Adelaide Desalination Plant Baited Remote Underwater Video Surveys - 2018

Report to AdelaideAqua Pty Ltd

James Brook (J Diversity Pty Ltd)

Rev 0, December 2018 ADP BRUV Surveys - 2018

Cover photo: Fish at Noarlunga Tyre Reef, including yellowtail scad Trachurus novaezelandiae and trevally Pseudocaranx spp., April 2018. Acknowledgements Dimitri Colella was the technical and field lead on this project. Trent Brockhouse and Andrew Dendunnen of Whyalla Diving Services, and Sasha Whitmarsh assisted in the field. Dr Bryan McDonald provided advice on statistical analysis and review.

Disclaimer The findings and opinions expressed in this publication are those of the author and do not necessarily reflect those of AdelaideAqua Pty Ltd. While reasonable efforts have been made to ensure the contents of this report are factually correct, the author does not accept responsibility for the accuracy and completeness of the contents. The author does not accept liability for any loss or damage that may be occasioned directly or indirectly through the use of, or reliance on, the contents of this report.

Preferred citation: Brook, J (2018), Adelaide Desalination Plant Baited Remote Underwater Video Fish Surveys – 2018. Report for AdelaideAqua Pty Ltd, prepared by J Diversity Pty Ltd.

Revision history Rev Date Comment Author Reviewed A 11/12/2018 Initial Draft J. Brook D. Colella B 12/12/2018 Minor changes J. Brook B McDonald 0 18/12/2018 Changes in response to review

2 ADP BRUV Surveys - 2018

Table of Contents Executive Summary ...... 6 1 Introduction ...... 7 2 Methods ...... 8 2.1 Baited Remote Underwater Video System ...... 8 2.2 Survey sites ...... 8 2.3 Deployment...... 10 2.4 Data analysis ...... 11 3 Results ...... 12 3.1 Autumn 2018 fish communities ...... 12 3.2 Spring 2018 fish communities ...... 15 3.3 Comparisons of control and impact sites over time ...... 18 3.3.1 Diversity measures ...... 18 3.3.2 Community structure ...... 20 3.4 Interannual differences ...... 21 3.5 Other factors influencing community structure ...... 21 4 Discussion ...... 23 5 References ...... 24 Appendix A – Species recorded during 2015 and 2018 surveys...... 26 Appendix B – Plates of species recorded ...... 31 Appendix C – PRIMER/PERMANOVA+ outputs ...... 39

Table of Tables Table 1. Survey sites and attributes ...... 10

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Table of Figures Figure 1. Baited remote underwater video unit. Source: adapted from Cappo et al. (2007)...... 8 Figure 2. BRUV survey sites. Source: DEW 2018a, b...... 9 Figure 3. Abundance of species per site during autumn survey, by family ...... 13 Figure 4. Richness of species per site during autumn survey, by family ...... 14 Figure 5. Principal Coordinates Analysis scatter plot of fish communities recorded during autumn survey...... 15 Figure 6. Abundance of species per site during spring survey, by family ...... 16 Figure 7. Richness of species per site during spring survey, by family ...... 17 Figure 8. Principal Coordinates Analysis scatter plot of fish communities recorded during spring survey...... 18 Figure 9. Mean abundance, richness and Shannon-Weiner diversity index value for replicates of autumn and spring surveys in 2015 and 2018...... 19 Figure 10. Principal Coordinates Analysis scatter plot of fish communities recorded during autumn and spring of 2015 and 2018, showing control vs impact (colour) and survey (shape)...... 20 Figure 11. Principal Coordinates Analysis scatter plot of fish communities recorded during autumn and spring of 2015 and 2018, showing patterns related to location (south vs north), protection (fished and unfished), and substrate (natural vs artificial)...... 22

Table of Plates Plate 1. Bottlenose dolphin Tursiops truncatus ...... 31 Plate 2. Western Australian salmon Arripis truttaceus ...... 31 Plate 3. Trevally Pseudocaranx spp...... 31 Plate 4. Yellow-tail scad Trachurus novaezelandiae ...... 31 Plate 5. Western talma Chelmonops curiosus ...... 31 Plate 6. Long-fin pike Dinolestes lewini ...... 31 Plate 7. Old wife Enoplosus armatus ...... 32 Plate 8. Silverbelly Parequula melbournensis ...... 32 Plate 9. Zebra fish Girella zebra ...... 32 Plate 10. Silver drummer Kyphosus sydneyanus ...... 32 Plate 11. Black-spotted wrasse Austrolabrus maculatus ...... 32 Plate 12. Brown-spotted wrasse Notolabrus parilus ...... 32 Plate 13. Western blue groper Achoerodus gouldii ...... 33 Plate 14. Spiny tailed leatherjacket Acanthaluteres brownii ...... 33 Plate 15. Toothbrush leatherjacket Acanthaluteres vittiger ...... 33 Plate 16. Blue-tail leatherjacket Eubalichthys cyanoura ...... 33 Plate 17. Six-spine leatherjacket Meuschenia freycineti ...... 33 Plate 18. Horseshoe leatherjacket Meuschenia hippocrepis ...... 33 Plate 19. Degen’s leatherjacket Thamnaconus degeni ...... 34 Plate 20. Bearded cod Pseudophycis barbata...... 34 Plate 21. Southern goatfish Upeneichthys vlamingii ...... 34 Plate 22. Gurnard perch Neosebastes spp...... 34 Plate 23. Blue rock whiting Haletta semifasciata ...... 34

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Plate 24 . Shaw's cowfish Aracana aurita ...... 34 Plate 25 . Rough bullseye Pempheris klunzingeri ...... 35 Plate 26 . Long-snouted boarfish Pentaceropsis recurvirostris ...... 35 Plate 27 . Wavy grubfish Parapercis haackei ...... 35 Plate 28 . Yank flathead Platycephalus speculator ...... 35 Plate 29 . Yellow-headed hulafish Trachinops noarlungae ...... 35 Plate 30 . Slimy mackerel Scomber australasicus ...... 35 Plate 31 . Sea sweep Scorpis aequipinnis ...... 36 Plate 32 . Banded sweep Scorpis georgiana ...... 36 Plate 33 . Moonlighter Tilodon sexfasciatus ...... 36 Plate 34 . King George whiting Sillaginodes punctatus ...... 36 Plate 35 . Whiting Sillago spp...... 36 Plate 36 . Snapper Pagrus auratus ...... 36 Plate 37 . Ringed toadfish Omegophora armilla ...... 37 Plate 38 . Port Jackson shark Heterodontus portusjacksoni ...... 37 Plate 39 . Broadnose sevengill shark Notorynchus cepedianus ...... 37 Plate 40 . Southern fiddler ray Trygonorrhina dumerilii ...... 37 Plate 41 . Western stingaree Trygonoptera mucosa ...... 37 Plate 42 . Sand crab Ovalipes australiensis ...... 37 Plate 43 . Red swimmer crab Nectocarcinus integrifrons...... 38 Plate 44 . Blue swimmer crab Portunus armatus ...... 38

5 ADP BRUV Surveys - 2018

Executive Summary The operators of the Adelaide Desalination Plant, AdelaideAqua Pty Ltd, are required by their discharge licence to monitor reef fish populations for two seasons in every third year. Baseline monitoring of fish communities undertaken prior to the construction of the desalination plant used stereo baited remote underwater video (BRUV) systems to measure diversity, abundance and size of fish in both seagrass and reef habitat, in the latter case the shallow reef inshore from the area most likely to be impacted by brine discharge. In response to an independent review and with the agreement of the Environment Protection Authority, Jacobs Pty Ltd retained the BRUV method but modified the design of the surveys undertaken in autumn and spring 2015, resetting the baseline to adopt an asymmetric ‘beyond BACI’ design. The artificial reef created by rock armour around the diffuser structures became the impact site, rather than the inshore reef and offshore seagrass, and four new reference sites were identified to collectively represent similar depth, substrate (reef), construction (artificial vs natural) and protection from fishing. Single-camera BRUV units were used to measure diversity and abundance (but not size). The current study describes the 2018 surveys, the first since the reset of the baseline in 2015, and uses the same design as the 2015 surveys. More than 3,000 specimens were recorded during the autumn and spring surveys, from 78 distinct including four species of crab, southern calamari and five species of shark or ray, with the remainder being bony fishes. The most diverse family was Monacanthidae (leatherjackets), with 10 species. The most abundant species were trevally, slender bullseyes and yellowtail scad in autumn and Degen’s leatherjacket and trevally in spring. Both abundance and richness were lower during the spring survey than the autumn survey in 2018. Degen’s leatherjacket, snapper and yellowtail scad were less abundant than in 2015, and trevally were more abundant. In both seasons during 2018 there were significant differences between the fish communities at each site, driven by a range of species including trevally, yellowtail scad, snapper, silverbelly and long-finned pike in autumn and Degen’s leatherjacket, silverbelly, Port Jackson shark, red swimmer crabs, sand crabs and goatfish in spring. These differences between sites are not unexpected given the differences in construction (natural vs artificial reefs), protection from fishing, and latitudinal differences, as well as a range of other physical factors. However, the key question is not whether there are differences between the sites, but whether there is any difference between the trajectories of the control sites collectively compared with the impact site. Analysis of the reef fish communities across seasonal surveys during 2015 (the baseline) and 2018 (the current study), each for two seasons, found no evidence that the ADP is having an impact on fish communities. There was no statistically significant difference between control and impact sites for diversity indices including abundance, species richness and Shannon-Weiner index, nor for multivariate analysis of fish communities. Changes in abundance and community structure between 2015 and 2018 were statistically significant, but changes at the control and impact sites were of similar magnitude. The same results were achieved whether the impact sites included or excluded replicates form locations near the intake structure that were established during 2015.

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1 Introduction The South Australian Government contracted AdelaideAqua Pty Ltd (the Client) to operate and maintain the Adelaide Desalination Plant, a reverse osmosis plant at Port Stanvac with an annual capacity of up to 100 gigalitres, for 20 years from 2012. Discharge from the desalination plant occurs through a diffuser consisting of six equally spaced risers along the final 140 metres of the outfall pipe, within an offshore exclusion zone. During construction, the diffuser was protected with artificial rocky reef. The exclusion zone contains little natural reef habitat but there is reef on the coastline inshore from the discharge point (SA Water 2008). The environmental impact statement for the ADP acknowledged the ecological sensitivity of the nearby subtidal reef habitats but found that measurable adverse impacts of the ADP on the marine environment within Gulf St Vincent would be unlikely (SA Water 2008). Fish assemblages have been monitored since 2009 using Baited Remote Underwater Video Systems (BRUVS), which is a non-destructive sampling method. Ongoing monitoring is required for two seasons in every third year under the current licence (EPA 2017). Initially, monitoring occurred near the inshore reef and over a seagrass community, as well as a reference site for each of these habitat types. This monitoring was undertaken by the environment agency of the South Australian Government. In 2015, in response to a review by Cheshire (2014) and with the approval of the EPA, the BRUVS surveys were redesigned to focus on reef habitat in general, and specifically that most likely to be impacted by the brine plume, namely the artificial diffuser reef (Jacobs 2015a). There is an underlying but previously unstated assumption that colonisation of this reef has reached a stable state, allowing impact-related change to be discernible. To improve the design, new reference sites were also chosen in 2015, to be consistent with the depth of the diffuser reef and/or to include artificial habitat or areas protected from fishing (Jacobs 2015a). There were two reference sites to the north and two to the south of the diffuser reef. A further decision was to discontinue fish size measurement and focus on abundance and diversity (Jacobs 2015a). The 2015 surveys by Jacobs (2015a, b) effectively reset the baseline for monitoring. The current BRUVs survey is the first since those surveys. J Diversity Pty Ltd was contracted to perform the 2018 surveys according to a specified scope (AdelaideAqua 2017). The aim of this report is to describe the fish assemblages from the 2018 surveys at the desalination discharge and reference sites, and compare them with the results from 2015, in a Before/After-Control/Impact (BACI) framework. The abundances for each replicate from the 2015 surveys (Jacobs 2015a, b) were provided to this study.

