Ecological Archives E096-225-A1

Ecological Archives E096-225-A1

Joleah B. Lamb, David H. Williamson, Garry P. Russ, and Bette L. Willis. 2015. Protected areas mitigate diseases of reef-building corals by reducing damage from fishing. Ecology 96:2555–2567. http://dx.doi.org/10.1890/14-1952.1

Appendix A. Additional tables, methods, and results.

Table A1. Permitted and restricted activities in three management zones surveyed in this study. Additional information available from www.gbrmpa.gov.au

Activity	Marine National Park MNP	Habitat Protection HP	Conservation Park CP
Line fishing	No	Yes	Limited ^a
Boating, diving, photography	Yes	Yes	Yes
Crabbing (trapping)	No	Yes	Limited ^b
Harvest fishing for aquarium fish, coral and beachworm	No	Permit	Permit
Harvest fishing for sea cucumber, trochus, tropical rock lobster	No	Permit	No
Limited collecting	No	Yes	Yes
Limited impact research (non-extractive)	Yes	Yes	Yes
Limited spearfishing (snorkel only)	No	Yes	Yes
Bait netting	No	Yes	Yes
Netting (other than bait netting)	No	Yes	No
Research (other than non-extractive)	Permit	Permit	Permit
Shipping (other than a designated shipping area)	Permit	Permit	Permit
Tourism program	Permit	Permit	Permit
Traditional use of marine resources	Permit	Permit	Permit
Trawling	No	No	No
Trolling	No	Yes c	Yes ^c

a One hand-held rod or one hand-held line per person, with no more than one hook attached

b Four crab pots or collapsible traps

c No more than three lines per person and up to six hooks combined total per person

Table A2. Fish species categorised into functional and taxonomic groups according to targeted fishery status in the Great Barrier Reef Marine Park.

Family	Species	Functional Group	Fishery status
Acanthuridae	Acanthurus blochii	Detritivore	Non-target
	Acanthurus dussumieri	Detritivore	Non-target
	Acanthurus grammoptilus	Detritivore	Non-target
	Acanthurus lineatus	Algal cropper	Non-target
	Acanthurus nigricauda	Detritivore	Non-target
	Acanthurus nigrofuscus	Algal cropper	Non-target
	Acanthurus xanthopterus	Detritivore	Non-target
	Ctenochaetus binotatus	Detritivore	Non-target
	Ctenochaetus striatus	Detritivore	Non-target
	Naso annulatus	Algal cropper	Non-target
	Naso brevirostris	Algal cropper	Non-target
	Naso lituratus	Algal cropper	Non-target
	Naso tuberosus	Algal cropper	Non-target
	Naso unicornis	Algal cropper	Non-target
	Prionurus microlepidotus	Algal cropper	Non-target
	Zebrasoma scopas	Algal cropper	Non-target
	Zebrasoma veliferum	Algal cropper	Non-target

Chaetodontidae	Chaetodon aureofasciatus	Corallivore	Non-target
	Chaetodon auriga	Corallivore	Non-target
	Chaetodon baronessa	Corallivore	Non-target
	Chaetodon citrinellus	Corallivore	Non-target
	Chaetodon flavirostris	Corallivore	Non-target
	Chaetodon lineolatus	Corallivore	Non-target
	Chaetodon lunula	Corallivore	Non-target
	Chaetodon lunulatus	Benthic carnivore	Non-target
	Chaetodon melannotus	Benthic carnivore	Non-target
	Chaetodon ornatissimus	Corallivore	Non-target
	Chaetodon plebeius	Corallivore	Non-target
	Chaetodon rafflesi	Corallivore	Non-target
	Chaetodon rainfordi	Corallivore	Non-target
	Chaetodon speculum	Corallivore	Non-target
	Chaetodon trifascialis	Corallivore	Non-target
	Chaetodon ulietensis	Benthic carnivore	Non-target
	Chaetodon vagabundus	Corallivore	Non-target
	Chelmon rostratus	Benthic carnivore	Non-target
	Coradion altivelis	Benthic carnivore	Non-target
	Coradion chrysostomus	Benthic carnivore	Non-target
	Heniochus acuminatus	Benthic carnivore	Non-target
	Heniochus monoceros	Benthic carnivore	Non-target
	Heniochus varius	Benthic carnivore	Non-target
	Parachaetodon ocellatus	Benthic carnivore	Non-target

