Zoe Richards, Maria Beger, Jean-Paul Hobbs, Tom Bowling, Karen Chong-Seng and Morgan Pratchett* FINAL REPORT November 10th, 2009

ASHMORE REEF NATIONAL NATURE RESERVE AND CARTIER ISLAND MARINE RESERVE MARINE SURVEY 2009 Zoe Richards, Maria Beger, Jean-Paul Hobbs, Tom Bowling, Karen Chong-Seng and Morgan Pratchett* FINAL REPORT November 10th, 2009 Produced for Department of the Environment, Water Heritage & the Arts *Corresponding author Dr Morgan Pratchett, ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville QLD 4811. E-mail: Morgan.Pratchett@jcu.edu.au, Telephone/ Fax: (07) 47815747/ 47816722

In responding to a tender from the Department of the Environment, Water, Heritage & the Arts, a team of researchers representing the ARC Centre of Excellence for Coral Reef Studies at James Cook University (JCU) completed surveys of the coral reef fauna at Ashmore Reef National Nature Reserve and Cartier Island Marine Reserve. The field team comprised Dr Maria Beger (University of Queensland), Ms Zoe Richards (James Cook University), Mr Jean-Paul Hobbs (James Cook University), and Mr Thomas Bowling (National Marine Science Centre). This report was prepared by the above-mentioned researchers, working in conjunction with Dr Morgan Pratchett, Ms Karen Chong-Seng, with further specific input from Dr Andrew Baird, Dr Nick Graham, and Professor David Yellowlees (ARC Centre of Excellence, James Cook University). Commonwealth of Australia 2009 This work is copyright. Apart from any use as permitted under the Copyright Act 1968, no part may be reproduced by any process without prior written permission from the Commonwealth. Requests and inquiries concerning reproduction and rights should be addressed to the Commonwealth Copyright Administration, Attorney General s Department, Robert Garran Offices, National Circuit, Barton ACT 2600 or posted at http://www.ag.gov.au/cca The views and opinions expressed in this publication are those of the authors and do not necessarily reflect those of the Australian Government or the Minister for the Environment, Heritage and the Arts or the Minister for Climate Change and Water. This report has been produced for the sole use of the party who requested it. The application or use of this report and of any data or information (including results of experiments, conclusions, and recommendations) contained within it shall be at the sole risk and responsibility of that party. JCU does not provide any warranty or assurance as to the accuracy or suitability of the whole or any part of the report, for any particular purpose or application. Address all correspondence regarding this report to Dr Morgan Pratchett. E-mail: Morgan.Pratchett@jcu.edu.au Page 2

1 Executive Summary Field-based surveys of demersal coral reef fishes (Acanthuridae, Chaetodontidae, Haemulidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae), commercially important invertebrates (trochus, sea cucumbers, clams and sea stars), coral biodiversity, habitat structure (percentage cover of hard and soft corals, sponges and algae) and coral health (the incidence of coral disease and coral predation) were undertaken at Ashmore and Cartier Reefs between April 28 th and May 7 th, 2009. Two habitats (shallow reef top and deep reef slope) were sampled at each of 8 sites established during the last comprehensive survey conducted in 2005. Pelagic fishes, as well as sharks, turtles and any other marine mega-fauna were also sampled along the reef front at each site, using replicate 500-m transects. Main findings include:- Mean abundance of demersal reef fishes has declined significantly since 2005, especially at Cartier Reef. This is attributable to localised declines in the abundance of Pomacentridae, Labridae, Scaridae and Siganidae, which may be explained by increased fishing effort and/ or changes in habitat structure between 2005 and 2009. Demersal fishes at Ashmore Reef, and especially the Pomacentridae, had very high and unprecedented parasite loads. For example, up to 90% of Chromis weberi within a given site were infected with cymothoid isopods. High parasitic loads are generally considered to be indicative of poor condition among reef fishes, but this would need to be tested for the specific situation. The slope of the size-spectra for all fishes surveyed at all study sites across both Ashmore and Cartier Reefs was -0.23, which is suggestive of moderate fishing pressure. However, size-spectra will need to be compared through time, and within other Commonwealth Marine Reserves, to test for sustained and ongoing fisheries effects. Densities of coral reef sharks at Ashmore and Cartier (whitetip sharks: 0.29 sharks.ha -1 ±0.13 SE, grey reef sharks 0.17 sharks.ha -1 ±0.09 SE) are equivalent to those reported in areas of the Great Barrier Reef that are subject to fishing, and less than one quarter of those reported for Cocos (Keeling) Islands. While there is no baseline data on shark abundance, the data is highly suggestive of sustained fishing for sharks. Densities of sea-snakes recorded in 2009 (1.42 individuals per hectare ±0.51 SE) were much lower than recorded in 2006 (4.67 individuals per hectare ±1.37 SE). The extent Page 3

and cause(s) of these declines are not known but clearly, more research is required to assess the population status and vulnerability of these species. Commercially important invertebrates (holuthurians, trochus and tridacnid clams) all exhibited significant declines in abundance from 2005 to 2009, based on comparable sampling conducted at the same 8 sites. Declines are apparent at both Ashmore Reefs and Cartier Island, and if anything, are more pronounced at Cartier Island. It is premature to ascribe these declines to over-fishing, but it is clear that either adult populations are experiencing higher than normal mortality rates or recruitment is insufficient to maintain these populations. Mean cover of hard (scleractinian) corals was 25.6% ±2.8 SE at Ashmore Reef and 29.4% ±1.8) at Cartier Island, which is 1.8-2.4 times higher compared to coral cover reported in 2005. Sustained increases in coral cover reflect recovery since the 1998 bleaching event, and are attributable to increased growth of existing colonies as well as apparent recruitment of new colonies. A total of 186 species of scleractinian coral were recorded across both Ashmore and Cartier Reefs, including 24 species that have not previously been recorded at these locations. While definitely present, densities of potentially devastating coral predators (Drupella snails and crown-of-thorns starfish, Acanthaster planci) were very low and currently causing negligible coral damage. Similarly, there was a low incidence of coral disease at Ashmore and Cartier Reefs, reflective of normal background levels of infection. Page 4