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2 Methods 2.1 Baited Remote Underwater Video System Each baited remote underwater video (BRUV) unit consisted of a high-definition GoPro Hero 4 Silver video camera mounted on a metallic frame (Figure 1) with the video camera orientated along a horizontal plane relative to the sea-floor. These cameras are functionally equivalent to the Hero 3+ Silver version selected for the previous study due to its relative low cost, ability to record in high definition, long battery life, wide-angle viewing, and image quality in low-light conditions (Jacobs 2015a). Only one camera was used on each unit because fish length measurement was not required.

Fra me

Figure 1. Baited remote underwater video unit. Source: adapted from Cappo et al. (2007).

The units were baited with 500 g of minced sardines (Sardinops sagax) in a plastic mesh bag mounted on a pole extending about 1.5 m in front of the cameras. The sardines create an odour plume which serves as an attractant. Each BRUV unit was linked to the sea surface via a floating rope and buoy system to enable ease of retrieval. The BRUV systems and their operation was consistent with standards developed by Miller et al. (2017) and, where applicable to single-camera BRUV units, Langlois et al. (2018), unless it would compromise consistency with the previous surveys by Jacobs (2015a, b). 2.2 Survey sites The sites identified by Jacobs (2015a, b) were retained for this survey. These sites implement a ‘beyond-BACI’ approach, with a single potential impact site (the desalination plant diffuser) and multiple controls (Underwood 1994). The four controls (reference reefs) are the Glenelg Tyre Reef (GTR) and Seacliff Reef (SCR) to the north, and Port Noarlunga Reef (PNR) and the Noarlunga Tyre Reef (NTR), including nearby

8 ADP BRUV Surveys - 2018 shipwreck H A Lumb to the south (Figure 2). Because the diffuser reef (ADP) is artificially constructed, two of the reference reefs, GTR and the NTR, were selected to represent an artificial reef in the north and south respectively. The Port Noarlunga Reef site was selected due to its location within a Marine Park Sanctuary Zone, which should provide it with a similar level of protection from fishing as the diffuser reef, which sits within the ADP Exclusion Zone that prohibits vessel access (Jacobs 2015a). The attributes relevant to the selection of the five sites are summarised in Table 1.

tyre reef (GTR)

Desalination plant diffuser (ADP) ♦ ♦ ♦ i, ♦ ♦

Noarlunga tyre reef (NTR) ♦ Exclusion zone markers

- Bathymetric contours

Figure 2. BRUV survey sites. Source: DEW 2018a, b.

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Table 1. Survey sites and attributes Site Acronym Use Protection Substrate Location Glenelg tyre reef GTR Control Fished Artificial North Seacliff reef SCR Control Fished Natural North Desalination plant diffuser ADP Impact Unfished Artificial South Port Noarlunga Reef PNR Control Unfished Natural South Noarlunga tyre reef NTR Control Fished Artificial South

A minimum of six replicate video drops were undertaken at each site. Consistent with the approach of Jacobs (2015a), a minimum of 50 m and preferably 100 m separated each replicate within the site to reduce the likelihood of bait plume interactions between units deployed concurrently. Greater distances between sites, in line with national standards (Langlois et al. 2008), would not be possible at some sites, including the diffuser reef. Replicates were generally positioned at the GPS locations used for (in common) for both of the 2015 surveys (Jacobs 2015a, b). An exception was at Port Noarlunga Reef, where there were snorkelers present at one of the marks. An important component of the baseline reset implemented by Jacobs (2015a) was to select an ‘impact’ site that is exposed to brine discharge, namely the ADP diffuser reef. During the 2015 surveys, two of the six replicates were near the intake structure, rather than the diffuser, assumedly because the line of diffuser structures was not long enough to allow six replicates to be spread at least 50 metres apart. Although the sites near the intake were retained for the 2018 survey to support consistency, additional replicates were undertaken near the diffuser as alternatives to the replicates near the intake, where discharged brine is likely to be well mixed and near ambient levels. These additional replicates allowed for a simple sensitivity analysis whereby the statistical tests for differences between control and impact sites were repeated after excluding the replicates near the intake. Marine Parks permit MR00119-1 provided for the survey work at the Port Noarlunga Reef site, within a Sanctuary Zone of the Encounter Marine Park. 2.3 Deployment Sampling was conducted in April (autumn) and September (spring), 2018. Each BRUVs unit was deployed for at least one hour during the window between one hour after sunrise and one hour before sunset (Langlois et al. 2018), before retrieval and downloading of footage. To prevent confounding effects from having too many cameras deployed at once in an area, the number of BRUVS deployed at any time was generally limited to three – this also enabled quicker retrieval of units and minimised time differences between site replicates. At the ADP diffuser site, half the replicates were done on the same day as northern sites, and the other half on the same day as southern sites.

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2.4 Data analysis One hour of video from each camera deployment (starting from when sediment settled after bottom contact) was analysed using the SeaGIS EventMeasure software (SeaGIS 2018) to log observations of fish and collate the abundance measure of each species. Fish identification was carried out with the aid of reference books (Edgar 2008, Gomon et al 2008, Hutchins and Swainston 1996). For each species or taxon, fish abundance was recorded as MaxN, which is the maximum number of individual fish (for each species or taxon) observed in a single frame throughout the deployment duration. MaxN is a conservative estimate of abundance, because counts are limited to those in the field of view at any one time, and when large numbers of fish are present, fish in the foreground can obscure others in the background (see reviews by Willis et al 2000 and Cappo et al 2003, 2004). Some species were not identifiable to species level and were therefore grouped into genus or family, e.g., trevally species could not be differentiated and were grouped as Pseudocaranx spp. Fish communities from each replicate were compared within and across the five sites using univariate and multivariate analyses. Univariate measures calculated for each replicate included the total abundance (sum of MaxN) of specimens, total number of species (richness) and the Shannon- Wiener diversity index were calculated for each hour of footage (i.e. each replicate). Shannon diversity was calculated by the DIVERSE routine of the PRIMER statistical package (Clarke and Gorley 2006). Multivariate datasets for each of the 2018 surveys, and for all four surveys from 2015 and 2018, were prepared using a fourth-root transformation to dampen the influence of abundant species (Clarke and Warwick 2001), and Bray-Curtis dissimilarity measure. Multivariate patterns were visualised by the Principle Components Analysis routine (PCO) of the PERMANOVA+ add-on (Anderson et al. 2008), including the display of the more strongly correlated species (R > 0.6). Permutational multivariate analysis of variance (PERMANOVA routine) was used to examine variation in the assemblages between the sites for each of the 2018 surveys. The full dataset was analysed using an asymmetric design with site as a random factor nested in use (control vs impact) as a fixed factor, orthogonal with year and season as random factors. The same design was used for statistical comparisons of the diversity measures (abundance, richness, Shannon-Weiner index). Species contributing the most to dissimilarity between different factors were explored using the SIMPER routine of PRIMER. Similar designs were used to test the statistical significance of factors including reef type (artificial vs natural), location (north vs south), and protection (fished vs unfished).

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3 Results Weather conditions during the survey were generally mild with flat seas and underwater visibility up to 10 m, although visibility was lower for one day of the autumn survey. Recreational fishing was noted at most of the control sites, except Port Noarlunga Reef, which is within a Marine Park Sanctuary Zone. The level of community surveillance of this zone was evident from the queries that the Marine Parks officer received in regard to our operations in the zone. A total of 3,141 specimens from 78 distinct taxa were recorded across the two surveys in 2018 (Appendix A). Photographs of many of these species are provided in Appendix B). 3.1 Autumn 2018 fish communities A total of 2,058 specimens were recorded from 70 distinct taxa, which included southern calamari Sepioteuthis australis and four crab species: sand crab Ovalipes australiensis, blue swimmer crab Portunus armatus, giant spider crab Leptomithrax gaimardii and the red swimmer crab Nectocarcinus integrifrons. There were four cartilaginous fish species: the Port Jackson shark Heterodontus portusjacksoni, southern fiddler ray Trygonorrhina dumerilii, smooth stingray Bathytoshia brevicaudata and the western stingaree Trygonoptera mucosa. No mammals were recorded. The 61 species of ray-finned fishes were recorded from 34 families (Appendix A). The most specious families were Monacanthidae (leatherjackets) with 10 species and Labridae (wrasses) with five species. The most abundant families were: Carangidae, with 599 fish, including 405 trevally Pseudocaranx spp. and 194 yellowtail scad Trachurus novaezelandiae; Pempherididae with 317 fish, including 251 slender bullseye Parapriacanthus elongatus and 66 Klunzinger’s bullseye Pempheris klunzingeri; and Monacanthidae with 200 fish, including 68 horseshoe leatherjacket Meuschenia hippocrepis. Abundances were highest at the PNR site, with high numbers of Carangids, and the NTR site, where the most abundant families were Pempherids and Monacanthids, with unidentified schooling fish also abundant (Figure 3). Species richness was highest at the NTR site and lowest at the ADP site (Figure 4).

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120

100 i 80 -- 60 Abundance

40

20

0 GTR SCR ADP PNR NTR

■ Arripidae ■ Carangidae ■ Chaetodontidae ■ Cheilodactylidae ■ Dasyatidae

■ Delphinidae ■ Dinolestidae ■ Enoplosidae ■ Gerreidae ■ Heterodontidae

■ Hexanchidae ■ Kyphosidae ■ Labridae ■ Loliginidae ■ Majidae

■ Monacanthidae ■ Moridae ■ Mullidae ■ Neosebastidae ■ Odacidae

■ Ostraciidae ■ Other ■ Paralichthyidae ■ Pempherididae ■ Pentacerotidae

■ Pinguipedidae ■ Platycephalidae ■ Plesiopidae ■ Polybiidae ■ Pomacentridae

■ Portunidae ■ Rhinobatidae ■ Scombridae ■ Scorpididae ■ Sepiidae

■ Serranidae ■ Sillaginidae ■ Sparidae ■ Sphyraenidae ■ Syngnathidae

■ Terapontidae ■ Tetraodontidae ■ Urolophidae

Figure 3. Abundance of species per site during autumn survey, by family

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20

18

16

14

12

10 Richness 8

6

4

2

0 GTR SCR ADP PNR NTR

■ Arripidae ■ Carangidae ■ Chaetodontidae ■ Cheilodactylidae ■ Dasyatidae

■ Delphinidae ■ Dinolestidae ■ Enoplosidae ■ Gerreidae ■ Heterodontidae

■ Hexanchidae ■ Kyphosidae ■ Labridae ■ Loliginidae ■ Majidae

■ Monacanthidae ■ Moridae ■ Mullidae ■ Neosebastidae ■ Odacidae

■ Ostraciidae ■ Other ■ Paralichthyidae ■ Pempherididae ■ Pentacerotidae

■ Pinguipedidae ■ Platycephalidae ■ Plesiopidae ■ Polybiidae ■ Pomacentridae

■ Portunidae ■ Rhinobatidae ■ Scombridae ■ Scorpididae ■ Sepiidae

■ Serranidae ■ Sillaginidae ■ Sparidae ■ Sphyraenidae ■ Syngnathidae

■ Terapontidae ■ Tetraodontidae ■ Urolophidae

Figure 4. Richness of species per site during autumn survey, by family

A Principal Coordinates Analysis scatter plot of the autumn 2018 fish community showed some grouping based on sites (Figure 5). A one-way PERMANOVA showed significant differences between all pairs of sites except between the Glenelg Tyre Reef and Seacliff Reef (Appendix C1). The species which most influenced the distribution of sites in the scatter plot included southern goatfish Upeneichthys vlamingii, brown-spotted wrasse Notolabrus parilus and blue swimmer crab Portunus armatus (Figure 5). SIMPER analysis showed that species making regular and relatively large contributions to the differences between sites included trevally Pseudocaranx spp., yellowtail scad Trachurus novaezelandiae, snapper Pagrus auratus, silverbelly Parequula melbournensis and long-finned pike Dinolestes lewini (Appendix C2).