Ephippidae	Platax orbicularis	Benthic carnivore	Non-target
	Platax teira	Benthic carnivore	Non-target
	Platax pinnatus	Benthic carnivore	Non-target
	Platax teira	Benthic carnivore	Non-target

Haemulidae	Diagramma pictum	Large predator	Secondary Target
	Plectorhinchus chaetodontoides	Large predator	Secondary Target
	Plectorhinchus flavomaculatus	Large predator	Secondary Target
	Plectorhinchus gibbosus	Large predator	Secondary Target
	Plectorhinchus lessonii	Large predator	Secondary Target
	Plectorhinchus unicolor	Large predator	Secondary Target

Kyphosidae	Kyphosus spp.	Algal cropper	Non-target
	Microcanthus strigatus	Benthic carnivore	Non-target

Labridae	Anampses geographicus	Benthic carnivore	Non-target
Labridae	Anampses neoguinaicus	Benthic carnivore	Non-target
	Bodianus axillaris	Benthic carnivore	Non-target
	Bodianus loxozonus	Benthic carnivore	Non-target
	Bodianus mesothorax	Benthic carnivore	Non-target
	Cheilinus chlorurus	Benthic carnivore	Non-target
	Cheilinus fasciatus	Benthic carnivore	Non-target
	Cheilinus trilobatus	Benthic carnivore	Non-target
	Cheilinus undulatus	Benthic carnivore	Non-target
	Choerodon anchorago	Benthic carnivore	Secondary target
	Choerodon cyanodus	Benthic carnivore	Secondary target
	Choerodon fasciatus	Benthic carnivore	Non-target
	Choerodon graphicus	Benthic carnivore	Secondary target
	Choerodon monostigma	Benthic carnivore	Secondary target
	Choerodon schoenleinii	Benthic carnivore	Secondary target
	Choerodon vitta	Benthic carnivore	Non-target
	Epibulus insidiator	Benthic carnivore	Non-target
	Gomphosus varius	Benthic carnivore	Non-target
	Halichoeres melanurus	Benthic carnivore	Non-target
	Hemigymnus fasciatus	Benthic carnivore	Non-target
	Hemigymnus melapterus	Benthic carnivore	Non-target
	Labrichthys unilineatus	Benthic carnivore	Non-target
	Labroides bicolor	Benthic carnivore	Non-target
	Labroides dimidiatus	Benthic carnivore	Non-target
	Labropsis australis	Benthic carnivore	Non-target
	Oxycheilinus diagramma	Benthic carnivore	Non-target
	Psuedolabrus guentheri	Benthic carnivore	Non-target
	Stethojulis bandanensis	Benthic carnivore	Non-target
	Stethojulis strigiventer	Benthic carnivore	Non-target
	Thalassoma hardwicke	Benthic carnivore	Non-target
	Thalassoma jansenii	Benthic carnivore	Non-target
	Thalassoma lunare	Benthic carnivore	Non-target
	Thalassoma lutescens	Benthic carnivore	Non-target

Lethrinidae	Gymnocranius spp.	Intermediate predator	Secondary target
	Lethrinus atkinsoni	Intermediate predator	Secondary target
	Lethrinus laticaudis	Intermediate predator	Secondary target
	Lethrinus lentjan	Intermediate predator	Secondary target
	Lethrinus miniatus	Intermediate predator	Primary target
	Lethrinus nebulosus	Intermediate predator	Secondary target
	Lethrinus obsoletus	Intermediate predator	Secondary target
	Lethrinus ornatus	Intermediate predator	Secondary target
	Monotaxis grandoculis.	Intermediate predator	Secondary target

Lutjanidae	Lutjanus argentimaculatus	Large predator	Secondary target
	Lutjanus carponotatus	Intermediate predator	Secondary target
	Lutjanus fulviflamma	Intermediate predator	Secondary target
	Lutjanus fulvus	Intermediate predator	Secondary target
	Lutjanus lemniscatus	Intermediate predator	Secondary target
	Lutjanus lutjanus	Intermediate predator	Secondary target
	Lutjanus monostigma	Intermediate predator	Secondary target
	Lutjanus quinquelineatus	Intermediate predator	Secondary target
	Lutjanus russelli	Intermediate predator	Secondary target
	Lutjanus sebae	Intermediate predator	Primary target
	Lutjanus vitta	Intermediate predator	Secondary target
	Symphorus nematophorus	Large predator	Non-target