Table of Contents 1. Executive Summary 3 2. Introduction 10 3. Methods 14 3.1 Distribution, abundance and size-structure of fishes 15 3.2 Commercially important invertebrates 16 3.3 Habitat structure and coral health 17 4. Findings 20 4.1 Distribution, abundance and size-structure of fishes 20 4.1.1 Abundance and species richness 20 4.1.2 Community structure 22 4.1.3 Temporal variation: 2005 versus 2009 25 4.1.4 Size-spectra analysis 28 4.1.5 Densities of reef sharks 30 4.1.6 Sea snakes 31 4.2 Commercially important invertebrates 34 4.2.1 Holothurians 34 4.2.2 Trochus 41 4.2.3 Clams 44 4.3 Habitat structure 48 4.3.1 Hard coral cover 48 4.3.2 Coral composition 51 4.3.3 Benthic structure 52 4.3.4 Coral diversity 56 4.4 Coral health 65 4.4.1 Coral predators 65 4.4.2 Coral disease 65 5. Conclusions 67 6. Recommendations 71 7. References 73 Page 5

List of Figures Figure 1. Location of Ashmore Reef National Nature Reserve within the area covered under the Memorandum of Understanding between Australian and Indonesia (the MOU Box) in the Indian Ocean (image from DEH 2005). Figure 2. Sites surveyed at Ashmore Reef and Cartier Island. Satellite imagery from NASA. Figure 3. Mean abundance (± SE) of demersal reef fishes in each depth zone (shallow reef crest or reef top, versus deeper reef slope) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). Figure 4. Mean species richness (± SE) of demersal reef fishes in each depth zone (shallow reef crest or reef top, versus deeper reef slope) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). 12 14 20 22 Figure 5. CDA of community structure of demersal reef fishes. 23 Figure 6. Mean abundance (± SE) of demersal fishes within each of the major reef fish families at each of the 8 survey sites across Ashmore Reef and Cartier Island. Figure 7. Inter-annual variation in the mean abundance (± SE) of demersal reef fishes at each of the 8 survey sites across Ashmore Reef and Cartier Island. Figure 8. Inter-annual variation in the mean abundance (± SE) of demersal reef fishes at Cartier Island. Figure 9. Size-spectra relationship for entire fish community surveyed across 8 replicate sites at Ashmore and Cartier Reef. Figure 10. Densities of reef sharks along reef fronts at Cocos (Keeling) Islands and throughout the Great Barrier Reef (GBR) in different management zones, to compare against overall densities recorded at Ashmore and Cartier Reefs. Figure 11. Comparison of mean density (+SE) of Sea Snakes recorded across all survey sites at Asmore Reef in 2006 (Kospartov et al. 2006) and 2009 (the present study). Figure 12. Total number of individuals of each species of holothurian known to exist in the Reserves. Species are presented in order of decreasing abundance. Species with no data were not encountered in the present survey. 24 26 27 29 30 32 35 Page 6

Figure 13. Mean number (± SE) of holothurians per hectare within shallow reef crest or deeper reef slopes at sites across Cartier Island and Ashmore Reef (sites 3-8). All other holothurian species were only recorded on the reef slope. Figure 14. Mean density of holothurian individuals (+SE) at survey sites in 2005, 2006 and 2009. 2006 data is for Ashmore Reef only. Figure 15. Mean density of trochus (+SE) at survey sites in 2005, 2006 and 2009. 2006 data is for Ashmore Reef only. Figure 16. Mean trochus basal shell width in the Reserves in 2006 and 2009 (2006 data excludes Cartier Island). Figure 17. Size frequency distribution of trochus recorded on transects in the Reserves in 2006 and 2009 (2006 data does not include Cartier Island). Figure 18. Mean (± SE) density of clams on shallow reef crest (white bars) or deeper reef slopes (grey bars) at sites across Cartier Island (sites 1-2) and Ashmore Reef (sites 3-8). Figure 19. Mean density of clams (+SE) at survey sites in 2005, 2006 and 2009. 2006 data is for Ashmore Reef only. Figure 20. Mean percent scleractinian coral cover (± SE) in each depth zone (shallow reef crest or reef top, versus deeper reef slope) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). Figure 21. Temporal variation in mean (± SE) cover of hard and soft corals at Cartier Island and Ashmore Reef, based on comparisons between this study and comparable surveys conducted by Skewes et al (1999) and Kospartov et al (2006). Figure 22. Temporal comparison of hard coral cover for i) the reef crest and ii) the reef slope, comparing coral cover recorded in 2009 to comparable data from surveys undertaken by Kospartov et al (2006). 36 37 42 43 43 45 46 49 49 50 Figure 23. CDA of community structure for hard corals,. 52 Figure 24. CDA of community structure for all coral reef benthos. 54 Figure 25. Proportional composition of major habitat categories within each depth zone across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). 55 Figure 26. Mean percent cover (± SE) of different genera of soft corals at Cartier 56 Page 7