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Transform: Fourth root Resemblance: S17 Bray Curtis similarity 60 Site T GTR SCR ...• ADP 40 ♦ PNR NTR T ■

♦ ■

20 ♦ Meuschenia hippocrepis

Notolabrus parilus Portunus armatus .... Tilodon sexfasciatus 0 ... ♦ ... Austrolabrus maculatus •

PCO2 (14.5% of total variation) variation) of total (14.5% PCO2 ♦ Upeneichthys vlamingii -20 T T • T • -40 -60 -40 -20 0 20 40 60 PCO1 (29.1% of total variation) Figure 5. Principal Coordinates Analysis scatter plot of fish communities recorded during autumn survey.

3.2 Spring 2018 fish communities A total of 1,803 ‘fish’ were recorded from 57 distinct taxa, which included four crab species (the same four as autumn) and the southern calamari Sepioteuthis australis. There were four cartilaginous fish species: the Port Jackson shark, southern fiddler ray, smooth stingray and the broadnose sevengill shark Notorynchus cepedianus. A bottlenose dolphin Tursiops truncatus was recorded at the Noarlunga tyre reef. The 47 species of ray-finned fishes were recorded from 27 families (Appendix A). The most specious families were Monacanthidae (leatherjackets) with nine species and Labridae (wrasses) with three species. The most abundant families were: Monacanthidae with 707 fish, including 558 Degen’s leatherjacket Thamnaconus degeni and 76 spiny-tail leatherjacket Acanthaluteres brownii; and Carangidae, with 234 fish, including 219 trevally. Abundances were highest at the ADP and NTR sites, due to the number of Monacanthids and Carangids, and at the latter site, Sillaginids (whitings) (Figure 6). Species richness was highest at the GTR site and lowest at the ADP site (Figure 7). Both abundance and richness were lower during the spring survey than the autumn survey in 2018.

15 ADP BRUV Surveys - 2018

120

100

80

60 Abundance

40

20

0 GTR SCR ADP PNR NTR

■ Arripidae ■ Carangidae ■ Chaetodontidae ■ Cheilodactylidae ■ Dasyatidae

■ Delphinidae ■ Dinolestidae ■ Enoplosidae ■ Gerreidae ■ Heterodontidae

■ Hexanchidae ■ Kyphosidae ■ Labridae ■ Loliginidae ■ Majidae

■ Monacanthidae ■ Moridae ■ Mullidae ■ Neosebastidae ■ Odacidae

■ Ostraciidae ■ Other ■ Paralichthyidae ■ Pempherididae ■ Pentacerotidae

■ Pinguipedidae ■ Platycephalidae ■ Plesiopidae ■ Polybiidae ■ Pomacentridae

■ Portunidae ■ Rhinobatidae ■ Scombridae ■ Scorpididae ■ Sepiidae

■ Serranidae ■ Sillaginidae ■ Sparidae ■ Sphyraenidae ■ Syngnathidae

■ Terapontidae ■ Tetraodontidae ■ Urolophidae

Figure 6. Abundance of species per site during spring survey, by family

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20

18

16

14

12

10 Richness 8

6

4

2

0 GTR SCR ADP PNR NTR

■ Arripidae ■ Carangidae ■ Chaetodontidae ■ Cheilodactylidae ■ Dasyatidae

■ Delphinidae ■ Dinolestidae ■ Enoplosidae ■ Gerreidae ■ Heterodontidae

■ Hexanchidae ■ Kyphosidae ■ Labridae ■ Loliginidae ■ Majidae

■ Monacanthidae ■ Moridae ■ Mullidae ■ Neosebastidae ■ Odacidae

■ Ostraciidae ■ Other ■ Paralichthyidae ■ Pempherididae ■ Pentacerotidae

■ Pinguipedidae ■ Platycephalidae ■ Plesiopidae ■ Polybiidae ■ Pomacentridae

■ Portunidae ■ Rhinobatidae ■ Scombridae ■ Scorpididae ■ Sepiidae

■ Serranidae ■ Sillaginidae ■ Sparidae ■ Sphyraenidae ■ Syngnathidae

■ Terapontidae ■ Tetraodontidae ■ Urolophidae

Figure 7. Richness of species per site during spring survey, by family

A Principal Coordinates Analysis scatter plot of the spring 2018 fish community showed some grouping based on sites (Figure 8). A one-way PERMANOVA showed significant differences between all pairs of sites except between the Adelaide Desalination Plant and Noarlunga Tyre Reef (Appendix C3). The species which most influenced the distribution of sites in the scatter plot included brown- spotted wrasse, sand crab Ovalipes australiensis and red swimmer crab Nectocarcinus integrifrons (Figure 8). SIMPER analysis showed that species making regular and relatively large contributions to the differences between sites included Degen’s leatherjacket Thamnaconus degeni, silverbelly Parequula melbournensis, Port Jackson shark Heterodontus portusjacksoni, red swimmer crab Nectocarcinus integrifrons, sand crab Ovalipes australiensis and southern goatfish Upeneichthys vlamingii (Appendix 4).

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Transform: Fourth root Resemblance: S17 Bray Curtis similarity 60 Site

♦ ______. __ T GTR • SCR .. ADP Notolabrus parilus PNR 40 ♦ ♦ Meuschenia hippocrepis ■ NTR Notolabrus tetricus Kyphosus sydneyanus Scorpis aequipinnis 20 Austrolabrus maculatus .. Thamnaconus degeni

Ovalipes australiensisI 0 ■ T ■ Parequula melbournensis T Omegophora armilla ♦ ♦ Scobinichthys granulatus PCO2 (17.5%of total variation)PCO2 Nectocarcinus integrifrons ■ .... -20 • T T •

-40 T -60 -40 -20 0 20 40 60 PCO1 (34.7% of total variation)

Figure 8. Principal Coordinates Analysis scatter plot of fish communities recorded during spring survey.

3.3 Comparisons of control and impact sites over time 3.3.1 Diversity measures The mean abundance, richness and Shannon-Weiner diversity index value for replicates (camera drops) of surveys in autumn and winter of both 2015 and 2018 are shown in Figure 9. Abundances at the impact site in each season in 2018 were about a third of their respective 2015 abundances but there was a smaller decrease between the years at the control sites. A PERMANOVA showed a significant difference between years (P<0.05), but not for control vs impact, season or any interaction between those factors (Appendix 5). Mean species richness at the impact site decreased across the four surveys while collectively increasing at the control sites for the 2015 and autumn 2018 surveys then decreasing to the lowest value for control sites during the spring 2018 survey. The Shannon-Weiner diversity index value was higher for 2018 than 2015 in both seasons and higher for autumn than spring in each year, but this pattern was consistent for both the control and impact sites. PERMANOVAs showed no significant difference between control and impact sites nor any significant interaction with year or season for either species richness or Shannon-Weiner diversity index (Appendix 6, 7).

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250

200

150

100 Abundance

50

0

18 16 14 12 10 8 Richness 6 4 2 0

2.5

2

1.5

1

Shannon-Weiner index 0.5

0 AUT SPR AUT SPR 2015 I 2018 ■ Control ■ Impact

Figure 9. Mean abundance, richness and Shannon-Weiner diversity index value for replicates of autumn and spring surveys in 2015 and 2018.

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3.3.2 Community structure A Principal Coordinates Analysis scatter plot of fish community data for the four surveys (autumn and spring in 2015 and 2018) suggests that there is no distinction between control and impact sites over time (Figure 10). A three-way PERMANOVA (use, year and season) showed a significant difference between years (P<0.05) but no significant difference between levels of use (control and impact), nor any interaction of use with year or season (Appendix C8). To test the sensitivity of this result to the inclusion or exclusion of replicates at the intake site, which is less likely to be impacted by brine discharge, the analysis was repeated after excluding the intake sites. The result was that the significance of the difference between years increased to the 0.01 level, but the use factor and its interactions with year or season remained insignificant (Appendix C9).

Transform: Fourth root Resemblance: S17 Bray Curtis similarity 40 Legend ... T ■ ♦ Impact ♦ T •Control lt'T .._ T T ♦ • 20 ~ Autumn 2015 ■ ... 'i T .... V Spring 2015 ... .. ♦ □ Autumn 2018 ♦.. _T T ◊ Spring 2018 ...,.... ♦ ♦ 0 ~ •• ■ T T T -20 T ♦

■ PCO2 (13.8% of total variation) variation) total of PCO2(13.8% -40 ...♦ -60 -60 -40 -20 0 20 40 60 PCO1 (23.4% of total variation)

Figure 10. Principal Coordinates Analysis scatter plot of fish communities recorded during autumn and spring of 2015 and 2018, showing control vs impact (colour) and survey (shape).

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3.4 Interannual differences The PERMANOVA tests described in Section 3.3.1 and Section 3.3.2 above showed significant differences in year for abundance and community structure. SIMPER analysis showed that Degen’s leatherjacket Thamnaconus degeni, snapper Pagrus auratus and yellowtail scad Trachurus novaezelandiae, which were less abundant in 2018 compared with 2015 and trevally Pseudocaranx spp., which were more abundant, collectively accounted for about 20% of the dissimilarity in community structure between those years, with the rest accounted for by small differences in a range of other species (Appendix C10). 3.5 Other factors influencing community structure Other factors have been suggested as important by Jacobs (2015a, b), including protection from fishing, which occurs at Port Noarlunga Reef (in a marine park Sanctuary Zone) and the ADP diffuser reef and intake structure (in the ADP exclusion zone); substrate, with the ADP and diffuser reef and intake structures being artificial reefs, and the location, with Seacliff Reef and Glenelg Tyre Reef to the north and the remaining sites to the south. The Principal Coordinates Analysis scatter plot of fish community data for the four surveys (autumn and spring in 2015 and 2018) is redisplayed showing protection, substrate and location factors (Figure 11). One-way PERMANOVA tests (with sites nested) for each of these factors showed that only the location factor was significant, also with a significant interaction with season and year (P < 0.05) (Appendix 11, 12 & 13).

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Transf orm: Fourth root Resemblance: S17 Bray Curtis similarity 40 Location South DNorth 20 on) i at i var l 0

-20 2 (13.8% of tota O

PC -40 ...... -60

40 Protection Protected Fished

) D 20 on i at ri a

l v 0

-20 13.8%of tota ( 2 O C

P -40 ...... -60 40 Substrate Artificial DNatural 20 on) i at i var l 0

-20 2 (13.8% of tota O

PC -40

-60 -60 -40 -20 0 20 40 60 PCO1 (23.4% of total variation) Figure 11. Principal Coordinates Analysis scatter plot of fish communities recorded during autumn and spring of 2015 and 2018, showing patterns related to location (south vs north), protection (fished and unfished), and substrate (natural vs artificial).

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4 Discussion The surveys by Jacobs (2015a, b) involved a significant redesign of the monitoring program, and form the baseline for this study. Surveys in both autumn and spring 2018 showed significant variability among the five sites surveyed. This is not unexpected, given the differences between reefs identified in Table 1, including significant differences between the northern and southern sites. Other differences include depth, relief and crevice size. Port Noarlunga reef extends to a maximum depth of about 8 metres, and sometimes shallower, along the outside of the reef and Seacliff Reef is about 12 metres deep, while the other sites are at least 20 metres deep. Port Noarlunga Reef has several metres of relief with large crevices; Seacliff Reef has only 0.5–1 metres of relief, and smaller crevices. The lower abundances at the northern sites (and some replicates of the ADP site), and significant interaction at community level between sites, year and season, may be partly because the visibility, although adequate, was lower on the day they were surveyed and fish are less likely to venture from shelter when visibility is low (Barrett and Buxton 2002). It is likely that the differences between the reefs are a complex interaction of these (and other) physical, environmental and species-specific behavioural factors. The key question is not whether there are differences between the sites, but whether there is any difference between the trajectories of the control sites collectively compared with the impact site. Analysis of the reef fish communities across seasonal surveys during 2015 (the baseline) and 2018 (the current study), each for two seasons, found no evidence that the ADP is having an impact on fish communities. There was no statistically significant difference between control and impact sites for diversity indices including abundance, species richness and Shannon-Weiner index, nor for multivariate analysis of fish communities. Changes in abundance and community structure between 2015 and 2018 were statistically significant, but changes at the control and impact sites were of similar magnitude. The lack of difference between control and impact sites was also apparent when the analysis of community structure was repeated without the replicates from near the intake structure, which is not likely to be exposed to elevated salinity. This is likely to mean that future survey designs can either focus on maintaining a 50 metre buffer between camera deployments, or can focus on deploying where impacts from brine discharge are most likely to occur. It is recommended that the next surveys, which are scheduled for 2021 (EPA 2017), occur at the same sites and at the same time, namely in or near the months of April and September. Consideration should be given whether the six replicates within the ADP site should be located such that they each interact with one of the six diffuser risers rather than the previous survey which located two of the replicates at the intake structure.