Mullidae	Parupeneus barberinus	Benthic carnivore	Non-target
	Parupeneus bifasciatus	Benthic carnivore	Non-target
	Parupeneus ciliatus	Benthic carnivore	Non-target
	Parupeneus indicus	Benthic carnivore	Non-target

Muraenidae	Echidna nebulosa	Intermediate predator	Non-target
	Gymnothorax favagineus	Intermediate predator	Non-target
	Gymnothorax javanicus	Intermediate predator	Non-target
	Gymnothorax meleagris	Intermediate predator	Non-target
	Gymnothorax undulatus	Intermediate predator	Non-target
	Gymnothorax javanicus	Intermediate predator	Non-target
	Gymnothorax meleagris	Intermediate predator	Non-target

Nemipteridae	Scolopsis bilineatus	Intermediate predator	Non-target
	Scolopsis margaritifer	Intermediate predator	Non-target
	Scolopsis monogramma	Intermediate predator	Non-target

Pomacanthidae	Centropyge bicolor	Benthic carnivore	Non-target
	Centropyge bispinosus	Benthic carnivore	Non-target
	Centropyge nox	Benthic carnivore	Non-target
	Centropyge tibicen	Benthic carnivore	Non-target
	Centropyge vrolikii	Benthic carnivore	Non-target
	Chaetodontoplus douboulayi	Benthic carnivore	Non-target
	Chaetodontoplus meredithi	Benthic carnivore	Non-target
	Pomacanthus imperator	Benthic carnivore	Non-target
	Pomacanthus semicirculatus	Benthic carnivore	Non-target
	Pomacanthus sexstriatus	Benthic carnivore	Non-target
	Pomacanthus xanthometapon	Benthic carnivore	Non-target
	Pygoplites diacanthus	Benthic carnivore	Non-target

Pomacentridae	Abudefduf bengalensis	Omnivorous pomacentrid	Non-target
	Abudefduf sexfasciatus	Omnivorous pomacentrid	Non-target
	Abudefduf vaigiensis	Omnivorous pomacentrid	Non-target
	Abudefduf whitleyi	Omnivorous pomacentrid	Non-target
	Abudefduf sexfasciatus	Omnivorous pomacentrid	Non-target
	Abudefduf vaigiensis	Omnivorous pomacentrid	Non-target
	Abudefduf whitleyi	Omnivorous pomacentrid	Non-target
	Acanthochromis polyacanthus	Omnivorous pomacentrid	Non-target
	Amblyglyphidodon aureus	Omnivorous pomacentrid	Non-target
	Amblyglyphidodon curacao	Omnivorous pomacentrid	Non-target
	Amblyglyphidodon leucogaster	Omnivorous pomacentrid	Non-target
	Amphiprion akindynos	Omnivorous pomacentrid	Non-target
	Amphiprion chrysopterus	Omnivorous pomacentrid	Non-target
	Amphiprion clarkia	Omnivorous pomacentrid	Non-target
	Amphiprion melanopus	Omnivorous pomacentrid	Non-target
	Amphiprion perideraion	Omnivorous pomacentrid	Non-target
	Chromis amboinensis	Planktivorous pomacentrid	Non-target
	Chromis atripectoralis	Planktivorous pomacentrid	Non-target
	Chromis atripes	Planktivorous pomacentrid	Non-target
	Chromis nitida	Planktivorous pomacentrid	Non-target
	Chromis retrofasciatus	Planktivorous pomacentrid	Non-target
	Chromis ternatensis	Planktivorous pomacentrid	Non-target
	Chromis weberi	Planktivorous pomacentrid	Non-target
	Chrysiptera rex	Omnivorous pomacentrid	Non-target
	Chrysiptera rollandi	Omnivorous pomacentrid	Non-target
	Chrysiptera talboti	Omnivorous pomacentrid	Non-target
	Dascyllus aruanus	Omnivorous pomacentrid	Non-target
	Dascyllus melanurus	Omnivorous pomacentrid	Non-target
	Dascyllus trimaculatus	Omnivorous pomacentrid	Non-target
	Dascyllus reticulatus	Omnivorous pomacentrid	Non-target
	Dischistodus melanotus	Territorial pomacentrid	Non-target
	Dischistodus perspicillatus	Territorial pomacentrid	Non-target
	Dischistodus prosopotaenia	Territorial pomacentrid	Non-target
	Dischistodus pseudochrysopoecilus	Territorial pomacentrid	Non-target
	Hemiglyphidodon plagiometapon	Territorial pomacentrid	Non-target
	Neoglyphidodon melas	Territorial pomacentrid	Non-target
	Neoglyphidodon nigroris	Territorial pomacentrid	Non-target
	Plectroglyphidodon dickii	Territorial pomacentrid	Non-target
	Plectroglyphidodon lacrymatus	Territorial pomacentrid	Non-target
	Pomacentrus adelus	Territorial pomacentrid	Non-target
	Pomacentrus amboinensis	Omnivorous pomacentrid	Non-target
	Pomacentrus australis	Omnivorous pomacentrid	Non-target
	Pomacentrus bankanensis	Territorial pomacentrid	Non-target
	Pomacentrus brachialis	Omnivorous pomacentrid	Non-target
	Pomacentrus chrysurus	Territorial pomacentrid	Non-target
	Pomacentrus coelestis	Omnivorous pomacentrid	Non-target
	Pomacentrus lepidogenis	Planktivorous pomacentrid	Non-target
	Pomacentrus moluccensis	Omnivorous pomacentrid	Non-target
	Pomacentrus nagasakiensis	Omnivorous pomacentrid	Non-target
	Pomacentrus vaiuli	Territorial pomacentrid	Non-target
	Pomacentrus wardi	Territorial pomacentrid	Non-target
	Stegastes apicalis	Territorial pomacentrid	Non-target
	Stegastes fasciolatus	Territorial pomacentrid	Non-target

