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Table S1. Family, , and Common Name of all 119 species of shallow-water reef identified in this study. The temperature affiliation, level of endemism, the abundance of each species over the entire survey area and frequency (Percentage of sites (n = 112) at which the species was observed) are also recorded for each species

Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Froese and of Acanthurus Inshore ACANTHURDIAE 6 3% Tropical Pauly 2019 Indo-Pacific grammoptilus Surgeonfish Randall 1956 (Bray 2019) Western Fairclough et Western Fairclough et APLODACTYLIDAE 12 9% Temperate westralis Seacarp al. 2011 Australia al. 2011 Froese and Froese and Western Ostorhinchus Pauly 2019 Pauly 2019 APOGONIDAE Striped 2 1% Temperate Australia victoriae Paxton et al. Paxton et al. Cardinalfish 1989 1989 Fishes of Shaw's Fairclough et ARACANIDAE Aracana aurita 7 6% Temperate Australia Australia Cowfish al. 2011 (Bray 2018) Western Fishes of Anoplocapros Fairclough et Smooth 4 4% Temperate Australia Australia amygdaloides al. 2011 Boxfish (Bray 2018) Fishes of Anoplocapros Whitebarred Fairclough et 4 4% Temperate Australia Australia lenticularis Boxfish al. 2011 (Bray 2018) Froese and Fishes of Latropiscis Sergeant Pauly 2019 Australia AULOPIDAE 5 3% Subtropical Australia purpurissatus Baker Paxton and (Bray and Niem 1999 Gomon 2018) Froese and Fishes of Centroberyx Pauly 2019 BERYCIDAE Swallowtail 2928 20% Temperate Indo-Pacific Australia lineatus May and (Bray 2017) Maxwell 1986

Froese and Froese and BLENNIIDAE Blenniidae sp Blennies 8 5% Tropical Pauly 2019 Other Pauly 2019 Nelson 1994 Nelson 1994

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Fishes of Callanthias Fairclough et CALLANTHIIDAE Splendid Perch 2 1% Temperate Indo-Pacific Australia australis al. 2011 (Bray 2018) Fishes of Chelmonops Fairclough et Australia CHAETODONTIDAE Western Talma 155 54% Temperate Australia curiosus al. 2011 (Bray and Gomon 2018) Chaetodon Western Fairclough et Western Fairclough et 49 11% Subtropical assarius Butterflyfish al. 2011 Australia al. 2011 Froese and Froese and Heniochus 4 3% Tropical Pauly 2019 Indo-Pacific Pauly, 2019 acuminatus Bannerfish Steene 1978 Steene 1978 Froese and Fishes of Bathytoshia Smooth Pauly 2019 DASYATIDAE 2 2% Temperate Indo-Pacific Australia brevicaudata Stingray Last et al. (Bray 2018) 2016 Froese and Fishes of Bathytoshia Pauly 2019 Black Stingray 1 1% Subtropical Indo-Pacific Australia lata Compagno (Bray 2018) 1999 Froese and Dinolestes Fishes of DINOLESTIDAE Longfin Pike 139 11% Temperate Pauly 2019 Australia lewini Australia Nelson 1984 Fishes of Enoplosus Fairclough et ENOPLOSIDAE Old Wife 570 32% Temperate Australia Australia armatus al. 2011 (Bray) Fishes of Parequula Fairclough et GERREIDAE Silverbelly 10 4% Temperate Australia Australia melbournensis al. 2011 (Bray) Fishes of Fairclough et GIRELLIDAE zebra Zebrafish 823 44% Temperate Australia Australia al. 2011 (Bray 2018) Girella Western Rock Fairclough et Western Fairclough et 47 12% Temperate tephraeops Blackfish al. 2011 Australia al. 2011

