puniceus, Pachymetopon aeneum GC/Medium/Bentho- pelagic/Within reef/Large Amathole groups (>50)/Adult 0.56 0.8 8.68 0.9 14.57 46.04 Pterogymnus laniarius IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus laticeps, Chrysoblephus groups (3-20)/Adult 0.94 1.06 8.63 0.91 14.48 60.52 puniceus, Pachymetopon aeneum GC/Large/Bentho- Argyrozona argyrozona, Cheimerius pelagic/Within reef/Small nufar, Chrysoblephus cristiceps, groups (3-20)/Juvenile 0.42 0.58 6.25 0.92 10.49 71.01 Polysteganus praeorbitalis

Average dissimilarity = 59.86 IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus puniceus, Pachymetopon groups (3-20)/Adult 1.41 0.55 8.47 1.28 14.14 14.14 aeneum IC/Medium/Bentho- pelagic/Within reef/Small Chrysoblephus puniceus, Pachymetopon groups (3-20)/Juvenile 0.88 1.04 6.27 1.07 10.48 24.63 aeneum GC/Large/Bentho- Cheimerius nufar, Chrysoblephus pelagic/Within reef/Small cristiceps, Lethrinus nebulosus, groups (3-20)/Juvenile 0.79 1.36 6.22 1.01 10.39 35.02 Polysteganus praeorbitalis GC/Large/Bentho- Cheimerius nufar, Chrysoblephus pelagic/Within reef/Small cristiceps, Lethrinus nebulosus,

Pondoland groups (3-20)/Adult 1.06 0.35 6.21 1.36 10.38 45.4 Polysteganus praeorbitalis IC/Large/Bentho- pelagic/Within reef/Small Argyrops spinifer, Chrysoblephus groups (3-20/)Juvenile 0.28 0.78 5.57 1.05 9.3 54.7 anglicus, Cymatoceps nasutus GC/Medium/Benthic/Within reef/Solitary/Adult 0.21 0.58 4.39 0.96 7.34 62.04 Epinephelus rivulatus IC/Large/Bentho- pelagic/Within reef/Small Argyrops spinifer, Chrysoblephus groups (3-20)/Adult 0.61 0.38 4.28 0.98 7.15 69.2 anglicus, Cymatoceps nasutus GC/Large/Benthic/Within Epinephelus marginatus, Epinephelus reef/Solitary/Adult 0.56 0.34 4.09 0.97 6.83 76.03 albomarginatus

b) Non-target Protected Exploited Av.Diss Diss/SD Contrib% Cum.% Species

Average dissimilarity =

72.41 GC/Large/Benthic/Within Haploblepharus fuscus, Poroderma reef/Solitary/Adult 0.48 1.1 36.64 1.15 50.59 50.59 africanum, Poroderma pantherinum Haploblepharus pictus, Scorpaena De Hoop De GC/Medium/Benthic/Within scrofa, Serranus knysnaensis, reef/Solitary/Adult 0.11 0.67 22.92 1.12 31.65 82.24 Haploblepharus edwardsii

Average dissimilarity = 66.43 GC/Large/Benthic/Within Haploblepharus fuscus, Poroderma reef/Solitary/Adult 0.72 0.64 31.02 0.93 46.69 46.69 africanum, Poroderma pantherinum

Tsitsikamma GC/Medium/Benthic/Within Haploblepharus pictus, Serranus reef/Solitary/Adult 0.43 0.39 21.34 0.86 32.13 78.82 knysnaensis, Haploblepharus edwardsii

11 Average dissimilarity =

57.57 GC/Large/Benthic/Within Haploblepharus fuscus, Poroderma reef/Solitary/Adult 0.75 0.96 28.42 0.84 49.37 49.37 africanum, Poroderma pantherinum

Bird Island Bird GC/Medium/Benthic/Within Serranus knysnaensis, Haploblepharus reef/Solitary/Adult 0.22 0.45 16.86 0.82 29.29 78.66 edwardsii

Average dissimilarity = 95.63 GC/Large/Benthic/Within Poroderma africanum, Poroderma reef/Solitary/Adult 0.06 0.34 41.48 0.92 43.37 43.37 pantherinum GC/Medium/Benthic/Within

Amathole reef/Solitary/Adult 0.1 0.19 22.32 0.63 23.34 66.71 Serranus knysnaensis IC/Small/Benthic/Within reef/Solitary/Adult 0.1 0.06 13.16 0.45 13.76 80.48 Cheilodactylus pixi

Average dissimilarity = 80.38 IC/Medium/Bentho- pelagic/Within reef/Small Parupeneus macronemus, Parupeneus groups (3-20)/Adult 0.62 0.73 16.52 0.77 20.55 20.55 rubescens GC/Medium/Benthic/Within reef/Solitary/Juvenile 0.06 0.43 10.38 0.63 12.91 33.46 Serranus knysnaensis GC/Medium/Bentho- pelagic/Within reef/Solitary/Adult 0.21 0.24 7.2 0.62 8.96 42.41 Sufflamen fraenatum IC/Small/Bentho- pelagic/Within Coris caudimacula, Parupeneus

Pondoland reef/Pairing/Adult 0.06 0.3 6.77 0.54 8.42 50.84 fraserorum IC/Medium/Bentho- pelagic/Within reef/Pairing/Adult 0.17 0.28 6.31 0.68 7.85 58.69 Bodianus bilunulatus, Cheilio inermis Herb-Omni/Medium/Bentho- pelagic/Within reef/Small groups (3-20)/Adult 0.16 0.19 5.79 0.51 7.2 65.89 Acanthurus dussumieri IC/Medium/Bentho- pelagic/Within reef/Small Parupeneus macronemus, Parupeneus groups (3-20)/Juvenile 0.05 0.21 3.77 0.5 4.69 70.58 rubescens