Scaridae	Bolbometapon muricatum	Excavating grazer	Non-target
	Cetoscarus bicolor	Excavating grazer	Non-target
	Chlorurus bleekeri	Excavating grazer	Non-target
	Chlorurus microrhinus	Excavating grazer	Non-target
	Chlorurus sordidus	Excavating grazer	Non-target
	Hipposcarus longiceps	Excavating grazer	Non-target
	Scarus altipinnis	Scraping grazer	Non-target
	Scarus chamaeleon	Scraping grazer	Non-target
	Scarus dimidiatus	Scraping grazer	Non-target
	Scarus flavipectoralis	Scraping grazer	Non-target
	Scarus frenatus	Scraping grazer	Non-target
	Scarus ghobban	Scraping grazer	Non-target
	Scarus globiceps	Scraping grazer	Non-target
	Scarus niger	Scraping grazer	Non-target
	Scarus psittacus	Scraping grazer	Non-target
	Scarus rivulatus	Scraping grazer	Non-target
	Scarus rubroviolaceus	Scraping grazer	Non-target
	Scarus schlegeli	Scraping scarid	Non-target
	Scarus spinus	Scraping grazer	Non-target
	Scarus tricolor	Scraping grazer	Non-target

Serranidae	Aethaloperca rogga	Intermediate predator	Secondary target
	Anyperodon leucogrammicus	Large predator	Secondary target
	Cephalopholis boenak	Intermediate predator	Non-target
	Cephalopholis cyanostigma	Intermediate predator	Secondary target
	Cephalopholis microprion	Intermediate predator	Non-target
	Cromileptes altivelis	Large predator	Primary target
	Diploprion bifasciatus	Intermediate predator	Non-target
	Epinephelus caerulopunctatus	Large predator	Secondary target
	Epinephelus fasciatus	Intermediate predator	Secondary target
	Epinephelus fuscoguttatus	Large predator	Secondary target
	Epinephelus lanceolatus	Large predator	Non-target
	Epinephelus merra	Intermediate predator	Secondary target
	Epinephelus ongus	Intermediate predator	Secondary target
	Epinephelus quoyanus	Intermediate predator	Secondary target
	Plectropomus laevis	Large predator	Primary target
	Plectropomus leopardus	Large predator	Primary target
	Plectropomus maculatus	Large predator	Primary target

Siganidae	Siganus argenteus	Algal cropper	Non-target
	Siganus corallinus	Algal cropper	Non-target
	Siganus doliatus	Algal cropper	Non-target
	Siganus fuscescens	Algal cropper	Non-target
	Siganus javus	Algal cropper	Non-target
	Siganus lineatus	Algal cropper	Non-target
	Siganus puellus	Algal cropper	Non-target
	Siganus punctatus	Algal cropper	Non-target
	Siganus spinus	Algal cropper	Non-target
	Siganus vulpinus	Algal cropper	Non-target