Island versus Ashmore Reef. Figure 27. Mean scleractinian species richness at the eight Reserve sites showing the deep sites have higher coral biodiversity than shallow sites. Figure 28. Regression of hard coral cover against species richness of scleractinian corals on each individual transect (n = 48). Figure 29. Major current systems in the southeast Indian Ocean and ocean basins around western Australia (from Domingues et al., 2007). 59 64 68 Plate 1. Fishes and reptiles in the Reserves. 33 Plate 2. Selection of invertebrates occurring in the Reserves. 47 Plate 3. Selection of hard coral occurring in the Reserves. 62 Plate 4. Soft coral and sea fans occurring within the Reserves. 63 Plate 5. Selection of degraded reef shots. 66 Page 8

List of Tables Table 1. GPS Co-ordinates of the 2009 survey sites 18 Table 2. ANOVA for i) abundance and ii) species richness of demersal reef fishes, testing for differences between depth zones and among sites at Ashmore. 21 Table 3. MANOVA for community structure of demersal reef fish,. 23 Table 4. Total number of fishes assigned to each size class based on comprehensive surveys of reef fish communities at 8 sites across both Ashmore and Cartier Reef 29 Table 5. ANOVA for total abundance of a) holothurians, b) trochus and c) clams. 38 Table 6. Comparisons of the density (individuals per hectare) of holothurian species on transects between 2006 and 2009. Table 7. ANOVA for hard coral cover, testing for differences between depth zones and among sites at Ashmore Reef and Cartier Island. Table 8. MANOVA for community structure of hard corals (based on the 10 most abundant genera). Table 9. Mean percent cover (± SE) of major benthic categories at Cartier Island and Ashmore Reef. 39 48 51 53 Table 10. MANOVA for community structure of coral reef benthos. 53 Table 11. New coral records from Ashmore Reef and Cartier Island Marine Reserves. Table 12. Species recorded in Kospartov et al. (2006) but not in the current survey. 57 57 Table 13. Regional comparison of scleractinian coral biodiversity. 58 Table 14. Ranked list of key hard coral species that occur within the Reserves. 61 Page 9

2 Introduction Coral reef ecosystems have enormous ecological, economic, social and cultural value both in Australia (Oxford Economics, 2009), and throughout the world (Moberg and Folke, 1999). However, coral reefs throughout the world are being rapidly degraded due to direct anthropogenic pressures (e.g., overfishing) and climate change (Hughes et al., 2003). Thus, the management and protection of coral reef organisms and ecosystems throughout Australia s territorial waters must remain a national imperative. Ashmore Reef National Nature Reserve and Cartier Island Marine Reserve (herein described collectively as the Reserves ) are two discontinuous exposed open ocean platform reefs located on the North-Western edge of the Sahul Shelf in North West Australia that are managed federally by the Department of Environment, Water, Heritage and the Arts (DEWHA). Ashmore Reef (12 17 S, 123 02 E) encloses an area of approximately 583 square kilometres and comprises three small vegetated islands, a number of sand cay, two lagoons and extensive reef. Cartier Island (12 32 S, 123 33 E) covers approximately 167 square kilometres and is located approximately 25 nautical miles to the south-east of Ashmore Reef. Cartier Island is an unvegetated sand cay surrounded by coral reef with an extensive reef flat and no lagoon. The Reserve description includes the seabed and substrata to 1000 metres depth, their boundaries are shown in Figure 1. The Reserves are protected for three reasons. Firstly, they have extremely high biodiversity with regionally and internationally significant fauna including marine invertebrates (coral, sponge, mollusc, crustacean, echinoderm and others), reef and pelagic fish, dugongs, turtles, sea snakes, seabirds and shorebirds. Secondly, the Reserves occur in a unique isolated oceanic location meaning that these systems are relatively undisturbed compared with many other coral reefs around the world. Thirdly, the Reserves are iconic and have extraordinary cultural value. For these reasons, Ashmore Reef National Nature Reserve is included on the Register of the National Estate and included on the World Conservation Union (IUCN) list of Coral Reefs of International Significance. The Reserves occur in a unique oceanographic setting because they are placed in the only area where low-latitude exchange of Pacific and Indian Ocean water masses can occur. A pressure gradient between the two oceans drives the Pacific through-flow current westward through the Timor Strait over winter months (May-September) (Wyrtki, 1987). Throughout summer months (November-March), the sea-level difference between the two Page 10