Table S9. Full model output of the sequential PERMANOVA of the multivariate species data based on adjusted Modified Gower (logbase 5) to test for significant effects protection (model 2) for the abundance (MaxN) of the target (a) and non-target (b) species. Visibility and per cent water column were fitted first and second to account for differences in the field of view between stereo-BRUVs samples and water temperature, depth and bottom type were fitted last to account for environmental effects. Values indicated in bold represent significant effect. df degrees of freedom, SS sum of squares, MS mean square, Pseudo-F F-ratios, P (perm) probability density. a) Target b) Non-target

Pseudo- Pseudo- Source df SS MS P(perm) SS MS P(perm) F F Visibility 1 16.55 16.55 42.003 0.0001 5.3726 5.3726 21.991 0.0001 Water column 1 1.2164 1.2164 3.0927 0.0011 1.3933 1.3933 5.714 0.0001 Water temperature 1 13.774 13.774 30.196 0.0001 3.6823 3.6823 12.918 0.0001 Depth 1 13.723 13.723 28.016 0.0001 3.5166 3.5166 11.451 0.0001 Bottom type 4 6.8469 1.7117 4.5772 0.0001 4.4333 1.1083 4.7947 0.0001 Location 4 35.306 8.8266 23.603 0.0001 13.571 3.3928 14.677 0.0001 Status 1 3.3959 3.3959 9.0807 0.0001 5.1965 5.1965 22.48 0.0001 Location x Status 4 8.990 2.2475 6.0099 0.0001 3.358 0.8396 3.6322 0.0001

Res 295 110.32 0.37397 68.19 0.23115

Total 312 210.12 108.71 Table S10. Full model output of the sequential PERMANOVA of the multivariate species data based on adjusted Modified Gower (logbase 5) to test for significant effects protection (model 2) for the biomass data of the target (a) and non-target (b) species. Visibility and per cent water column were fitted first and second to account for differences in the field of view

12 between stereo-BRUVs samples and water temperature, depth and bottom type were fitted last to account for environmental effects. Values indicated in bold represent significant effect. df degrees of freedom, SS sum of squares, MS mean square, Pseudo-F F-ratios, P (perm) probability density. b) Non- a) Target target Pseudo- Pseudo- Source df SS MS P(perm) SS MS P(perm) F F Visibility 1 146.63 146.63 37.923 0.0001 32.381 32.381 9.8145 0.0001 Water column 1 8.7101 8.7101 2.2409 0.0083 21.366 21.366 6.4586 0.0004 Temp 1 107.94 107.94 24.822 0.0001 32.163 32.163 9.173 0.0001 Depth 1 83.724 83.724 18.298 0.0001 14.823 14.823 4.1132 0.0037 Bottom type 4 57.463 14.366 3.8729 0.0001 31.228 7.8071 2.4157 0.0015 Location 4 296.63 74.158 19.993 0.0001 146.17 36.543 11.307 0.0001 Status 1 25.357 25.357 6.8362 0.0001 30.064 30.064 9.3024 0.0001 Location x Status 4 87.036 21.759 5.8661 0.0001 34.349 8.5871 2.6571 0.0011 Res 266 986.67 3.7093 859.67 3.2318 Total 283 1800.2 1202.2

Table S11: Sequential pairwise analyses based on adjusted Modified Gower (logbase 5) to investigate the significant interaction between ‘location’ (fixed) and ‘status’ (fixed; model 2) of the abundance of the target (a) and non-target (b) species and the biomass of the target (c) and non-target (d) species. Values indicated in bold represent significant effect. t t statisic, P (perm) probability density Abundance Biomass a) Target b) Non-target c) Target d)Non-target t P(perm) t P(perm) t P(perm) t P(perm) De Hoop 3.0658 0.0001 3.4463 0.0001 2.7734 0.0001 2.991 0.0004 Tsitsikamma 2.357 0.0001 4.0247 0.0001 2.2511 0.0001 2.1367 0.0036 Bird Island 2.122 0.0001 2.0998 0.001 1.9072 0.0004 1.5597 0.0466 Amathole 1.7657 0.0066 2.0947 0.0046 2.1672 0.0002 1.6208 0.0611 Pondoland 2.3951 0.0001 1.5899 0.0061 1.9906 0.0009 0.902 0.5668

Table S12: Arrangement of the five South African marine protected areas according to the classification of the management criteria set out by (Edgar et al., 2014).

Governance Effectiveness Age Size Isolation Total NEOLI Tsitsikamma National Park MPA 1 1 1 1 2 4 De Hoop MPA 1 2 1 1 1 4 Pondoland MPA 1 1 2 1 1 4 Amathole MPA 1 2 1 1 3 3 Bird Island MPA 1 2 2 2 1 2

13 Table S13: Management features and classification criteria for Table S12 High (1) Medium (2) Low (3) Governance No-take Within MPA but some fishing Openly fished (no-take) allowed Effectiveness Well enforced Moderate policing Little attempt to control (enforced) Age (old) > 10 years old 5 - 10 years old < 5 years old Size (large) > 100 km2 1-100 km2 < 1km2 Isolation MPA zone isolated from fishing Small (1–20%) percentage of Shallow (<25m) reef (isolated) areas by depth (>25m) or sand zone boundary breached by habitat extends barriers of at least 20m width. continuous shallow reef habitat continuously across MPA boundary

Figure S1. Model fit of the generalised additive model testing the effect of family and maximum attainable size on the size at maturity.

14

Figure S2. The predicted relationships between maximum attainable size and size at maturity for the fish families included in the generalised additive model. Data source: FishBase (Froese & Pauly 2014).

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