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5 References AdelaideAqua (2017), Scope of Work. Document provided to tenderers for 2018 BRUV surveys. Anderson MJ, Gorely RN & Clarke KR (2008), PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods. PRIMER-E. Plymouth, UK. Barrett NS, Buxton CD (2002), Examining underwater visual census techniques for the assessment of population structure and biodiversity in temperate coastal marine protected areas. Tasmanian Aquaculture and Fisheries Technical Report Series 11:1-114. Cappo M, Harvey E, Malcolm HA and Speare P (2003), Potential of video techniques to monitor diversity abundance and size of fish in studies of marine protected areas. In: Beumer JP, Grant A, Smith DC (eds) Aquatic protected areas - What works best and how do we know? Proc World Congr on Aquat Protected Areas Australian Society for fish Biology, North Beach, Western Australia, p 455- 464 Cappo M, Speare P and De'ath G (2004), Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reefal areas of the Great Barrier Reef Marine Park. Journal of Experimental Marine Biology and Ecology 302:123-152 Cappo M, De'ath G and Speare P (2007), Inter-reef vertebrate communities of the Great Barrier Reef Marine Park determined by baited remote underwater video stations. Marine Ecology Progress Series 350:209-221. Cheshire, A (2014), Assessment of the environmental performance of the Adelaide Desalination Plant based on a review of all documentation provided in compliance with EPA licencing requirements: June-2014. Report number 22 in a series prepared for AdelaideAqua Pty Ltd. Science to Manage Uncertainty Pty Ltd. Clarke KR and Gorley RN (2006), PRIMER v6: User Manual/Tutorial. PRIMER-E Ltd, Plymouth. Clarke KR and Warwick RM (2001), Change in Marine Communities: An approach to Statistical Analysis and Interpretation. Plymouth Marine Laboratory, Plymouth. DEW (2018a), EGIS data: Topography - Bathymetry - Navigation Chart, Department for Environment and Water, Adelaide, South Australia, viewed June 2018, http://location.sa.gov.au/lms/Reports/ReportMetadata.aspx?p_no=1121&pu=y&pa=dewnr. DEW (2018b), EGIS data: State Marine Benthic Habitats, viewed September 2018, http://location.sa.gov.au/lms/Reports/ReportMetadata.aspx?p_no=1233&pu=y&pa=dewnr. Department for Environment and Water, Adelaide, South Australia. Edgar, GJ (2008), Australian Marine Life – The Plants and Animals of Temperate Waters, 2nd Edition, New Holland, Sydney. EPA (2017), Licence No. 39143: ADELAIDEAQUA PTY LIMITED. Environment Protection Authority, Adelaide. Gomon M, Bray D and Kuiter R (2008), Fishes of Australia's southern coast. Reed New Holland, Sydney.

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Hutchins, B & Swainston, R (1986), Sea fishes of southern Australia: complete field guide for anglers and divers. Swainston Publishing, Perth. Jacobs (2015a), ADP 2015 Fish Survey: ADP Autumn BRUVS survey report. Prepared by Dr. G. Barbara for AdelaideAqua. Jacobs (2015b), ADP 2015 Fish assemblage survey: Spring BRUVS survey report. Prepared by Dr. G. Barbara for AdelaideAqua. Langlois, T, Williams, J, Monk, J, Bouchet, P, Currey, L, Goetze, J, Harasti, D, Huveneers, C, Ierodiaconou, D, Malcolm, H & Whitmore, S (2018), Marine sampling field manual for benthic stereo BRUVS (Baited Remote Underwater Videos). In: Field Manuals for Marine Sampling to Monitor Australian Waters, National Environmental Science Programme, Hobart, Tasmania. Miller D, Colella D, Holland S and Brock D (2017), Baited Remote Underwater Video Systems (BRUVS): Application and data management for the South Australian marine parks program, DEWNR Technical note 2017/20, Government of South Australia, Department of Environment, Water and Natural Resources, Adelaide SA Water (2008), Proposed Adelaide Desalination Plant Environmental Impact Statement. SA Water, Adelaide. SeaGIS (2018), EventMeasure User guide Updated: October 2018 (version 5.22). SeaGIS Pty Ltd, Bacchus Marsh, Victoria. Underwood AJ (1994), On beyond BACI: sampling designs that might reliably detect environmental disturbances. Ecological Applications 4:3-15. Willis TJ, Millar RB, Babcock RC (2000), Detection of spatial variability in relative density of fishes: comparison of visual census, angling, and baited underwater video. Marine Ecology Progress Series 198:249-260

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Appendix A – Species recorded during 2015 and 2018 surveys. Note: Numbers in column ‘Plate’ are references to Appendix B.

CAAB 2015 2018 Class Family Genus Species Code Plate Common name Aut Spr Aut Spr Mammalia Delphinidae Tursiops truncatus 41116019 1 Bottlenose dolphin 1

Actinopterygii Arripidae Arripis georgianus 37344001 Tommy rough 2 48 2

Arripis truttaceus 37344004 2 Western Australian salmon 8

Carangidae Pseudocaranx 37337924 3 Trevally 59 13 405 219 Trachurus novaezelandiae 37337003 4 Yellow-tail scad 236 179 194 15 Trachurus declivis 37337002 Jack mackerel 110

Chaetodontidae Chelmonops curiosus 37365066 5 Western talma 13 4 22 4 Cheilodactylidae Cheilodactylus nigripes 37377001 Magpie perch 11 12 13 7 Dactylophora nigricans 37377005 Dusky morwong 4 7 10 1 Dinolestidae Dinolestes lewini 37327041 6 Long-fin pike 74 39 55 53 Enoplosidae Enoplosus armatus 37366001 7 Old wife 7 6 14 6 Gerreidae Parequula melbournensis 37349001 8 Silverbelly 62 28 58 65 Kyphosidae Girella zebra 37361008 9 Zebra fish 20 11 16 24 Kyphosus sydneyanus 37361001 10 Silver drummer 88 124 96 26

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CAAB 2015 2018 Class Family Genus Species Code Plate Common name Aut Spr Aut Spr Actinopterygii Labridae 37384900 Wrasse 1 (cont.) Achoerodus gouldii 37384002 13 Western blue groper 1 Austrolabrus maculatus 37384025 11 Black-spotted wrasse 34 26 53 32

Notolabrus parilus 37384022 12 Brown-spotted wrasse 7 9 16 7 Notolabrus tetricus 37384003 Blue-throat wrasse 6 10 5 3 Pictilabrus laticlavius 37384020 Senator wrasse 3 3 Monacanthidae 37465903 Leatherjacket 8 2 Acanthaluteres 37465905 Leatherjacket 3 Acanthaluteres brownii 37465001 14 Spiny tailed leatherjacket 96 402 74 152 Acanthaluteres spilomelanurus 37465043 Bridled leatherjacket 1 Acanthaluteres vittiger 37465002 15 Toothbrush leatherjacket 29 14 26 15 Brachaluteres jacksonianus 37465025 Pygmy leatherjacket 4 1 2 Eubalichthys cyanoura 37465055 16 Blue-tail leatherjacket 1 Eubalichthys mosaicus 37465003 Mosaic leatherjacket 2 2 12 2 Meuschenia flavolineata 37465035 Yellow-stripe leatherjacket 1 1

Meuschenia freycineti 37465036 17 Six-spine leatherjacket 40 13 28 9

Meuschenia galii 37465040 Blue-lined leatherjacket 2

Meuschenia hippocrepis 37465004 18 Horseshoe leatherjacket 42 115 68 34 Scobinichthys granulatus 37465007 Rough leatherjacket 12 26 18 10 Thamnaconus degeni 37465037 19 Degen’s leatherjacket 1464 2317 7 558

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CAAB 2015 2018 Class Family Genus Species Code Plate Common name Aut Spr Aut Spr Actinopterygii Moridae Pseudophycis barbata 37224003 20 Bearded cod 4

(cont.) Mullidae Upeneichthys vlamingii 37355029 21 Southern goatfish 67 53 39 52 Neosebastidae Neosebastes 37287927 22 Gurnard perch 5 2 6

Odacidae Haletta semifasciata 37385009 23 Blue rock whiting 57 7 Heteroscarus acroptilus 37385010 Rainbow cale 6 2

Neoodax balteatus 37385005 Little rock whiting 2 8 Olisthops cyanomelas 37385001 Herring cale 2 Siphonognathus 37385905 Weed whiting 3 Siphonognathus attenuatus 37385004 Short-nose weed whiting 1

Siphonognathus beddomei 37385006 Pencil weed whiting 1

Ostraciidae Aracana aurita 37466017 24 Shaw's cowfish 11 6 1 7 Aracana ornata 37466001 Ornate cowfish 4 6 3 4 Aracana 37466903 Cowfish 1

Paralichthyidae 37460924 Flounder 1

Pempherididae 37357904 Bullseye 2

Parapriacanthus elongatus 37357002 Slender bullseye 251

Pempheris klunzingeri 37357003 25 Rough bullseye 66 1

Pempheris multiradiata 37357001 Common bullseye 43 2 Pentacerotidae Paristiopterus gallipavo 37367001 Yellow spotted Boarfish 2 Pentaceropsis recurvirostris 37367003 26 Long-snouted boarfish 2 1 2

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CAAB 2015 2018 Class Family Genus Species Code Plate Common name Aut Spr Aut Spr Actinopterygii Pinguipedidae Parapercis haackei 37390004 27 Wavy grubfish 36 16 24 22 (cont.) Platycephalidae Platycephalus 37296913 Flathead 1 1

Platycephalus bassensis 37296003 Sand flathead 1 2

Platycephalus speculator 37296037 28 Yank flathead 5 8 2 2

Plesiopidae Trachinops noarlungae 37316017 29 Yellow-headed hulafish 99 125 51 37 Pomacentridae Parma victoriae 37372006 Victorian scalyfin 5 2 5 4 Scombridae Scomber australasicus 37441001 30 Slimy mackerel 63

Scorpididae Scorpis aequipinnis 37361004 31 Sea sweep 24 36 16 Scorpis georgiana 37361015 32 Banded sweep 3 1 Tilodon sexfasciatus 37361003 33 Moonlighter 22 14 22 2 Serranidae Hypoplectrodes nigroruber 37311037 Banded sea perch 2 2

Sillaginidae Sillaginodes punctatus 37330001 34 King George whiting 12 81 Sillago 37330904 35 Whiting 136 17 17 126 Sillago bassensis 37330002 Southern school whiting 98 Sparidae Pagrus auratus 37353001 36 Snapper 283 324 145 50 Sphyraenidae Sphyraena novaehollandiae 37382002 Snook 4

Syngnathidae Phyllopteryx taeniolatus 37282932 Weedy seadragon 1

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CAAB 2015 2018 Class Family Genus Species Code Plate Common name Aut Spr Aut Spr Actinopterygii Terapontidae Pelates octolineatus 37321020 Western striped grunter 1 1

(cont.) Omegophora armilla 37467002 37 Ringed toadfish 4 6 1 6 Torquigener pleurogramma 37467030 Banded toadfish 1

Omegophora cyanopunctata 37467048 Blue-spotted pufferfish 1 (Unknown) 37000000 Unidentified schooling fish 100 13

Elasmobranchii Bathytoshia Dasyatis brevicaudata 37035001 Smooth stingray 1 4 1 1 Heterodontidae Heterodontus portusjacksoni 37007001 38 Port Jackson shark 28 16 47