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

West Glaucosoma Fairclough et Western Fairclough et GLAUCOSOMATIDAE Australian 60 20% Subtropical hebraicum al. 2011 Australia al. 2011 Dhufish Fishes of Plectorhinchus Goldspotted Fairclough et HAEMULIDAE 111 35% Tropical Indo-Pacific Australia flavomaculatus Sweetlips al. 2011 (Bray) Froese and Fishes of Diagramma Painted 3 2% Subtropical Pauly 2019 Indo-Pacific Australia labiosum Sweetlips Kuiter 1993 (Bray 2017) Froese and Pauly 2019 Fishes of Plectropomus Common Coral 4 2% Tropical Haemstra Indo-Pacific Australia leopardus Trout and Randall (Bray 2019) 1993 Fishes of Heterodontus Port Jackson Fairclough et HETERODONTIDAE 1 1% Temperate Australia Australia portusjacksoni Shark al. 2011 (Bray 2019) Silver Fishes of Drummer Fairclough et KYPHOSIDAE sydneyanus / 826 64% Temperate Indo-Pacific Australia / Gladius Sea al. 2011 gladius (Bray) Chub Western Buffalo Kyphosus Bream / Grey Fairclough et Fairclough et cornelii / bigibbus 1249 46% Subtropical Australia Drummer / al. 2011 al. 2011 / vaigiensis Brassy Drummer Fishes of Notolabrus Brownspotted Fairclough et LABRIDAE 1374 94% Temperate Australia Australia parilus al. 2011 (Bray 2019) Coris Western King Lek et al. Western Fairclough et 7053 91% Subtropical auricularis Wrasse 2011 Australia al. 2011

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Pseudolabrus Redband Fairclough et Western Fairclough et 1078 69% Temperate biserialis Wrasse al. 2011 Australia al. 2011 Fishes of Ophthalmolepis Southern Fairclough et 993 63% Temperate Australia Australia lineolatus Maori Wrasse al. 2011 (Bray 2019) Fishes of Olisthops Fairclough et 491 62% Temperate Australia Australia cyanomelas al. 2011 (Bray)

Fishes of Austrolabrus Blackspotted Fairclough et 274 47% Temperate Australia Australia maculatus Wrasse al. 2011 (Bray 2018) Halichoeres Brownfield's Fairclough et Western Fairclough et 235 42% Subtropical brownfieldi Wrasse al. 2011 Australia al. 2011 Fishes of Achoerodus Western Shepherd 174 41% Temperate Australia Australia gouldii Blue Groper 2007 (Bray 2018) Fishes of Bodianus Western Cossington et Australia 60 26% Temperate Australia frenchii Foxfish al. 2010 (Gomon and Bray 2019) Cure et al. Choerodon Baldchin 2015 Western Fairclough et 95 26% Subtropical rubescens Groper Cure et al. Australia al. 2011 2018 Fishes of Pictilabrus Senator Fairclough et 32 18% Temperate Australia Australia laticlavius Wrasse al. 2011 (Bray) Froese and Froese and Anampses Scribbled Pauly 2019 Pauly 2019 169 17% Tropical Indo-Pacific geographicus Wrasse Westneat Westneat, 2001 2001

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Froese and Fishes of Thalassoma Sevenband Pauly 2019 Western 73 16% Tropical Australia septemfasciatum Wrasse Parenti and Australia (Bray 2018) Randall 2000 Thalassoma Fairclough et Fishes of Moon Wrasse 57 14% Tropical Indo-Pacific lunare al. 2011 Australia Froese and Scarus ghobban Bluebarred Fairclough et Pauly 2019 105 13% Tropical Indo-Pacific / schlegeli al. 2011 Parenti and Randall 2000 Fishes of Thalassoma Green Moon Fairclough et 116 10% Tropical Indo-Pacific Australia lutescens Wrasse al. 2011 (Bray) Fishes of Labroides Common Fairclough et 17 8% Tropical Indo-Pacific Australia dimidiatus Cleanerfish al. 2011 (Bray 2017) Little Rainbow Fairclough et Western Fairclough et Dotalabrus alleni 30 6% Temperate Wrasse al. 2011 Australia al. 2011 Fishes of Eupetrichthys Snakeskin Fairclough et 14 6% Temperate Australia Australia angustipes Wrasse al. 2011 (Bray 2018) Fishes of Heteroscarus Fairclough et Rainbow Cale 5 4% Temperate Australia Australia acroptilus al. 2011 (Bray 2017) Froese and Fishes of Chlorurus Greenfin Pauly 2019 4 2% Tropical Indo-Pacific Australia sordidus Parrotfish Eschmeyer (Bray 2017) 1997 Froese and Froese and Anampses Blacktail 3 1% Tropical Pauly 2019 Indo-Pacific Pauly 2019 melanurus Wrasse Myers 1991 Myers 1991 Dotalabrus Castelnau's Froese and Fishes of 2 1% Temperate Australia aurantiacus Wrasse Pauly 2019 Australia