Zanclidae	Zanclus cornutus	Benthic carnivore	Non-target

Table A3. Mean prevalence^a of coral disease at sites within reserves and sites open to fishing, and results (F statistics) of univariate 3-level nested analysis of variance (ANOVA) comparing disease prevalence between sites differing in fishing status (fished vs protected), wave exposure (sheltered versus exposed) and among replicate sites nested within these two factors (all replicate site comparisons were significant; results not shown). n: denotes number of transects. Colonies surveyed = 80,866

Variable	Reserve (n = 62)	Fished (n = 60)	ANOVA
Variable	Mean ± SE prevalence	Mean ± SE prevalence	Exposure	Fishing status	Exposure × Fishing Status
Total disease	0.98 ± 0.15	4.05 ± 0.36	3.6 (ns)	43.4 (***)	< 0.01 (ns)
Skeletal eroding band	0.55 ± 0.09	2.34 ± 0.25	2.7 (ns)	35.0 (***)	0.2 (ns)
Brown band	0.14 ± 0.06	0.65 ± 0.09	0.4 (ns)	11.7 (**)	0.3 (ns)
Black band	0.01 ± 0.007	0.16 ± 0.05	1.5 (ns)	2.3 (ns)	0.2 (ns)
White syndrome	0.24 ± 0.05	0.81 ± 0.08	4.0 (ns)	30.2 (***)	0.1 (ns)
Growth anomalies	0.02 ± 0.01	0.06 ± 0.02	1.3 (ns)	2.1 (ns)	0.03 (ns)
Atramentous necrosis	-	0.05 ± 0.02	0.03 (ns)	3.6 (ns)	0.2 (ns)

a Mean prevalence calculated as the percentage of colonies with disease for each disease type or as a percentage of the total number of diseased corals per transect. Analyses performed on data transformed to the square root. ***: P < 0.001; **: P <0.01; *: P < 0.05; ns: not significant

Table A4. Comparisons of included model variables between reserves (n = 63 transects) and fished locations (n = 60 transects). Results (F statistics) of a 2-level nested ANOVA comparing abundance or disease prevalence between reserve status (fished vs protected) and replicate sites (nested within reserve status).