Hexanchidae Notorynchus cepedianus 37005002 39 Broadnose sevengill shark 1 Rhinobatidae Trygonorrhina dumerilii 37027011 40 Southern fiddler ray 12 4 20 8 Urolophidae Trygonoptera mucosa 37038015 41 Western stingaree 2

Malacostraca Majidae Leptomithrax gaimardii 28880010 Giant spider crab 6 31 1 2 Naxia aurita 28880007 Smooth seaweed crab 2

Polybiidae Ovalipes australiensis 28911003 42 Sand crab 1 4 5 55 Portunidae Nectocarcinus integrifrons 28911010 43 Red swimmer crab 2 9 8 43 Portunus armatus 28911005 44 Blue swimmer crab 21 7

Cephalopoda Loliginidae Sepioteuthis australis 23617005 Southern calamari 6 3 1 2 Sepiidae Sepia apama 23607001 Giant cuttlefish 1 3

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Appendix B – Plates of species recorded

Plate 1. Bottlenose dolphin Tursiops truncatus Plate 2. Western Australian salmon Arripis truttaceus

Plate 3. Trevally Pseudocaranx spp. Plate 4. Yellow-tail scad Trachurus novaezelandiae

Plate 5. Western talma Chelmonops curiosus Plate 6. Long-fin pike Dinolestes lewini

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Plate 7. Old wife Enoplosus armatus Plate 8. Silverbelly Parequula melbournensis

Plate 9. Zebra fish Girella zebra Plate 10. Silver drummer Kyphosus sydneyanus

Plate 11. Black-spotted wrasse Austrolabrus Plate 12. Brown-spotted wrasse Notolabrus parilus maculatus

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Plate 13. Western blue groper Achoerodus gouldii Plate 14. Spiny tailed leatherjacket Acanthaluteres brownii

Plate 15. Toothbrush leatherjacket Acanthaluteres Plate 16. Blue-tail leatherjacket Eubalichthys cyanoura vittiger

Plate 17. Six-spine leatherjacket Meuschenia Plate 18. Horseshoe leatherjacket Meuschenia freycineti hippocrepis

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Plate 19. Degen’s leatherjacket Thamnaconus degeni Plate 20. Bearded cod Pseudophycis barbata

Plate 21. Southern goatfish Upeneichthys vlamingii Plate 22. Gurnard perch Neosebastes spp.

Plate 23. Blue rock whiting Haletta semifasciata Plate 24. Shaw's cowfish Aracana aurita

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Plate 25. Rough bullseye Pempheris klunzingeri Plate 26. Long-snouted boarfish Pentaceropsis recurvirostris

Plate 27. Wavy grubfish Parapercis haackei Plate 28. Yank flathead Platycephalus speculator

Plate 29. Yellow-headed hulafish Trachinops Plate 30. Slimy mackerel Scomber australasicus noarlungae

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Plate 31. Sea sweep Scorpis aequipinnis Plate 32. Banded sweep Scorpis georgiana

Plate 33. Moonlighter Tilodon sexfasciatus Plate 34. King George whiting Sillaginodes punctatus

Plate 35. Whiting Sillago spp. Plate 36. Snapper Pagrus auratus

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Plate 37. Ringed toadfish Omegophora armilla Plate 38. Port Jackson shark Heterodontus portusjacksoni

Plate 39. Broadnose sevengill shark Notorynchus Plate 40. Southern fiddler ray Trygonorrhina dumerilii cepedianus

Plate 41. Western stingaree Trygonoptera mucosa Plate 42. Sand crab Ovalipes australiensis

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Plate 43. Red swimmer crab Nectocarcinus Plate 44. Blue swimmer crab Portunus armatus integrifrons

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Appendix C – PRIMER/PERMANOVA+ outputs

1. Autumn 2018 comparison by site PERMANOVA Permutational MANOVA

Resemblance worksheet Name: Aut18 Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type I (sequential) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Site Si Fixed 5

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Si 4 26251 6562.9 4.0136 0.0001 9893 0.0001 Res 26 42514 1635.2 Total 30 68765

PAIR-WISE TESTS

Term 'Si'

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Unique Groups t P(perm) perms P(MC) ADP, GTR 1.6775 0.0092 1287 0.0304 ADP, NTR 1.8672 0.0056 2873 0.016 ADP, PNR 2.4857 0.0007 2891 0.0016 ADP, SCR 1.6847 0.0138 2919 0.0286 GTR, NTR 1.4296 0.0492 462 0.0917 GTR, PNR 2.2421 0.0023 462 0.0035 GTR, SCR 1.2988 0.12 462 0.1619 NTR, PNR 2.2586 0.0021 461 0.0014 NTR, SCR 2.2507 0.0032 462 0.0023 PNR, SCR 2.6165 0.0023 462 0.0025

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2. Autumn 2018 species contributing to differences between sites SIMPER Similarity Percentages - species contributions

One-Way Analysis

Data worksheet Name: Data3 Data type: Abundance Sample selection: 13-20,41-45,64-69,90-95,113-118 Variable selection: All

Parameters Resemblance: S17 Bray Curtis similarity Cut off for low contributions: 50.00%

Factor Groups Sample Site ADP_2018_AUT_1 ADP ADP_2018_AUT_2 ADP ADP_2018_AUT_4 ADP

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ADP_2018_AUT_5 ADP ADP_2018_AUT_6 ADP ADP_2018_AUT_7 ADP ADP_2018_AUT_8 ADP ADP_2018_AUT_9 ADP GTR_2018_AUT_1 GTR GTR_2018_AUT_2 GTR GTR_2018_AUT_3 GTR GTR_2018_AUT_4 GTR GTR_2018_AUT_5 GTR NTR_2018_AUT_1 NTR NTR_2018_AUT_2 NTR NTR_2018_AUT_3 NTR NTR_2018_AUT_4 NTR NTR_2018_AUT_5 NTR NTR_2018_AUT_6 NTR PNR_2018_AUT_1 PNR PNR_2018_AUT_2 PNR PNR_2018_AUT_3 PNR PNR_2018_AUT_4 PNR PNR_2018_AUT_5 PNR

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PNR_2018_AUT_6 PNR SCR_2018_AUT_1 SCR SCR_2018_AUT_2 SCR SCR_2018_AUT_3 SCR SCR_2018_AUT_4 SCR SCR_2018_AUT_5 SCR SCR_2018_AUT_6 SCR

Group ADP Average similarity: 39.30

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Pseudocaranx spp_ 2.08 13.44 1.61 34.20 34.20 Pagrus auratus 1.08 4.46 1.02 11.35 45.55 Portunus armatus 0.65 3.27 0.72 8.32 53.87

Group GTR Average similarity: 42.55

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Pagrus auratus 1.34 4.45 1.10 10.46 10.46

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Austrolabrus maculatus 1.03 3.76 1.12 8.83 19.29 Parequula melbournensis 1.04 3.68 1.12 8.65 27.94 Enoplosus armatus 0.95 3.60 1.10 8.45 36.39 Pseudocaranx spp_ 1.03 3.47 1.12 8.16 44.55 Upeneichthys vlamingii 0.94 3.13 1.09 7.37 51.92

Group NTR Average similarity: 49.66

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Trachurus novaezelandiae 1.99 7.89 3.11 15.89 15.89 Pagrus auratus 1.67 7.19 4.45 14.48 30.37 Pseudocaranx spp_ 1.75 5.36 1.16 10.80 41.17 Austrolabrus maculatus 1.13 3.50 1.34 7.05 48.22 Acanthaluteres brownii 1.02 3.17 1.34 6.38 54.60

Group PNR Average similarity: 51.62

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Meuschenia hippocrepis 1.77 8.80 7.86 17.05 17.05

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Scorpis aequipinnis 1.41 6.40 4.22 12.40 29.44 Kyphosus sydneyanus 1.36 5.65 4.96 10.95 40.40 Notolabrus parilus 1.03 5.13 7.28 9.94 50.34

Group SCR Average similarity: 41.50

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Parequula melbournensis 1.29 10.00 2.96 24.09 24.09 Portunus armatus 1.06 8.09 3.25 19.49 43.58 Upeneichthys vlamingii 1.03 5.97 1.20 14.38 57.96

Groups ADP & GTR Average dissimilarity = 69.04

Group ADP Group GTR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Pseudocaranx spp_ 2.08 1.03 4.23 1.83 6.13 6.13 Trachurus novaezelandiae 0.00 1.26 3.90 1.05 5.66 11.78 Parequula melbournensis 0.35 1.04 2.87 1.54 4.16 15.94 Acanthaluteres brownii 0.00 0.95 2.82 1.55 4.09 20.03

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Scobinichthys granulatus 0.00 0.94 2.72 1.84 3.94 23.97 Pagrus auratus 1.08 1.34 2.59 1.08 3.75 27.71 Acanthaluteres vittiger 0.00 0.88 2.54 1.03 3.68 31.39 Enoplosus armatus 0.25 0.95 2.54 1.37 3.67 35.07 Dinolestes lewini 0.87 0.86 2.46 1.10 3.57 38.63 Austrolabrus maculatus 0.59 1.03 2.35 1.19 3.41 42.04 Kyphosus sydneyanus 0.00 0.86 2.32 1.19 3.36 45.40 Upeneichthys vlamingii 0.66 0.94 1.96 0.97 2.84 48.24 Thamnaconus degeni 0.16 0.60 1.92 1.11 2.79 51.03

Groups ADP & NTR Average dissimilarity = 66.33

Group ADP Group NTR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Trachurus novaezelandiae 0.00 1.99 5.89 2.56 8.88 8.88 Acanthaluteres brownii 0.00 1.02 2.82 2.08 4.25 13.13 Scomber australasicus 0.00 1.04 2.62 0.97 3.95 17.08 Pseudocaranx spp_ 2.08 1.75 2.57 0.94 3.87 20.95 Austrolabrus maculatus 0.59 1.13 2.25 1.26 3.39 24.33 Parequula melbournensis 0.35 0.74 2.22 1.01 3.35 27.68

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Pagrus auratus 1.08 1.67 2.15 1.00 3.24 30.93 Dinolestes lewini 0.87 0.80 2.13 1.18 3.21 34.13 Eubalichthys mosaicus 0.25 0.90 2.05 1.43 3.09 37.22 Portunus armatus 0.65 0.00 2.01 1.21 3.03 40.25 Chelmonops curiosus 0.56 0.93 1.87 1.15 2.83 43.08 Tilodon sexfasciatus 0.27 0.74 1.82 1.23 2.74 45.82 Trygonorrhina dumerilii 0.63 0.00 1.82 1.22 2.74 48.56 Scobinichthys granulatus 0.00 0.67 1.78 1.35 2.68 51.24

Groups GTR & NTR Average dissimilarity = 59.30

Group GTR Group NTR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Trachurus novaezelandiae 1.26 1.99 2.87 1.09 4.84 4.84 Pseudocaranx spp_ 1.03 1.75 2.83 1.64 4.77 9.61 Scomber australasicus 0.28 1.04 2.37 1.04 3.99 13.60 Portunus armatus 0.86 0.00 2.11 1.69 3.56 17.16 Acanthaluteres vittiger 0.88 0.00 2.03 1.04 3.43 20.59 Chelmonops curiosus 0.20 0.93 2.03 1.47 3.42 24.01 Eubalichthys mosaicus 0.24 0.90 1.92 1.60 3.23 27.25

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Parequula melbournensis 1.04 0.74 1.89 1.17 3.19 30.43 Enoplosus armatus 0.95 0.36 1.88 1.22 3.17 33.61 Kyphosus sydneyanus 0.86 0.17 1.86 1.23 3.14 36.75 Dinolestes lewini 0.86 0.80 1.85 1.20 3.12 39.87 Cheilodactylus nigripes 0.20 0.70 1.68 1.11 2.84 42.70 Tilodon sexfasciatus 0.26 0.74 1.68 1.28 2.83 45.53 Pagrus auratus 1.34 1.67 1.47 0.86 2.48 48.01 Upeneichthys vlamingii 0.94 0.70 1.46 0.94 2.46 50.47