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Russell 1988 (Bray 2018)

Fishes of Haletta Blue Fairclough et 2 1% Temperate Australia Australia semifasciata Weed-Whiting al. 2011 (Bray) Fishes of Pseudojuloides Long Green Fairclough et 1 1% Tropical Indo-Pacific Australia elongatus Wrasse al. 2011 (Bray 2018) Froese and Fishes of Scarus Sixband Pauly 2019 2 1% Tropical Indo-Pacific Australia frenatus Parrotfish Parenti and (Bray) Randall 2000 Fishes of Stethojulis Redspot Fairclough et 1 1% Temperate Indo-Pacific Australia bandanensis Wrasse al. 2011 (Bray 2018) Bluethroat Suezichthys Fairclough et Western Fairclough et Rainbow 1 1% Subtropical cyanolaemus al. 2011 Australia al. 2011 Wrasse Fishes of Psammoperca Waigieu Fairclough et LATIDAE 20 9% Tropical Australia Australia waigiensis Seaperch al. 2011 (Bray 2018) Fishes of Redlip Fairclough et Western LATRIDAE 88 34% Subtropical Australia rubrolabiatus al. 2011 Australia (Bray 2019) Froese and Fishes of Pauly 2019 Blue Morwong 85 27% Temperate Australia Australia valenciennesi May and (Bray 2019) Maxwell 1986 Froese and Dactylophora Dusky Fairclough et Pauly 2019 41 17% Temperate Australia nigricans Morwong al. 2011 May and Maxwell 1986

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Cheilodactylus Magpie Fairclough et Western Fairclough et 27 11% Temperate gibbosus Morwong al. 2011 Australia al. 2011 Froese and Fishes of Cheilodactylus Pauly 2019 14 7% Temperate Indo-Pacific Australia nigripes May and (Bray 2019) Maxwell 1986 Froese and Froese and Pauly 2019 Lethrinus Pauly 2019 LETHRINIDAE Grass Emperor 1 1% Tropical Carpenter Indo-Pacific laticaudis Carpenter and and Allen Allen 1989 1989 Froese and Fishes of Lutjanus Stripey LUTJANIDAE 1 1% Tropical Pauly, 2019 Indo-Pacific Australia carponotatus Snapper Allen 1985 (Bray 2017) Fishes of Neatypus Footballer Fairclough et MICROCANTHIDAE 592 34% Temperate Australia Australia obliquus Sweep al. 2011 (Bray) Froese and Fishes of Tilodon Moonlighter 60 23% Subtropical Pauly 2019 Australia Australia sexfasciatus Kuiter 1993 (Bray 2018) Fishes of Microcanthus Fairclough et Stripey 1 1% Temperate Indo-Pacific Australia strigatus al. 2011 (Bray 2019) Fishes of Meuschenia Bluelined Fairclough et MONACANTHIDAE 93 30% Temperate Australia Australia galii Leatherjacket al. 2011 (Bray) Fishes of Meuschenia Yellowstriped Fairclough et 223 29% Temperate Australia Australia flavolineata Leatherjacket al. 2011 (Bray) Fishes of Meuschenia Horseshoe Fairclough et 32 12% Temperate Australia Australia hippocrepis Leatherjacket al. 2011 (Bray 2019)

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Fishes of Meuschenia Sixspine Fairclough et 24 5% Temperate Australia Australia freycineti Leatherjacket al. 2011 (Bray 2017) Froese and Fishes of Acanthaluteres Spinytail Pauly 2019 16 4% Subtropical Australia Australia brownii Leatherjacket May and (Bray 2018) Maxwell 1986 Fishes of Scobinichthys Rough Fairclough et 4 3% Temperate Australia Australia granulatus Leatherjacket al. 2011 (Bray) Acanthaluteres Toothbrush Fairclough et Fishes of 1 1% Temperate Australia vittiger Leatherjacket al. 2011 Australia Froese and Pauly 2019 Fishes of Eubalichthys Bluespotted 3 1% Tropical Allen and Australia Australia caeruleoguttatus Leatherjacket Swainston (Bray 2018) 1988 Froese and Fishes of Eubalichthys Mosaic Pauly 2019 1 1% Temperate Australia Australia mosaicus Leatherjacket May and (Bray) Maxwell 1986 Fishes of Upeneichthys Bluespotted Fairclough et MULLIDAE 112 26% Temperate Australia Australia vlamingii Goatfish al. 2011 (Bray) Fishes of Parupeneus Blacksaddle Fairclough et 69 21% Tropical Indo-Pacific Australia spilurus Goatfish al. 2011 (Bray) Froese and Parupeneus Fairclough et Rosy Goatfish 2 2% Tropical Indo-Pacific Pauly 2019 chrysopleuron al. 2011 Randall 2004 Froese and Fishes of Myliobatis Southern MYLIOBATIDAE 1 1% Temperate Pauly 2019 Indo-Pacific Australia tenuicaudatus Eagle Ray Francis 1993 (Bray)