	Reserve Status		ANOVA
Variable	Reserve mean ± SE	Fished mean ± SE	Status	Site (Status)	Difference
(A) Coral Assemblages and cover
Coral density	740.3 ± 154.6	582.7 ± 145.8	0.1(ns)	9.6(***)	No
Coral genera diversity Coral genera richness	2.4 ± 0.2 6.1 ± 0.3	2.6 ± 0.2 6.1 ± 0.2	1.3(ns) 0.6(ns)	1.9(*) 1.6()	No No
Total coral cover	26.3 ± 1.9	26.5 ± 2.4	0.4(ns)	5.7(***)	No
Acroporidae	5.3 ± 0.9	7.1 ± 0.9	1.1(ns)	3.4(***)	No
Agaricidae	1.3 ± 0.3	1.6 ± 0.7	0.02(ns)	1.7(*)	No
Faviidae	4.5 ± 0.8	3.7 ± 0.6	1.5(ns)	5.6(***)	No
Fungidae	0.1 ± 0.05	0.1 ± 0.04	0.03(ns)	1.0(ns)	No
Merulinidae	0.4 ± 0.1	0.9 ± 0.3	0.8(ns)	4.7(***)	No
Mussidae	0.7 ± 0.2	0.5 ± 0.1	1.3(ns)	1.5(ns)	No
Oculiniidae	1.0 ± 0.7	0.3 ± 0.07	0.5(ns)	2.6(***)	No
Pectiniidae	1.0 ± 0.3	1.1 ± 0.3	0.5(ns)	5.4(***)	No
Pocilloporidae	0.9 ± 0.2	0.9 ± 0.3	0.009(ns)	1.3(ns)	No
Poritidae	10.4 ± 2.0	9.7 ± 2.5	0.002(ns)	8.2(***)	No
Siderastreidae	0.2 ± 0.09	0.2 ± 0.1	0.3(ns)	1.1(ns)	No
Other hard coral	0.4 ± 0.1	0.2 ± 0.1	2.4(ns)	3.1(***)	No
(B) Benthic characteristics and coral health
Sediment grain size	8.1 ± 0.5	6.9 ± 0.4	1.4(ns)	1.7(*)	No
Coral physical damage	0.9 ± 0.1	3.5 ± 0.9	8.2(**)	1.6(*)	Fished > Reserve
Sediment tissue death	2.2 ± 0.3	2.4 ± 0.3	0.8(ns)	3.6(***)	No
Derelict fishing line	2.1 ± 1.5	6.5 ± 1.8	6.8(**)	3.0(***)	Fished > Reserve
Site complexity	13.3 ± 0.6	12.6 ± 0.7	0.2(ns)	7.6(***)	No
Macroalgae cover	2.5 ± 0.7	4.3 ± 1.3	1.9(ns)	5.4(***)	No
Coral Drupella scars	0.5 ± 0.2	0.9 ± 0.2	3.5(ns)	5.8(***)	No
Coral bleaching	0.6 ± 0.08	1.0 ± 0.2	5.0(*)	1.7(ns)	Fished > Reserve
(C) Fish assemblages and functional groups
Density of coral trout	2.7 ± 0.4	1.0 ± 0.2	13.2(***)	1.1(ns)	Reserve > Fished
Taxonomic diversity	71.9 ± 1.1	76.0 ± 0.9	5.1(*)	2.9(***)	Reserve > Fished
Total species	37.5 ± 0.9	37.1 ± 0.5	0.004(ns)	3.2(***)	No
Total individuals	281.8 ± 13.5	271.6 ± 16.2	0.2(ns)	4.2(***)	No
Algal croppers	6.8 ± 1.6	4.5 ± 0.5	1.0(ns)	2.1(ns)	No
Scraping grazers	17.9 ± 1.9	18.1 ± 2.8	0.05(ns)	3.7(ns)	No
Benthic carnivores	16.1 ± 1.0	19.1 ± 1.2	1.4(ns)	4.2(***)	No
Excavating grazers	1.5 ± 0.5	2.6 ± 0.6	3.4(ns)	1.1(ns)	No
Om. Pomacentrids	135.1 ± 8.9	144.1 ± 10.6	0.4(ns)	8.3(***)	No
Terr. Pomacentrids	11.3 ± 1.7	18.7 ± 1.8	3.6(ns)	6.4(***)	No
Plank. Pomacentrids	63.4 ± 7.1	31.4 ± 6.6	5.0(*)	3.4(***)	Reserve > Fished
Corallivores	7.1 ± 0.6	6.7 ± 0.5	0.05(ns)	3.6(***)	No
Dentrivores	2.0 ± 0.3	2.0 ± 0.3	0.03(ns)	1.7(*)	No
Other primary target pred.	2.4 ± 0.2	1.6 ± 0.3	3.7(ns)	1.3(ns)	No
Secondary target pred.	7.3 ± 2.2	11.4 ± 1.1	2.9(ns)	0.8(ns)	No
Non-target pred.	9.7 ± 0.5	11.5 ± 0.7	3.8(ns)	1.9(**)	No

Data square root transformed to meet assumptions of variance where necessary.

***: P < 0.001; **: P <0.01; *: P < 0.05; ns: not significant.

Table A5. Results of distance-based multivariate linear model (DISTLM) for coral disease prevalence showing the proportion of variation explained by significant zoning, environmental and biological variables (P < 0.005).

	Percentage variation explained by individual axes
Axis	% explained variation out of fitted model		% explained variation out of total variation
	Individual	Cumulative	Individual	Cumulative
Protection Status	89.70	89.70	39.65	39.65
SedDeath	7.81	97.52	3.45	43.10
GrainSize	1.66	99.17	0.73	43.83
Damage	0.60	99.77	0.26	44.10
Fishing line	0.23	100.00	0.10	44.23

Table A6. Pearson correlations between reserve status or environmental variables and each of the two dbRDA axes.

	Protection status	SedDeath	Grainsize	Damage	Fishing line
RDA1	-0.902	-0.007	-0.201	0.527	0.346
RDA2	0.034	0.856	0.487	-0.258	0.293

Table A7. Mean prevalence of six coral diseases in three management zones in the Whitsunday Island region (see Table 1). n = number of transects per management zone. SE = standard error of the mean, SEB = skeletal eroding band, WS = white syndromes, BBD = black band disease, BrB = brown band disease, GA = growth anomalies, and AtN = atramentous necrosis. Number of colonies surveyed = 80,866.