Groups ADP & PNR Average dissimilarity = 74.62

Group ADP Group PNR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Meuschenia hippocrepis 0.38 1.77 4.42 2.22 5.93 5.93 Pseudocaranx spp_ 2.08 0.93 4.25 1.78 5.69 11.62 Kyphosus sydneyanus 0.00 1.36 4.12 3.61 5.52 17.14 Scorpis aequipinnis 0.13 1.41 3.99 2.64 5.34 22.48 Notolabrus parilus 0.15 1.03 2.89 2.67 3.88 26.36 Tilodon sexfasciatus 0.27 0.92 2.33 1.44 3.13 29.48 Arripis truttaceus 0.00 0.75 2.24 1.30 3.01 32.49

48 ADP BRUV Surveys - 2018

Dinolestes lewini 0.87 0.50 2.24 1.21 3.01 35.50 Pagrus auratus 1.08 0.78 2.24 1.23 3.00 38.50 Austrolabrus maculatus 0.59 0.96 2.11 1.18 2.83 41.33 Portunus armatus 0.65 0.17 2.00 1.13 2.69 44.01 Acanthaluteres brownii 0.00 0.70 1.97 1.37 2.64 46.65 Meuschenia freycineti 0.56 0.92 1.96 1.11 2.63 49.28 Trygonorrhina dumerilii 0.63 0.00 1.94 1.23 2.60 51.88

Groups GTR & PNR Average dissimilarity = 70.29

Group GTR Group PNR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Meuschenia hippocrepis 0.24 1.77 4.18 2.40 5.95 5.95 Scorpis aequipinnis 0.20 1.41 3.31 2.11 4.71 10.66 Trachurus novaezelandiae 1.26 0.00 3.26 1.06 4.64 15.30 Enoplosus armatus 0.95 0.00 2.46 1.75 3.50 18.80 Pagrus auratus 1.34 0.78 2.33 1.36 3.32 22.12 Notolabrus parilus 0.20 1.03 2.32 1.86 3.30 25.42 Scobinichthys granulatus 0.94 0.00 2.30 1.86 3.27 28.68 Kyphosus sydneyanus 0.86 1.36 2.21 1.22 3.15 31.83

49 ADP BRUV Surveys - 2018

Parequula melbournensis 1.04 0.36 2.17 1.32 3.09 34.92 Tilodon sexfasciatus 0.26 0.92 2.15 1.56 3.06 37.99 Acanthaluteres vittiger 0.88 0.00 2.14 1.04 3.05 41.04 Portunus armatus 0.86 0.17 2.01 1.41 2.87 43.90 Arripis truttaceus 0.00 0.75 1.93 1.27 2.75 46.65 Trachinops noarlungae 0.34 0.60 1.92 0.83 2.73 49.39 Dinolestes lewini 0.86 0.50 1.92 1.28 2.73 52.12

Groups NTR & PNR Average dissimilarity = 64.41

Group NTR Group PNR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Trachurus novaezelandiae 1.99 0.00 4.95 2.75 7.69 7.69 Meuschenia hippocrepis 0.33 1.77 3.55 2.42 5.51 13.21 Pseudocaranx spp_ 1.75 0.93 2.93 1.62 4.55 17.76 Kyphosus sydneyanus 0.17 1.36 2.84 2.18 4.41 22.17 Scorpis aequipinnis 0.40 1.41 2.61 1.65 4.05 26.22 Scomber australasicus 1.04 0.00 2.26 0.97 3.51 29.73 Pagrus auratus 1.67 0.78 2.21 1.39 3.43 33.17 Eubalichthys mosaicus 0.90 0.00 2.08 2.10 3.23 36.39

50 ADP BRUV Surveys - 2018

Parequula melbournensis 0.74 0.36 1.77 1.05 2.75 39.14 Trachinops noarlungae 0.32 0.60 1.74 0.81 2.70 41.85 Arripis truttaceus 0.17 0.75 1.68 1.22 2.60 44.45 Dinolestes lewini 0.80 0.50 1.53 1.12 2.37 46.82 Scobinichthys granulatus 0.67 0.00 1.52 1.36 2.36 49.18 Chelmonops curiosus 0.93 0.50 1.48 1.09 2.30 51.48

Groups ADP & SCR Average dissimilarity = 68.28

Group ADP Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Pseudocaranx spp_ 2.08 0.53 6.94 1.79 10.17 10.17 Parequula melbournensis 0.35 1.29 4.16 2.16 6.09 16.26 Pagrus auratus 1.08 0.73 3.17 1.17 4.64 20.90 Dinolestes lewini 0.87 0.22 3.02 1.14 4.43 25.33 Scobinichthys granulatus 0.00 0.73 2.67 1.24 3.91 29.24 Upeneichthys vlamingii 0.66 1.03 2.46 1.05 3.61 32.84 Heterodontus portusjacksoni 0.58 0.40 2.44 0.99 3.57 36.41 Meuschenia freycineti 0.56 0.86 2.35 1.08 3.44 39.86 Austrolabrus maculatus 0.59 0.39 2.22 1.04 3.25 43.10

51 ADP BRUV Surveys - 2018

Sillago spp_ 0.54 0.00 2.21 0.72 3.23 46.33 Chelmonops curiosus 0.56 0.20 1.96 0.99 2.87 49.21 Pempheris klunzingeri 0.46 0.26 1.83 0.64 2.68 51.89

Groups GTR & SCR Average dissimilarity = 61.70

Group GTR Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Trachurus novaezelandiae 1.26 0.20 3.89 1.08 6.31 6.31 Pagrus auratus 1.34 0.73 3.05 1.15 4.94 11.25 Enoplosus armatus 0.95 0.17 2.82 1.40 4.58 15.83 Austrolabrus maculatus 1.03 0.39 2.70 1.25 4.37 20.20 Acanthaluteres vittiger 0.88 0.44 2.61 1.00 4.24 24.43 Acanthaluteres brownii 0.95 0.45 2.55 1.28 4.13 28.56 Pseudocaranx spp_ 1.03 0.53 2.40 1.13 3.89 32.46 Dinolestes lewini 0.86 0.22 2.34 1.10 3.79 36.25 Kyphosus sydneyanus 0.86 0.17 2.32 1.16 3.76 40.01 Meuschenia freycineti 0.44 0.86 1.97 1.11 3.20 43.21 Trygonorrhina dumerilii 0.20 0.67 1.93 1.07 3.12 46.33 Scobinichthys granulatus 0.94 0.73 1.80 0.91 2.91 49.24

52 ADP BRUV Surveys - 2018

Thamnaconus degeni 0.60 0.17 1.79 1.01 2.90 52.14

Groups NTR & SCR Average dissimilarity = 71.16

Group NTR Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Trachurus novaezelandiae 1.99 0.20 5.39 1.95 7.57 7.57 Pseudocaranx spp_ 1.75 0.53 4.14 1.48 5.81 13.38 Portunus armatus 0.00 1.06 3.12 3.99 4.38 17.77 Pagrus auratus 1.67 0.73 2.96 1.22 4.16 21.92 Scomber australasicus 1.04 0.00 2.65 0.95 3.72 25.65 Austrolabrus maculatus 1.13 0.39 2.59 1.41 3.64 29.29 Chelmonops curiosus 0.93 0.20 2.54 1.60 3.57 32.86 Eubalichthys mosaicus 0.90 0.00 2.46 2.02 3.46 36.32 Acanthaluteres brownii 1.02 0.45 2.42 1.52 3.40 39.72 Parequula melbournensis 0.74 1.29 2.24 1.17 3.15 42.87 Dinolestes lewini 0.80 0.22 2.09 1.25 2.93 45.80 Cheilodactylus nigripes 0.70 0.17 2.05 1.13 2.88 48.68 Trygonorrhina dumerilii 0.00 0.67 1.92 1.27 2.69 51.37

53 ADP BRUV Surveys - 2018

Groups PNR & SCR Average dissimilarity = 75.52

Group PNR Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Meuschenia hippocrepis 1.77 0.33 4.68 2.21 6.20 6.20 Scorpis aequipinnis 1.41 0.00 4.41 3.52 5.84 12.04 Kyphosus sydneyanus 1.36 0.17 3.86 2.14 5.12 17.16 Parequula melbournensis 0.36 1.29 3.09 1.52 4.09 21.25 Portunus armatus 0.17 1.06 2.88 2.01 3.82 25.07 Tilodon sexfasciatus 0.92 0.17 2.45 1.52 3.25 28.31 Pseudocaranx spp_ 0.93 0.53 2.45 1.11 3.24 31.56 Notolabrus parilus 1.03 0.36 2.43 1.47 3.21 34.77 Austrolabrus maculatus 0.96 0.39 2.41 1.29 3.19 37.96 Upeneichthys vlamingii 0.55 1.03 2.29 1.13 3.03 41.00 Pagrus auratus 0.78 0.73 2.28 1.25 3.02 44.02 Arripis truttaceus 0.75 0.00 2.28 1.27 3.02 47.04 Parapriacanthus elongatus 0.53 0.58 2.24 0.61 2.97 50.01

54 ADP BRUV Surveys - 2018

3. Spring 2018 comparison by site PERMANOVA Permutational MANOVA

Resemblance worksheet Name: Spr18 Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type I (sequential) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Site Si Fixed 5

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Si 4 39693 9923.3 4.6898 0.0001 9894 0.0001 Res 28 59246 2115.9 Total 32 98939

PAIR-WISE TESTS

Term 'Si'

Unique

55 ADP BRUV Surveys - 2018

Groups t P(perm) perms P(MC) ADP, GTR 2.7954 0.0003 4319 0.0002 ADP, NTR 1.1013 0.2671 8128 0.291 ADP, PNR 1.6483 0.0271 1982 0.0371 ADP, SCR 2.1128 0.0017 1987 0.0053 GTR, NTR 3.3254 0.0011 2873 0.0001 GTR, PNR 2.7585 0.0019 462 0.0018 GTR, SCR 1.514 0.0387 462 0.0782 NTR, PNR 1.9129 0.0153 1285 0.0192 NTR, SCR 2.5567 0.001 1287 0.0013 PNR, SCR 1.8078 0.017 126 0.0276

56 ADP BRUV Surveys - 2018

4. Spring 2018 species contributing to differences between sites SIMPER Similarity Percentages - species contributions

One-Way Analysis

Data worksheet Name: Data3 Data type: Abundance Sample selection: 21-29,46-51,70-77,96-100,119-123 Variable selection: All

Parameters Resemblance: S17 Bray Curtis similarity Cut off for low contributions: 50.00%

Factor Groups Sample Site ADP_2018_SPR_10 ADP ADP_2018_SPR_11 ADP ADP_2018_SPR_12 ADP

57 ADP BRUV Surveys - 2018

ADP_2018_SPR_4 ADP ADP_2018_SPR_5 ADP ADP_2018_SPR_6 ADP ADP_2018_SPR_7 ADP ADP_2018_SPR_8 ADP ADP_2018_SPR_9 ADP GTR_2018_SPR_1 GTR GTR_2018_SPR_2 GTR GTR_2018_SPR_3 GTR GTR_2018_SPR_4 GTR GTR_2018_SPR_5 GTR GTR_2018_SPR_6 GTR NTR_2018_SPR_10 NTR NTR_2018_SPR_11 NTR NTR_2018_SPR_12 NTR NTR_2018_SPR_3 NTR NTR_2018_SPR_4 NTR NTR_2018_SPR_7 NTR NTR_2018_SPR_8 NTR NTR_2018_SPR_9 NTR PNR_2018_SPR_1 PNR

58 ADP BRUV Surveys - 2018

PNR_2018_SPR_2 PNR PNR_2018_SPR_3 PNR PNR_2018_SPR_4 PNR PNR_2018_SPR_5 PNR SCR_2018_SPR_1 SCR SCR_2018_SPR_2 SCR SCR_2018_SPR_3 SCR SCR_2018_SPR_5 SCR SCR_2018_SPR_6 SCR

Group ADP Average similarity: 30.89

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Thamnaconus degeni 1.90 11.72 1.10 37.93 37.93 Ovalipes australiensis 0.97 6.06 0.83 19.63 57.56