oceans is smaller and this causes the westward through-flow current to weaken enabling the South Java Current and the Eastern Gyral Current (Sprintall et al., 2002) to recirculate over the inshore part of the Sahul shelf. Ashmore Reef and Cartier Island occur on the edge of the continental shelf and border the Timor Strait so they are influenced by these seasonal circulation regimes (Cresswell et al., 1993). Hence, because the Reserves occur in a transition zone and receive water of mixed origins, they supports an exceptionally high biodiversity of marine life. The Reserves also have high cultural value because traditional Indonesian fishers (particularly people of Palau Roti which is only 150km away) have fished reefs in this region since the early eighteenth century (Fox 1998, Stacey 1999). In recognition of traditional fishing grounds in the North West Shelf, a Memorandum of Understanding (MOU) between the Australian and Indonesian governments was established in 1974, and reviewed in 1989, sets out arrangements by which traditional fishers may access marine resources in the region. The MOU allows for continued Indonesian traditional fishing activities in an area known as the MOU Box, which includes Ashmore and Cartier Reserves. Traditional Indonesian fishermen are permitted to visit the MOU Box area including a small area known as West Island Lagoon in the Ashmore Reef Reserve. Access to the remaining area of Ashmore Reef Reserve and all of Cartier Island Reserve is prohibited unless under authorisation from the Director of National Parks. Despite this MOU arrangement, illegal harvesting and fishing of holothurians, trochus, clams, turtles, sharks and other resources remain a constant threat in the Reserves. The Australian Customs Service (Customs) has provided a compliance and enforcement presence at Ashmore for many years, however it became clear that a dedicated vessel was required to protect the reserve s unique environment. As such, in April 2008, the Customs vessel, Ashmore Guardian, has since provided a near permanent presence at Ashmore, offering an unparalleled level of protection. In 2006 the suspicion of illegal fishing prompted DEWHA to conduct additional reactive Reserve-wide surveys of commercially targeted invertebrates (trochus, holothurians and tridacnid clams). This survey generally indicated that giant clams (Tridacna gigas), valuable species of sea cucumber (Holuthuria. nobilis, H. fuscogilva) and large individuals of trochus (Trochus niloticus) had had declined between 2005 and 2006, possibly due to overexpolitation. Detecting statistically significant declines in stock numbers is a challenge at the Reserve-wide level, and the stocks of some species of macroinvertebrates have proven difficult to monitor because for example some species (e.g. trochus) are cryptic, while others such as holothurians tend to aggregate and are difficult to detect. Page 11

Figure 1. Location of Ashmore Reef National Nature Reserve within the area covered under the Memorandum of Understanding between Australian and Indonesia (the MOU Box) in the Indian Ocean (image from DEH 2005). The last full marine survey of Ashmore and Cartier Reef s undertaken in 2005 (Kospartov et al., 2006) showed low levels of hard coral cover (10% at Ashmore, 16% at Cartier). The benthic communities were dominated by coralline and turf alga and there was substantial evidence of recent coral mortality. It was interpreted that the poor condition of benthic communities related to the 2003 coral bleaching events. Of concern in the Kospartov Page 12

et al. (2006) report is that few large mature coral individuals or coral recruits were observed. Also, it is important to note that this survey reports an apparent decline in coral biodiversity since surveys were first undertaken in 1986 (Marsh et al., 1993). Fish communities in the reserves were found to be diverse in 2005 and there were high densities of finfish stocks. In 2005, fish densities were observed to have increased at Cartier Island, but not at Ashmore. This could indicate healthy unfished stocks on the reef, or a positive effect of the closure to fishing (Kospartov et al., 2006). However the density of valuable marine invertebrates has declined since the start of the monitoring programme. The condition of the coral community is of particular interest to interpreting the medium-long term resilience of the Reserve reef communities as a whole. Since their inscription as protected areas (Ashmore in 1983; Cartier in 2000), monitoring of the marine resources in the Reserves has been conducted in accordance with the Reserves Management Plans (Environment Australia 2002). With the expiration of the Reserves management plan in June 2009, interim management arrangements have been enacted through the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act). A new management plan is being formulated as part of the North West bioregional planning process. The long-term monitoring of the Reserves provides a key performance measure critical to ensuring optimal management of marine resources. In the current survey we implement a rigorous sampling methodology, based on fixed-area (transect-based) surveys for fishes, benthic invertebrates and habitat structure, which will maximise resolution and precision for detecting temporal and spatial changes in coral reef ecosystems. The results of the current survey have been compared, where possible to the critical baseline information provided in previous surveys to give a more comprehensive understanding of the marine environment inside the Reserves. Surveys include small and large reef fish biodiversity, hard coral biodiversity, benthic cover estimates, holothurians, trochus and clams diversity and biomass. We also report on coral health and comment on other significant aspects of community condition and status. We make management recommendations to benefit the marine resources of the Reserve. Page 13

3 Methods Extensive surveys of coral reef fishes (Acanthuridae, Chaetodontidae, Haemulidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae), commercially important invertebrates (trochus, sea cucumbers, clams and sea stars), and hard structure (percentage cover of hard and soft corals, sponges and algae) were successfully completed at Ashmore and Cartier Reefs between April 28 th and May 7 th, 2009. Sampling was undertaken at 8 sites (Figure 2, Table 1) corresponding with survey sites established in 2005 by Kospartov et al. (2006). Re-sampling of specific sites (even though replicate transects were deployed randomly) removes the confounding influence of inherent spatial variation in coral reef habitats and organisms, thereby maximising the opportunity to detect significant changes in the size and abundance, or percentage cover, of key taxa. To ensure data were comparable between surveys, we replicated the methods used in previous surveys. Slight changes were made to the survey methods and sampling design to increase resolution, precision and statistical power to facilitate future comparisons as well as comparisons with other Commonwealth Reserves. Figure 2. Sites surveyed at Ashmore Reef and Cartier Island. Satellite imagery from NASA. Sources: http://earth.jsc.nasa.gov/newsletter/coralreefs/ch11/sts060-75-25.htm. http://oceancolor.gsfc.nasa.gov/cgi/landsat.pl?path=110&row=69&y=- 1900&sub=main_page&n=0&t=321. Page 14