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Froese and Pentapodus Western Western Fairclough et NEMIPTERIDAE 25 6% Subtropical Pauly 2019 vitta Butterfish Australia al. 2011 Russell 1990 Froese and Fairclough et Pauly 2019 ODACIDAE Weed Whiting 621 34% Temperate Australia spp al. 2011 Gomon and Paxton 1985 Froese and Fishes of Orectolobus Spotted Pauly 2019 ORECTOLOBIDAE 1 1% Temperate Australia Australia maculatus Wobbegong Compagno (Bray 2018) 1984 Koeda et al. Koeda et al. PEMPHERIDAE Pempheris spp Bullseyes 24873 69% Tropical Other 2014 2014

Fishes of Parapercis Fairclough et PINGUIPEDIDAE Wavy Grubfish 1 1% Temperate Australia Australia haackei al. 2011 (Bray) Fishes of Fairclough et PLESIOPIDAE Trachinops spp Hulafishes 14699 51% Temperate Australia Australia al. 2011 (Bray) Fishes of Paraplesiops Southern Fairclough et 8 6% Temperate Australia Australia meleagris Blue Devil al. 2011 (Bray) Fishes of Cnidoglanis Estuary Fairclough et Australia PLOTOSIDAE 1 1% Temperate Australia macrocephalus Cobbler al. 2011 (Gomon and Bray 2018) McCulloch's Fairclough et Western Fairclough et POMACENTRIDAE Parma mccullochi 1544 90% Temperate Scalyfin al. 2011 Australia al. 2011 Chromis Blackhead Fairclough et Western Fairclough et 10320 54% Temperate klunzingeri Puller al. 2011 Australia al. 2011 Parma Western Fairclough et Western Fairclough et 537 41% Subtropical occidentalis Scalyfin al. 2011 Australia al. 2011

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Froese and Pomacentrus Fairclough et Miller's Damsel 1500 27% Tropical Indo-Pacific Pauly, 2019 milleri al. 2011 Allen 1991 Fishes of Fairclough et Parma victoriae Scalyfin 113 21% Temperate Australia Australia al. 2011 (Bray 2018) Fishes of Abudefduf Bengal Fairclough et 81 12% Tropical Indo-Pacific Australia bengalensis Sergeant al. 2011 (Bray 2018) West Chromis Fairclough et Western Fairclough et Australian 146 7% Subtropical westaustralis al. 2011 Australia al. 2011 Puller Fishes of Stegastes Western Fairclough et 5 4% Tropical Indo-Pacific Australia obreptus Gregory al. 2011 (Bray 2019) Froese and Froese and Bicolor Parma bicolor 3 2% Subtropical Pauly 2019 Australia Pauly 2019 Scalyfin Allen 1991 Allen 1991 Froese and Fishes of Abudefduf Banded 3 1% Tropical Pauly 2019 Indo-Pacific Australia septemfasciatus Sergeant Allen 1991 (Bray 2018) Froese and Fishes of Abudefduf Scissortail 5 1% Tropical Pauly 2019 Indo-Pacific Australia sexfasciatus Sergeant Allen 1991 (Bray 2018) Fishes of Abudefduf Indo-Pacific Fairclough et 1 1% Tropical Indo-Pacific Australia vaigiensis Sergeant al. 2011 (Bray 2019) Froese and Froese and Dischistodus Honeyhead 2 1% Tropical Pauly 2019 Indo-Pacific Pauly 2019 prosopotaenia Damsel Allen 1991 Allen 1991 Western Froese and Fishes of Neopomacentrus Western Australian 5 1% Tropical Pauly 2019 Australia aktites Australia Demoiselle Allen et al. (Bray 2018)

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

2017

Labracinus Lined Fairclough et Western Fairclough et PSEUDOCHROMIDAE 16 8% Tropical lineatus Dottyback al. 2011 Australia al. 2011