Group GTR Average similarity: 57.14

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.%

59 ADP BRUV Surveys - 2018

Nectocarcinus integrifrons 1.52 10.38 4.79 18.17 18.17 Parequula melbournensis 1.39 9.26 4.71 16.21 34.38 Upeneichthys vlamingii 1.24 8.19 5.17 14.34 48.72 Sillaginodes punctatus 1.17 5.55 1.33 9.71 58.43

Group NTR Average similarity: 44.52

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Thamnaconus degeni 1.87 12.43 1.36 27.92 27.92 Heterodontus portusjacksoni 0.95 6.56 1.58 14.74 42.65 Ovalipes australiensis 1.02 6.23 1.03 14.00 56.65

Group PNR Average similarity: 30.70

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Heterodontus portusjacksoni 1.26 10.06 0.97 32.77 32.77 Meuschenia hippocrepis 1.03 3.11 0.62 10.13 42.90 Scorpis aequipinnis 0.90 2.91 0.61 9.47 52.37

60 ADP BRUV Surveys - 2018

Group SCR Average similarity: 30.87

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Nectocarcinus integrifrons 0.88 6.67 1.14 21.61 21.61 Scobinichthys granulatus 0.86 6.49 1.13 21.02 42.63 Meuschenia freycineti 0.60 2.98 0.62 9.66 52.28

Groups ADP & GTR Average dissimilarity = 87.04

Group ADP Group GTR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.90 0.17 7.71 1.48 8.86 8.86 Nectocarcinus integrifrons 0.13 1.52 6.11 2.43 7.02 15.88 Parequula melbournensis 0.29 1.39 4.94 1.77 5.67 21.55 Sillaginodes punctatus 0.00 1.17 4.78 1.97 5.49 27.04 Ovalipes australiensis 0.97 0.00 4.19 1.34 4.82 31.86 Upeneichthys vlamingii 0.35 1.24 4.15 1.40 4.77 36.63 Acanthaluteres brownii 0.15 0.95 3.63 1.30 4.17 40.80 Acanthaluteres vittiger 0.24 1.03 3.61 1.52 4.15 44.94

61 ADP BRUV Surveys - 2018

Heterodontus portusjacksoni 0.84 0.00 3.56 1.70 4.09 49.03 Parapercis haackei 0.13 0.92 3.51 1.76 4.03 53.06

Groups ADP & NTR Average dissimilarity = 64.26

Group ADP Group NTR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.90 1.87 5.41 1.13 8.42 8.42 Pseudocaranx spp_ 0.60 1.06 5.26 1.24 8.19 16.61 Sillago bassensis 0.16 1.14 5.23 1.08 8.13 24.74 Parequula melbournensis 0.29 0.91 3.68 1.32 5.73 30.47 Pagrus auratus 0.78 0.27 3.52 1.03 5.48 35.95 Sillago spp_ 0.11 0.67 3.36 0.61 5.22 41.17 Ovalipes australiensis 0.97 1.02 3.11 0.97 4.84 46.02 Upeneichthys vlamingii 0.35 0.55 2.46 1.01 3.83 49.85 Portunus armatus 0.11 0.50 2.44 0.95 3.79 53.65

Groups GTR & NTR Average dissimilarity = 81.68

62 ADP BRUV Surveys - 2018

Group GTR Group NTR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 0.17 1.87 7.10 1.77 8.70 8.70 Nectocarcinus integrifrons 1.52 0.00 5.90 3.88 7.22 15.92 Sillago bassensis 0.00 1.14 4.41 1.07 5.40 21.31 Sillaginodes punctatus 1.17 0.00 4.27 1.98 5.23 26.54 Ovalipes australiensis 0.00 1.02 4.21 1.56 5.16 31.70 Acanthaluteres vittiger 1.03 0.00 3.75 2.08 4.59 36.29 Heterodontus portusjacksoni 0.00 0.95 3.73 2.21 4.57 40.86 Pseudocaranx spp_ 0.25 1.06 3.73 1.19 4.56 45.42 Parapercis haackei 0.92 0.00 3.32 2.07 4.06 49.48 Acanthaluteres brownii 0.95 0.31 3.12 1.23 3.82 53.30

Groups ADP & PNR Average dissimilarity = 81.33

Group ADP Group PNR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.90 0.00 9.61 1.41 11.81 11.81 Meuschenia hippocrepis 0.22 1.03 4.36 1.24 5.37 17.18 Heterodontus portusjacksoni 0.84 1.26 4.28 1.07 5.26 22.44

63 ADP BRUV Surveys - 2018

Pseudocaranx spp_ 0.60 0.62 4.15 0.81 5.10 27.53 Ovalipes australiensis 0.97 0.48 4.14 1.18 5.09 32.62 Pagrus auratus 0.78 0.48 4.05 1.07 4.98 37.60 Scorpis aequipinnis 0.00 0.90 3.91 1.14 4.81 42.41 Sillago bassensis 0.16 0.54 3.70 0.77 4.55 46.96 Kyphosus sydneyanus 0.00 0.76 3.42 1.07 4.21 51.16

Groups GTR & PNR Average dissimilarity = 88.25

Group GTR Group PNR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Heterodontus portusjacksoni 0.00 1.26 5.69 1.58 6.45 6.45 Upeneichthys vlamingii 1.24 0.00 5.33 2.55 6.04 12.49 Nectocarcinus integrifrons 1.52 0.24 5.32 1.96 6.02 18.51 Parequula melbournensis 1.39 0.20 4.83 2.25 5.47 23.98 Sillaginodes punctatus 1.17 0.00 4.63 1.86 5.24 29.22 Acanthaluteres vittiger 1.03 0.00 4.07 1.94 4.61 33.83 Meuschenia hippocrepis 0.00 1.03 3.66 1.17 4.15 37.98 Parapercis haackei 0.92 0.00 3.59 1.94 4.07 42.06 Acanthaluteres brownii 0.95 0.40 3.29 1.21 3.73 45.78

64 ADP BRUV Surveys - 2018

Scorpis aequipinnis 0.00 0.90 3.25 1.16 3.68 49.46 Austrolabrus maculatus 0.87 0.66 2.89 1.10 3.27 52.73

Groups NTR & PNR Average dissimilarity = 76.60

Group NTR Group PNR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.87 0.00 8.99 1.76 11.74 11.74 Sillago bassensis 1.14 0.54 4.70 1.20 6.14 17.87 Pseudocaranx spp_ 1.06 0.62 4.26 1.17 5.56 23.43 Meuschenia hippocrepis 0.25 1.03 3.82 1.24 4.99 28.42 Ovalipes australiensis 1.02 0.48 3.48 1.32 4.54 32.95 Parequula melbournensis 0.91 0.20 3.46 1.39 4.51 37.46 Scorpis aequipinnis 0.00 0.90 3.45 1.16 4.50 41.96 Heterodontus portusjacksoni 0.95 1.26 3.10 1.72 4.05 46.01 Kyphosus sydneyanus 0.00 0.76 3.00 1.10 3.92 49.93 Sillago spp_ 0.67 0.00 2.99 0.53 3.91 53.83

Groups ADP & SCR Average dissimilarity = 89.32

65 ADP BRUV Surveys - 2018

Group ADP Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.90 0.00 9.06 1.44 10.14 10.14 Acanthaluteres brownii 0.15 1.01 4.93 0.87 5.52 15.67 Ovalipes australiensis 0.97 0.00 4.72 1.29 5.29 20.95 Scobinichthys granulatus 0.00 0.86 4.70 1.73 5.27 26.22 Nectocarcinus integrifrons 0.13 0.88 4.37 1.52 4.90 31.12 Upeneichthys vlamingii 0.35 0.95 4.20 1.07 4.70 35.82 Parequula melbournensis 0.29 0.90 4.04 1.03 4.52 40.34 Pagrus auratus 0.78 0.20 3.51 0.90 3.93 44.27 Heterodontus portusjacksoni 0.84 0.20 3.42 1.31 3.83 48.11 Pseudocaranx spp_ 0.60 0.42 3.40 0.65 3.81 51.91

Groups GTR & SCR Average dissimilarity = 63.64

Group GTR Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Acanthaluteres brownii 0.95 1.01 4.00 1.08 6.28 6.28 Acanthaluteres vittiger 1.03 0.00 3.89 1.97 6.11 12.39

66 ADP BRUV Surveys - 2018

Sillaginodes punctatus 1.17 0.48 3.62 1.32 5.69 18.08 Upeneichthys vlamingii 1.24 0.95 3.52 1.39 5.53 23.62 Parequula melbournensis 1.39 0.90 3.43 1.18 5.39 29.01 Austrolabrus maculatus 0.87 0.20 3.11 1.19 4.89 33.90 Parapercis haackei 0.92 0.20 2.96 1.47 4.66 38.56 Dinolestes lewini 0.33 0.82 2.68 1.12 4.21 42.76 Meuschenia freycineti 0.17 0.60 2.41 1.07 3.78 46.54 Nectocarcinus integrifrons 1.52 0.88 2.32 1.85 3.65 50.19

Groups NTR & SCR Average dissimilarity = 87.19

Group NTR Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.87 0.00 8.50 1.80 9.75 9.75 Sillago bassensis 1.14 0.00 4.90 1.04 5.62 15.38 Ovalipes australiensis 1.02 0.00 4.72 1.50 5.41 20.79 Pseudocaranx spp_ 1.06 0.42 4.28 1.20 4.91 25.70 Acanthaluteres brownii 0.31 1.01 4.24 0.91 4.86 30.56 Nectocarcinus integrifrons 0.00 0.88 4.10 1.81 4.70 35.26 Scobinichthys granulatus 0.00 0.86 4.04 1.79 4.64 39.90

67 ADP BRUV Surveys - 2018

Upeneichthys vlamingii 0.55 0.95 3.66 1.16 4.20 44.10 Parequula melbournensis 0.91 0.90 3.51 1.25 4.02 48.12 Heterodontus portusjacksoni 0.95 0.20 3.34 1.52 3.83 51.94

Groups PNR & SCR Average dissimilarity = 86.47

Group PNR Group SCR Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Heterodontus portusjacksoni 1.26 0.20 5.66 1.48 6.55 6.55 Acanthaluteres brownii 0.40 1.01 4.63 0.85 5.35 11.90 Scobinichthys granulatus 0.00 0.86 4.54 1.64 5.25 17.15 Upeneichthys vlamingii 0.00 0.95 4.10 0.96 4.74 21.90 Meuschenia hippocrepis 1.03 0.00 4.05 1.14 4.68 26.58 Parequula melbournensis 0.20 0.90 3.88 1.06 4.49 31.07 Nectocarcinus integrifrons 0.24 0.88 3.78 1.33 4.37 35.44 Scorpis aequipinnis 0.90 0.00 3.60 1.12 4.16 39.60 Dinolestes lewini 0.00 0.82 3.28 1.11 3.79 43.39 Sillago bassensis 0.54 0.00 3.19 0.71 3.68 47.08 Kyphosus sydneyanus 0.76 0.20 3.08 1.05 3.57 50.64

68 ADP BRUV Surveys - 2018

5. Abundance PERMANOVA Permutational MANOVA

Resemblance worksheet Name: abundance Data type: Distance Selection: All Resemblance: D1 Euclidean distance

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Use Us Fixed 2 Site Si Random 5 Year Ye Random 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Us 1 48042 48042 0.96298 0.5209 9958 0.5074 Ye 1 1.4527E5 1.4527E5 5.4738 0.0495 9968 0.0929 Se 1 99.537 99.537 0.66684 0.6799 9962 0.6191 Si(Us) 3 1.5898E5 52993 1.6476 0.1986 9950 0.2783 UsxYe 1 35756 35756 1.1444 0.4285 9971 0.3976 UsxSe 1 2218.2 2218.2 0.45651 0.8011 9953 0.7642 YexSe 1 1473 1473 0.14551 0.6999 9816 0.8258

69 ADP BRUV Surveys - 2018

Si(Us)xYe 3 70817 23606 2.1726 0.2185 9964 0.2649 Si(Us)xSe 3 45455 15152 1.3945 0.366 9970 0.4019 UsxYexSe 1 14886 14886 1.2103 0.3475 9832 0.345 Si(Us)xYexSe 3 32595 10865 4.8108 0.0033 9949 0.0046 Res 103 2.3262E5 2258.5 Total 122 7.374E5