3.1 The distribution, abundance and size-structure of coral reef fishes The size and abundance for coral reef fishes, as well as other large reef-associated marine fauna, were surveyed using underwater visual census along replicate transects, with transect dimensions (length and width) adjusted according to the size and abundance of the focal species. For demersal (habitat-associated) reef fishes, surveys were completed in both shallow (2-5 metres depth) reef crest habitats and deeper (8-10 metres depth) reef slope habitats. Surveys were undertaken along three replicate 50-m belt transects within each depth zone at every study site. Larger fishes (e.g. Acanthuridae, Labridae, Lethrinidae, Scaridae, and Serranidae) were surveyed 2.5m either side of the transect path (giving a sample area of 250m 2 per transect), while smaller more site attached species (Chaetodontidae, and especially Pomacentridae) were documented 1m either side of the transect tape (giving a sample area of 100m 2 per transect). In addition to counting fish from each species within each family, we also estimated total length (to the nearest cm) for each individual fish. Variation in the abundance of habitat-associated coral reef fishes (between years, between depth zones, and among sites) was analysed using analysis of variance (ANOVA), based on log-transformed counts of fish abundance. Separate analyses were conducted for each family of fishes to test for significant changes in abundance through time, and so significant differences were interpreted very cautiously given the potential for elevated Type I error rates. Community structure of fish assemblages (based on relative abundance of fishes in each of the major families) was also analysed using MANOVA, testing for differences between depth zones and among sites. The extent of similarity in fish assemblages was then displayed using a CDA. The CDA plots display each combination of site and depth zone in a two dimensional space to illustrate the relative similarity in community structure. In addition structural coefficients are plotted in the space to assist with interpretation. The size composition of reef fish communities was characterised using size-spectra, which is the relative abundance of fishes in different size classes regardless of taxonomy. In order to explore the size structure of reef fishes in Ashmore and Cartier all data on the size of individual fishes was aggregated across all sites. Fishes were assigned to one of 13 different 5cm size classes, ranging 5cm up to 60cm (Table 3). The slopes of the sizespectra were calculated from linear regressions of log10 (x+1) numbers per size class on the rescaled log10 mid-point of each length class. In order to calculate the mid-point height as opposed to the intercept, we also centered the regression around the independent variable (size classes). The resulting slopes of the size-spectra respond to changes in mortality rates, Page 15

thereby providing a useful metric of community response to fisheries exploitation (e.g., Graham et al 2005). Values obtained for Ashmore and Cartier Reefs were compared to values obtained from locations in Fiji (Graham et al 2005), where differential slopes of sizespectra have been related to spatial variation in fishing pressure. To survey larger and highly mobile reef-associated fishes (including Carangidae and sharks), as well as marine mammals and reptiles, three replicate 500-m long underwater visual transects were conducted along the reef front at each study site, following Robbins et al (2006). Transects were run approximately parallel with the reef crest and approximately 10-m from the reef edge. All pelagic fishes and megafauna (sharks and rays, marine mammals and reptiles) were recorded within 10-m of the transect path, giving a total sample area of 10,000m 2 (1 hectare). In contrast to previous studies at Ashmore and Cartier (e.g., Kospartov et al. 2006), which use only a single large transect per site, replication of these long swims facilitates future site-level comparisons of pelagic fishes and sharks. Overall densities of reef sharks (white tip shark and grey reef sharks) will be compared to published estimates of shark densities from Cocos (keeling) Islands and areas of the Great Barrier Reef that are subject to different management regimes (Robbins et al. 2006), to provide some indication of relative fishing pressure for sharks. 3.2 The distribution and abundance of commercially important invertebrates Species-level surveys of commercially important invertebrates (trochus, sea cucumbers, clams and sea stars) were conducted on the reef flat (at least 10-m from the reef crest) and reef slope (8-10m) at each of the 8 study sites. Five replicate 10m wide and 100- m long transects were conducted in each depth zone at every study site. Large transectareas are necessary to effectively survey these often rare and highly aggregated taxa, but it is also necessary to ensure replication at every study site. The occurrence of sea snakes was also recorded on these invertebrate transects. Count data for individual invertebrates is reported as no. per hectare, and variation in individual size and abundance of commercially-important invertebrates is analysed independently for each species. Sampling methodologies used in this study are similar to those used previously (1 x 500m transect) though the lack of replication in the last study (Kospartov et al. 2006) prohibit any formal statistical comparisons through time. By implementing a well replicated transect-based survey method within well-defined habitats, this will facilitate data comparisons between Ashmore and Cartier Reefs and other reefs Page 16