Froese and Fishes of Scorpis Pauly 2019 SCORPIDIDAE Banded Sweep 187 45% Temperate Australia Australia georgiana May and (Bray 2017) Maxwell 1986 Fishes of Scorpis Fairclough et Sea Sweep 251 32% Temperate Australia Australia aequipinnis al. 2011 (Bray) Epinephelides Fairclough et Fairclough et SERRANIDAE Breaksea Cod 88 38% Subtropical Australia armatus al. 2011 al. 2011 Fishes of Australia Caesioscorpis Blowhole Fairclough et Western 102 5% Temperate Fishes of theagenes Perch al. 2011 Australia Australia (Bray 2018) Epinephelus Chinaman Fairclough et Fairclough et 8 4% Tropical Australia rivulatus Rockcod al. 2011 al. 2011 Froese and Fishes of Pauly 2019 Caesioperca rasor Barber Perch 27 3% Temperate Australia Australia May and (Bray) Maxwell 1986 Fishes of Fairclough et Othos dentex Harlequin Fish 3 3% Temperate Australia Australia al. 2011 (Bray 2018) Fishes of Acanthistius Western Fairclough et 5 2% Temperate Australia Australia serratus Wirrah al. 2011 (Bray)

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Common Frequency Supporting Supporting Family Scientific Name Abundance Affiliation Endemism Name (%) Reference Reference

Fishes of Hypoplectrodes Banded Fairclough et 2 1% Temperate Australia Australia nigroruber Seaperch al. 2011 (Bray 2018) Froese and Fishes of Siganus Black Pauly 2019 SIGANIDAE 758 10% Tropical Indo-Pacific Australia fuscescens Rabbitfish Woodland (Bray 2018) 1990

Fishes of Rhabdosargus Fairclough et SPARIDAE Tarwhine 208 5% Temperate Indo-Pacific Australia sarba al. 2011 (Bray)

Froese and Fishes of Chrysophrys Snapper 24 4% Subtropical Pauly 2019 Indo-Pacific Australia auratus Paulin 1990 (Bray 2017) Fishes of Froese and Sphyraena Striped Australia SPHYRAENIDAE 112 20% Tropical Pauly 2019 Indo-Pacific obtusata Barracuda (Bray and Rose 1984 Shultz 2019) Fishes of Pelsartia Fairclough et TERAPONTIDAE Sea Trumpeter 1 1% Temperate Australia Australia humeralis al. 2011 (Bray 2018) Froese and Fishes of Omegophora Bluespotted Pauly 2019 TETRAODONTIDAE 13 9% Subtropical Australia Australia cyanopunctata Toadfish Eschmeyer (Bray) 1999

Trygonoptera Striped Fairclough et Western Fairclough et UROLOPHIDAE 3 3% Temperate ovalis Stingaree al. 2011 Australia al. 2011

Urolophus Circular Fairclough et Western Fairclough et 1 1% Temperate circularis Stingaree al. 2011 Australia al. 2011

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Figure S1 (A) Canonical Analysis of Principal Coordinates (CAP) plot of shallow-water reef fish assemblages using the two Fisheries management regions of SWA: West Coast and South Coast (m = 12, n = 112) as a factor of groups. The resulting leave-one-out allocation success of observations is also shown. (B) Canonical Analysis of Principal

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Coordinates (CAP) plot of shallow-water reef fish assemblages using the three IMCRA mesoscale bioregions of SWA: Central West Coast, Leeuwin Naturaliste and WA South Coast (m = 39, n = 112) as a factor of groups. The resulting leave-one-out allocation success of observations is also shown.

Figure S2 (A) Canonical Analysis of Principal Coordinates (CAP) plot of shallow-water reef fish assemblages using the five-assemblage structure of SWA: Geraldton, Jurien Bay and Perth, South-West Capes, Albany and Bremer Bay, and Esperance (m = 12, n = 112) as a factor of groups. The resulting leave-one-out allocation success of

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observations is also shown. (B) Canonical Analysis of Principal Coordinates (CAP) plot of shallow-water reef fish assemblages using the six-assemblage structure of SWA: Geraldton, Jurien Bay, Perth, South-West Capes, Albany and Bremer Bay, and Esperance (m = 36, n = 112) as a factor of groups. The resulting leave-one-out allocation success of observations is also shown.

15