6. Richness PERMANOVA Permutational MANOVA

Resemblance worksheet Name: richness Data type: Distance Selection: All Resemblance: D1 Euclidean distance

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Use Us Fixed 2 Site Si Random 5 Year Ye Random 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC)

70 ADP BRUV Surveys - 2018

Us 1 68.94 68.94 0.69512 0.6614 9961 0.6178 Ye 1 32.274 32.274 0.45969 0.738 9968 0.7516 Se 1 109.83 109.83 1.241 0.4234 9958 0.5012 Si(Us) 3 239.85 79.951 2.6636 0.1363 9952 0.1706 UsxYe 1 80.298 80.298 1.6984 0.3171 9951 0.3043 UsxSe 1 2.1109 2.1109 0.96512 0.5142 9968 0.5749 YexSe 1 107.41 107.41 3.1679 0.1703 9847 0.1754 Si(Us)xYe 3 100.12 33.374 1.109 0.472 9965 0.4708 Si(Us)xSe 3 23.819 7.9398 0.26385 0.8495 9960 0.8485 UsxYexSe 1 29.13 29.13 0.92406 0.4118 9851 0.4329 Si(Us)xYexSe 3 90.276 30.092 1.5428 0.2125 9970 0.2098 Res 103 2009 19.505 Total 122 3081.7

7. Shannon-Weiner diversity index PERMANOVA Permutational MANOVA

Resemblance worksheet Name: shannon Data type: Distance Selection: All Resemblance: D1 Euclidean distance

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Use Us Fixed 2

71 ADP BRUV Surveys - 2018

Site Si Random 5 Year Ye Random 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Us 1 4.8151 4.8151 1.5965 0.2828 9966 0.3181 Ye 1 1.3317 1.3317 1.7563 0.3185 9972 0.3078 Se 1 0.84652 0.84652 0.92945 0.5235 9966 0.5118 Si(Us) 3 10.378 3.4594 1.7232 0.2629 9965 0.2607 UsxYe 1 0.12096 0.12096 0.63877 0.6549 9971 0.6588 UsxSe 1 5.4244E-4 5.4244E-4 0.38952 0.7918 9956 0.7747 YexSe 1 3.6979E-2 3.6979E-2 0.10024 0.7751 9851 0.9645 Si(Us)xYe 3 2.8795 0.95983 1.6183 0.3479 9961 0.3552 Si(Us)xSe 3 4.1755 1.3918 2.3467 0.2519 9961 0.2471 UsxYexSe 1 0.15306 0.15306 0.26906 0.6397 9839 0.7185 Si(Us)xYexSe 3 1.7793 0.5931 2.9579 0.0351 9951 0.0344 Res 103 20.653 0.20051 Total 122 48.56

72 ADP BRUV Surveys - 2018

8. All surveys (2015 and 2018) comparison by use, year and season PERMANOVA Permutational MANOVA

Resemblance worksheet Name: BothYears Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Use Us Fixed 2 Site Si Random 5 Year Ye Fixed 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms Us 1 17981 17981 0.93521 0.5444 9856 Ye 1 17775 17775 2.4003 0.0151 9922 Se 1 13843 13843 1.9894 0.0662 9887 Si(Us) 3 60817 20272 3.3164 0.0024 9804 UsxYe 1 4214 4214 1.533 0.1308 9932 UsxSe 1 3301.93301.9 0.50193 0.8698 9888

73 ADP BRUV Surveys - 2018

YexSe 1 5512.25512.2 0.86724 0.5524 9928 Si(Us)xYe 3 120684022.7 0.70127 0.8099 9909 Si(Us)xSe 3 183386112.7 3.818 0.0001 9886 UsxYexSe 1 2423.12423.1 0.40272 0.9379 9934 Si(Us)xYexSe 3 172095736.3 3.5828 0.0001 9902 Res 103 1.6491E5 1601 Total 122 3.4568E5

74 ADP BRUV Surveys - 2018

9. All surveys by use, year and season excluding replicates from near intake structure

PERMANOVA Permutational MANOVA

Resemblance worksheet Name: WithoutIntake Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Use Us Fixed 2 Site Si Random 5 Year Ye Random 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Us 1 15562 15562 0.83719 0.7342 9892 0.6824 Ye 1 15734 15734 2.7783 0.0036 9919 0.0102 Se 1 11749 11749 1.7834 0.0699 9925 0.0755 Si(Us) 3 60817 20272 2.5661 0.0007 9910 0.0009 UsxYe 1 4107.54107.5 1.6558 0.0967 9932 0.079

75 ADP BRUV Surveys - 2018

UsxSe 1 3081.93081.9 1.0981 0.4102 9933 0.3871 YexSe 1 3733 3733 0.65762 0.7422 9943 0.741 Si(Us)xYe 3 120684022.7 0.70127 0.8178 9923 0.8182 Si(Us)xSe 3 183386112.7 1.0656 0.435 9925 0.4316 UsxYexSe 1 1930.41930.4 0.34006 0.9664 9920 0.957 Si(Us)xYexSe 3 172095736.3 3.7761 0.0001 9877 0.0001 Res 97 1.4735E5 1519.1 Total 116 3.2117E5

76 ADP BRUV Surveys - 2018

10. Species contributing to differences between years SIMPER Similarity Percentages - species contributions

One-Way Analysis

Data worksheet Name: Data3 Data type: Abundance Sample selection: All Variable selection: All

Parameters Resemblance: S17 Bray Curtis similarity Cut off for low contributions: 50.00%

Group 2015 Average similarity: 31.45

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.%

77 ADP BRUV Surveys - 2018

Thamnaconus degeni 1.72 5.93 0.63 18.87 18.87 Pagrus auratus 1.22 4.25 0.88 13.51 32.38 Upeneichthys vlamingii 0.88 3.67 1.03 11.66 44.04 Parequula melbournensis 0.75 2.73 0.75 8.67 52.70

Group 2018 Average similarity: 25.18

Species Av.Abund Av.Sim Sim/SD Contrib% Cum.% Pseudocaranx spp_ 0.96 2.53 0.55 10.06 10.06 Parequula melbournensis 0.72 2.48 0.60 9.83 19.89 Upeneichthys vlamingii 0.68 2.26 0.65 8.97 28.87 Pagrus auratus 0.73 1.93 0.54 7.66 36.53 Heterodontus portusjacksoni 0.51 1.77 0.45 7.01 43.54 Austrolabrus maculatus 0.62 1.52 0.55 6.02 49.56 Meuschenia freycineti 0.47 1.28 0.49 5.10 54.66

Groups 2015 & 2018 Average dissimilarity = 75.25

78 ADP BRUV Surveys - 2018

Group 2015 Group 2018 Species Av.Abund Av.Abund Av.Diss Diss/SD Contrib% Cum.% Thamnaconus degeni 1.72 0.60 6.03 1.07 8.02 8.02 Pagrus auratus 1.22 0.73 3.62 1.17 4.81 12.82 Pseudocaranx spp_ 0.41 0.96 3.30 0.97 4.38 17.20 Trachurus novaezelandiae 0.71 0.33 2.63 0.84 3.49 20.69 Parequula melbournensis 0.75 0.72 2.52 1.03 3.35 24.05 Acanthaluteres brownii 0.60 0.54 2.48 0.93 3.30 27.35 Upeneichthys vlamingii 0.88 0.68 2.42 1.03 3.22 30.56 Meuschenia hippocrepis 0.52 0.44 2.26 0.86 3.00 33.56 Austrolabrus maculatus 0.56 0.62 2.23 1.03 2.96 36.52 Heterodontus portusjacksoni 0.30 0.51 2.15 0.86 2.85 39.37 Kyphosus sydneyanus 0.48 0.34 1.99 0.85 2.64 42.01 Meuschenia freycineti 0.46 0.47 1.95 0.98 2.59 44.60 Dinolestes lewini 0.41 0.47 1.94 0.90 2.58 47.18 Scobinichthys granulatus 0.40 0.32 1.72 0.85 2.29 49.47 Acanthaluteres vittiger 0.38 0.24 1.65 0.74 2.19 51.65

79 ADP BRUV Surveys - 2018

11. Location (north vs south) PERMANOVA Permutational MANOVA

Resemblance worksheet Name: BothYears Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Location2 Lo Fixed 2 Site Si Random 5 Year Ye Random 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Lo 1 36570 36570 1.8347 0.0152 9889 0.0447 Ye 1 13960 13960 1.9778 0.0416 9924 0.0817 Se 1 15234 15234 1.7362 0.0778 9927 0.1128 Si(Lo) 3 41159 13720 2.0576 0.0065 9883 0.0082 LoxYe 1 7134.87134.8 0.79418 0.7213 9915 0.6798 LoxSe 1 6205.26205.2 0.62898 0.8786 9922 0.8463

80 ADP BRUV Surveys - 2018

YexSe 1 5666.95666.9 1.735 0.1368 9943 0.1195 Si(Lo)xYe 3 9401.73133.9 0.93998 0.5594 9923 0.5608 Si(Lo)xSe 3 154625154.1 1.5459 0.1365 9933 0.134 LoxYexSe 1 10006 10006 3.0636 0.0151 9936 0.0108 Si(Lo)xYexSe 3 10002 3334 2.0824 0.0016 9877 0.0028 Res 103 1.6491E5 1601 Total 122 3.4568E5

12. Protection (fished vs unfished) PERMANOVA Permutational MANOVA

Resemblance worksheet Name: BothYears Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data Number of permutations: 9999

Factors Name Abbrev.Type Levels Protection Pr Fixed 2 Site Si Random 5 Year Ye Random 2 Season Se Random 2

81 ADP BRUV Surveys - 2018

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Pr 1 25210 25210 1.2568 0.2111 9882 0.2373 Ye 1 17785 17785 1.7236 0.0811 9931 0.1372 Se 1 15148 15148 1.3496 0.2238 9936 0.2592 Si(Pr) 3 54524 18175 2.4008 0.0014 9905 0.0025 PrxYe 1 4943.74943.7 0.81883 0.6988 9927 0.6833 PrxSe 1 5726.95726.9 0.77762 0.7418 9936 0.7327 YexSe 1 8904.38904.3 2.0334 0.0812 9943 0.0708 Si(Pr)xYe 3 116773892.4 0.90204 0.601 9930 0.602 Si(Pr)xSe 3 164265475.2 1.2688 0.2711 9925 0.2725 PrxYexSe 1 7439.97439.9 1.7001 0.1422 9945 0.1312 Si(Pr)xYexSe 3 129454315.1 2.6952 0.0002 9886 0.0002 Res 103 1.6491E5 1601 Total 122 3.4568E5

13. Substrate (natural vs artificial) PERMANOVA Permutational MANOVA

Resemblance worksheet Name: BothYears Data type: Similarity Selection: All Transform: Fourth root Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial) Fixed effects sum to zero for mixed terms Permutation method: Unrestricted permutation of raw data

82 ADP BRUV Surveys - 2018

Number of permutations: 9999

Factors Name Abbrev.Type Levels Substrate Su Fixed 2 Site Si Random 5 Year Ye Random 2 Season Se Random 2

PERMANOVA table of results Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Su 1 21839 21839 0.98626 0.5102 9873 0.4869 Ye 1 15134 15134 1.7721 0.0714 9927 0.1055 Se 1 14429 14429 1.6495 0.1028 9928 0.1353 Si(Su) 3 55420 18473 2.652 0.0004 9881 0.0005 SuxYe 1 3378.93378.9 1.2763 0.2633 9926 0.2479 SuxSe 1 7066.87066.8 1.7002 0.0909 9933 0.0824 YexSe 1 7434.87434.8 1.3445 0.2532 9941 0.2535 Si(Su)xYe 3 129654321.6 0.76589 0.7423 9929 0.7484 Si(Su)xSe 3 143154771.8 0.84567 0.6534 9926 0.6681 SuxYexSe 1 2743.92743.9 0.49621 0.8688 9941 0.8673 Si(Su)xYexSe 3 169285642.6 3.5243 0.0001 9885 0.0001 Res 103 1.6491E5 1601 Total 122 3.4568E5

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