systems around the world, as well as enabling better temporal comparisons through future surveys. 3.3 Habitat structure Biological and physical structure of benthic reef habitats was documented using 3 replicate 50-m point- intercept transects, with 100 uniformly distributed points (50cm apart) per transect, as utilised in extensive regional surveys of coral reef habitats on the Great Barrier Reef (e.g., Pratchett et al., 2006) and throughout the Indo-Pacific (Pratchett et al. 2009). All scleractinian (hard) corals underlying specific survey points were identified to genus, providing a rigorous measure of coral cover and composition to facilitate spatial and temporal comparisons. Hard coral cover, soft coral cover and algal cover are all reported as percentages as per the accepted scientific standard. Moreover, coral diversity, benthic cover and composition were documented along the same transects used to quantify size and abundance of fishes, allowing for fine-scale comparisons of fish and habitat structure. Replicate measures of topographic complexity, which is a fundamental component of reef habitats (Graham et al. 2006), were also obtained at the start of each transect, using the five-point scale formalised by Wilson et al. (2007). Variation in mean coral cover (both among sites and among years) was analysed using univariate parametric analyses (ANOVA) following appropriate (square root arcsine) transformation of proportional cover. Community structure of benthic assemblages was then analysed using multivariate analyses (MANOVA and CDA). Two separate analyses of benthic composition were conducted; Firstly to explore variation in broad habitat categories (e.g., hard coral, soft-coral turf algae, macroalage) and secondly, to assess variation in the taxonomic composition (family-level) of hard coral assemblages. To document coral biodiversity as well colony level measures of coral health, all coral colonies >5cm diameter were surveyed 1-m either side of the transect path, and identified to species. Three replicated 50m transects were conducted at two depths. This provided a rigorous measure of species diversity, with controls for area surveyed as well as number of colonies surveyed. The number of species per unit area provides a standardised measure of coral diversity that can be later compared among Commonwealth Marine reserves, taking account of variation in coral cover and colony density. Whilst surveying corals along 50 x 2m belt transects, any evidence of adverse coral health, such as coral bleaching, recent coral predation and coral disease was also recorded. In addition, the size and abundance of A. planci was quantified, and the density of Drupella spp, were recorded along each transect. Page 17

Table 1. GPS Co-ordinates of the 2009 survey sites Equivalent 2005 Site Number Start Latitude (degrees South) Start Longitude (degrees East) End Latitude (degrees South) End Longitude (degrees East) Replicate Location Site Number Reef fish/benthic Transects - Deep Cartier South Site 1 D13 12.54.684 123.55.236 12.54.606 123.55.698 Reef fish/benthic Trans. - Shallow Cartier South Site 1 D14 12.54.589 123.55.249 12.54.519 123.55.706 Pelagic Transect 1 Cartier South Site 1 D13 12.32.701 123.33.690 12.32.764 123.33.419 Pelagic Transect 2 Cartier South Site 1 D13 12.32.764 123.33.419 12.32.819 123.33.078 Pelagic Transect 3 Cartier South Site 1 D13 12.32.819 123.33.078 12.32.864 123.32.798 Invert Transects - Deep Cartier South Site 1 D13 12.32.819 123.33.078 12.32.984 123.32.798 Invert Transects - Shallow Cartier South Site 1 D14 12.32.651 123,33,074 12.32.642 123.33.137 Reef fish/benthic Transects - Deep Cartier North Site 2 D15 12.52.374 123.55.849 12.54.393 123.55.386 Reef fish/benthic Trans. - Shallow Cartier North Site 2 D16 12.52.419 123.55.858 12.54.436 123.55.428 Pelagic Transect 1 Cartier North Site 2 D15 12.31.387 123.32.973 12.31.404 123.33.252 Pelagic Transect 2 Cartier North Site 2 D15 12.31.404 123.33.252 12.31.412 123.33.550 Pelagic Transect 3 Cartier North Site 2 D15 12.31.412 123.33.550 12.31.421 123.33.834 Invert Transects - Deep Cartier North Site 2 D15 12.31.447 123.33.510 12.31.444 123.32.957 Invert Transects - Shallow Cartier North Site 2 D16 12.31.521 123.33.235 12.31.638 123.33.484 Reef fish/benthic Transects - Deep Ashmore South Site 3 D1 12.29.14 123.11.65 12.29.06 123.12.12 Reef fish/benthic Trans. - Shallow Ashmore South Site 3 D2 12.28.97 123.12.13 12.28.97 123.12.13 Pelagic Transect 1 Ashmore South Site 3 D1 12.17.483 123.07.329 12.17.472 123.07.052 Pelagic Transect 2 Ashmore South Site 3 D1 12.17.472 123.07.052 12.17.530 123.06.782 Pelagic Transect 3 Ashmore South Site 3 D1 12.17.530 123.06.782 12.17.587 123.06.482 Invert Transects - Deep Ashmore South Site 3 D1 12.17.476 123.06.990 12.17.546 123.06.715 Invert Transects - Shallow Ashmore South Site 3 D2 12.17.371 123.06.984 12.17.280 123.07.238 Reef fish/benthic Transects - Deep Ashmore SW Site 4 D3 12.26.63 122.96.19 12.26.47 122.9576 Reef fish/benthic Trans. - Shallow Ashmore SW Site 4 D4 12.26.67 122.96.24 12.26.12 122.9514 Pelagic Transect 1 Ashmore SW Site 4 D3 12.16.140 122.57.924 12.15.999 122.57.691 Pelagic Transect 2 Ashmore SW Site 4 D3 12.15.999 122.57.691 12.15.857 122.57.456 Pelagic Transect 3 Ashmore SW Site 4 D3 12.15.857 122.57.456 12.15.801 122.57.454 Invert Transects - Deep Ashmore SW Site 4 D3 12.15.864 122.57.442 12.15.782 122.57.171 Invert Transects - Shallow Ashmore SW Site 4 D4 12.15.804 122.57.725 12.15.627 122.57.517 Page 18