	Reserves (60 transects)	Fished (33 transects)	Limited fishing (27 transects)	ANOVA
				ANOVA
	Prev ± SE	Prev ± SE	Prev ± SE	Zone	Site (Zone)
SEB	0.5 ± 0.1	1.5 ± 0.3	3.3 ± 0.3	35.2 (***)	32.1 (ns)
WS	0.2 ± 0.05	0.6 ± 0.1	1.0 ± 0.1	18.7 (***)	0.2 (ns)
BrB	0.1 ± 0.06	0.5 ± 0.2	0.9 ± 0.2	8.5 (***)	1.2 (ns)
BBD	0.01 ± 0.007	0.08 ± 0.03	0.3 ± 0.1	2.3 (ns)	1.3 (ns)
GA	0.02 ± 0.02	0.07 ± 0.03	0.03 ± 0.02	1.4 (ns)	1.2 (ns)
AtN	-	0.02 ± 0.02	0.1 ± 0.1	1.9 (ns)	0.8 (ns)

a Mean prevalence calculated as the percentage of colonies with disease for each management zone as a percentage of the total number of corals per transect. Analyses performed on data transformed to the square root. ***: P < 0.001; **: P <0.01; *: P < 0.05; ns: not significant.

Supplemental Methods

Sampling sediment and grain size classification

Each sediment core was sampled by driving a 60 ml plastic syringe with the end removed perpendicularly into the sediment in order to not disturb the layers. Replicate cores for each site were placed in a sterile 50 ml polypropylene tube until examined for grain size classification. Replicate sediment cores were classified into an incremental categorical scale ranging between 1 (very coarse) and 10 (very fine) by taking the mode of 5 measurements for each sample: (1) 1410–2000μm; (2) 1000–1410μm; (3) 710–1000μm; (4) 500–710μm; (5) 250–500μm; (6) 250–350μm; (7) 177–250μm; (8) 125–177μm; (9) 88-–125μm; and (10) 62–88μm.

Supplemental Results

Taxonomic comparisons of disease prevalence

Table A8. Mean taxonomic prevalence^a of coral disease at sites within reserves (n = 63 transects) and sites open to fishing (n = 60 transects). N = number of surveyed colonies.

		Coral disease prevalence (%)
Coral Family	N	SEB	WS	BrB	BBD	GA	AtN	Total
Fished
Acroporidae	4958	4.31	1.47	1.72	1.27	0.16	0.16	9.08
Agariciidae	790	0.45	0.54	0.14	1.30	-	-	2.44
Faviidae	2488	1.05	0.22	0.04	0.19	0.04	-	1.53
Fungiidae	214	-	-	-	-	0.15	-	0.15
Merulinidae	355	0.89	0.29	-	1.64	-	-	2.82
Mussidae	695	1.05	1.53	0.36	0.25	-	-	3.18
Oculiniidae	516	5.02	0.30	-	2.00	-	-	7.32
Pectiniidae	592	0.12	1.39	0.13	0.72	-	-	2.36
Pocilloporidae	1507	10.44	-	0.61	2.02	-	-	13.07
Poritidae	22507	0.45	1.56	0.19	0.27	-	-	2.47
Siderastreidae	89	0.69	0.25	0.03	0.26	0.01	-	1.24
Reserve
Acroporidae	4947	0.84	0.24	0.27	0.23	0.04	0.01	1.64
Agariciidae	1178	0.43	0.27	-	-	0.11	-	0.80
Faviidae	3669	0.16	0.03	-	-	-	-	0.18
Fungiidae	209	-	-	-	-	-	-	-
Merulinidae	337	-	0.42	-	-	-	-	0.42
Mussidae	1024	0.12	0.64	-	0.18	-	-	0.93
Oculiniidae	432	1.92	0.40	-	0.73	-	-	3.04
Pectiniidae	737	0.29	0.52	-	0.31	-	-	1.12
Pocilloporidae	707	3.96	-	0.07	0.81	-	-	4.84
Poritidae	32383	0.16	0.58	-	0.03	-	-	0.77
Siderastreidae	73	-	-	-	1.56	-	-	1.56

a Mean taxonomic prevalence of disease was calculated as the percentage of colonies with disease for each disease type per coral family at the transect level (n = 3 transects per site).

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