Reef fish/benthic Transects - Deep Ashmore East Site 5 D5 12.25.45 123.15.69 12.24.71 123.16.04 Reef fish/benthic Trans. - Shallow Ashmore East Site 5 D6 12.24.94 123.15.62 12.25.35 123.15.46 Pelagic Transect 1 Ashmore East Site 5 D5 12.15.039 123.09.649 12.15.291 123.09.456 Pelagic Transect 2 Ashmore East Site 5 D5 12.15.291 123.09.456 12.15.498 123.09.261 Pelagic Transect 3 Ashmore East Site 5 D5 12.15.498 123.09.261 12.15.685 123.09.068 Invert Transects - Deep Ashmore East Site 5 D5 12.15.135 123.09.439 12.15.320 123.09.241 Invert Transects - Shallow Ashmore East Site 5 D6 12.14.884 123.09.245 12.15.118 123.09.111 Reef fish/benthic Transects - Deep Ashmore North Site 6 D9 12.18.41 123.10.57 12.18.45 123.11.124 Reef fish/benthic Trans. - Shallow Ashmore North Site 6 D10 12.18.45 123.10.67 12.18.53 123.11.11 Pelagic Transect 1 Ashmore North Site 6 D9 12.13.980 122.59.457 12.14.116 122.59.213 Pelagic Transect 2 Ashmore North Site 6 D9 12.14.116 122.59.213 12.14.245 122.58.948 Pelagic Transect 3 Ashmore North Site 6 D9 12.14.245 122.58.948 12.14.339 122.58.728 Invert Transects - Deep Ashmore North Site 6 D9 12.11.078 123.06.596 12.11.047 123.06.328 Invert Transects - Shallow Ashmore North Site 6 D10 12.13.980 122.59.457 12.14.116 122.59.213 Reef fish/benthic Transects - Deep Ashmore Lagoon Site 7 D7 12.23.08 122.99.75 12.23.07 122.99.42 Reef fish/benthic Trans. - Shallow Ashmore Lagoon Site 7 D8 12.23.27 122.99.57 12.23.05 122.99.27 Pelagic Transect 1 Ashmore Lagoon Site 7 D7 12.11.074 123.06.568 12.11.074 123.06.454 Pelagic Transect 2 Ashmore Lagoon Site 7 D7 12.11.045 123.06.139 12.11.097 123.06.022 Pelagic Transect 3 Ashmore Lagoon Site 7 D7 12.11.105 123.05.934 12.11.123 123.05.731 Invert Transects - Deep Ashmore Lagoon Site 7 D7 12.11.074 123.06.568 12.11.094 123.06.454 Invert Transects - Shallow Ashmore Lagoon Site 7 D8 12.11.105 123.05.934 12.11.123 123.05.731 Reef fish/benthic Transects - Deep Ashmore Mid. Lag. Site 8 D11 12.20.06 123.08.29 12.20.06 123.08.29 Reef fish/benthic Trans. - Shallow Ashmore Mid. Lag Site 8 D12 12.20.74 123.06.63 12.20.92 123.07.27 Pelagic Transect 1 Ashmore Mid. Lag Site 8 D11 12.12.490 123.04.444 12.12.526 123.04.213 Pelagic Transect 2 Ashmore Mid. Lag Site 8 D11 12.12.527 123.04.134 12.12.407 123.03.926 Pelagic Transect 3 Ashmore Mid. Lag Site 8 D11 12.11.338 123.04.649 12.11.091 123.04.536 Invert Transects - Deep Ashmore Mid. Lag Site 8 D11 12.11.338 123.04.649 12.11.091 123.04.536 Invert Transects - Shallow Ashmore Mid. Lag Site 8 D12 12.12.490 123.04.444 12.12.526 123.04.213 Page 19

4 Findings 4.1 The distribution, abundance and size-structure of coral reef fishes 4.1.1 Abundance and diversity of reef fishes A total of 13,564 fishes were counted during visual surveys of fishes within specified families (Acanthuridae, Chaetodontidae, Haemulidae, Kyphosidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae) across 48 transects surveyed at Ashmore Reef and Cartier Island in 2009, corresponding with a mean of 282.6 (±103.1 SE) fishes per transect. The abundance of fishes varied significantly among sites (ANOVA, Table 2), ranging from 202.8 fishes per transect (±14.9 SE) at site 4 on the south-west side of Ashmore reef, up to 407.8 fishes per transect (±39.1 SE) at site 3 on the south-east side of Ashmore. Overall abundance was also fairly consistent among zones within a given site (Table 2, Figure 3). 600 500 Crest Slope No. per transect 400 300 200 100 0 1 2 3 4 5 6 7 8 Sites Figure 3. Mean abundance (± SE) of demersal reef fishes in each depth zone (shallow reef crest or reef top, versus deeper reef slope) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). Page 20

A total of 273 species of fishes were recorded during visual surveys of fishes within specified families (Acanthuridae, Chaetodontidae, Haemulidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae). The number of species recorded on a single transect varied greatly among transects (even within a given site) ranging from 11 to 73, with a mean of 45.6 (±39.1 SE) species per transect. In all, the mean species richness did not vary greatly among sites, but was significantly different between zones (Table 2) and generally higher on the reef slope compared to the reef crest (Figure 4). The only exception to this pattern was at site 8 (in the Ashmore lagoon) were fish diversity was actually higher on the reef crest compared to the associated reef slope. Table 2. ANOVA for i) abundance and ii) species richness of demersal reef fishes, testing for differences between depth zones and among sites at Ashmore Reef and Cartier Island. Raw counts were log(x+1) transformed to improve normality. i) Log Abundance Source df MS F Sig. Site 7 0.07 2.41 0.04 Zone 1 0.01 0.12 0.73 Site * Zone 7 0.02 0.82 0.58 Error 32 0.03 ii) Species Richness Source df MS F Sig. Site 7 282.9 3.04 0.01 Zone 1 892.7 9.61 0.00 Site * Zone 7 221.9 2.39 0.04 Error 32 92.9 Page 21

70 60 Crest Slope No. species per transect 50 40 30 20 10 0 1 2 3 4 5 6 7 8 Sites Figure 4. Mean species richness (± SE) of demersal reef fishes in each depth zone (shallow reef crest or reef top, versus deeper reef slope) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). 4.1.2 Community structure of demersal reef fishes Demersal reef fish assemblages were strongly dominated by the family Pomacentridae, which accounted for 59% (8,011/ 13,546) of individuals counted. It is important to remember however, that we specifically excluded several other families of reef fishes (Apogonidae, Blennidae, and Gobiidae) which are generally cryptic, but often very abundant within coral reef habitats. Other dominant families recorded during these surveys were the Labridae and Acanthuridae, which each accounted for approximately 13.3% of fishes counted. Overall community structure varied significantly and among sites, but there was also significant variation among zones within sites (MANOVA, Table 3). The greatest difference was between Cartier Island (sites 1 and 2) and Ashmore reef (sites 3-8), where Balistidae were much more abundant around Cartier Island (Figure 5), while Siganidae were only found at Ashmore Reef (Figure 6). There was also marked spatial variation in the abundance of some other families, such as the Lethrinidae (Figure 6), which could be compared to spatial variation in fishing intensity if this data was available. Page 22

Table 3. MANOVA for community structure of demersal reef fish, testing for differences between depth zones and among sites at Ashmore Reef and Cartier Island. Families included in this analysis were Acanthuridae, Balistidae, Chaetodontidae, Haemulidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae. Raw counts were log(x+1) transformed to improve normality. Effect Value F Hypothesis df Error df Sig. Site 3.68 2.22 91 182 0.00 Zone 0.79 5.79 13 20 0.00 Site * Zone 3.31 1.80 91 182 0.00 8 Axis 2 21.0% Mullidae Lutjanidae 2-S 1-C 1-S Balistidae Pomacanthidae Serranidae 5-S 4-S 6-C -8 8-S 3-C Scaridae 8 8-C 3-S 6-S Lethrinidae Axis 1 Haemulidae 4-C 5-C 7-S Pomacentridae 38.1% 7-C Chaetodontidae 2-C Labridae -8 Figure 5. CDA of community structure of demersal reef fishes, comparing the shallow reef crest (open circles), versus deeper reef slope (grey circles) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). The influence of key families on community structure are indicated by structural vectors. Page 23

Mean no. per Transect 100 90 80 70 60 50 40 30 20 10 0 Acanthuridae 1 2 3 4 5 6 7 8 50 40 30 20 10 0 Lutjanidae Crest Slope 1 2 3 4 5 6 7 8 Sites Mean no. per Transect 25 20 15 10 5 0 Chaetodontidae 1 2 3 4 5 6 7 8 16 14 12 10 8 6 4 2 0 Mullidae 1 2 3 4 5 6 7 8 Mean no. per Transect 90 80 70 60 50 40 30 20 10 0 Labridae 1 2 3 4 5 6 7 8 9 8 7 6 5 4 3 2 1 0 Pomacanthidae 1 2 3 4 5 6 7 8 Mean no. per Transect 16 14 12 10 8 6 4 2 0-2 Lethrinidae 1 2 3 4 5 6 7 8 400 350 300 250 200 150 100 50 0 Pomacentridae 1 2 3 4 5 6 7 8 Sites Sites Figure 6. Mean abundance (± SE) of demersal fishes within each of the major reef fish families at each of the 8 survey sites across Ashmore Reef and Cartier Island. Page 24

Mean no. per Transect 12 10 8 6 4 2 Serranidae 70 60 50 40 30 20 10 Scaridae Crest Slope 0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8 Sites Siganidae 5 ean no. per T rans ect M 4 3 2 1 0 1 2 3 4 5 6 7 8 Sites Figure 6. continued 4.1.3 Temporal variation in reef fishes: 2005 versus 2009 Based on a subset of families counted in both 2005 and 2009 (Acanthuridae, Chaetodontidae, Haemulidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae) there has been a significant decline through time in abundance of coral reef fishes at Ashmore Reef and Cartier Island (ANOVA, F= 10.3, df =1,7, p = 0.002). At Ashmore Reef, declines in abundance of reef fishes were only apparent at site 6 (on the north-east corner) due to a decline in the abundance of Pomacentridae. In 2005, there were in excess of 1,000 damselfish recorded on 2 of the 3 transects surveyed at site 6, whereas mean densities of pomacentrids across all other sites were <200 fishes per transect. At the two sites at Cartier Island, however, there was a consistent decline in the abundance of reef fishes from 2005 to 2009 (Figure 7), and this is only partly attributable to changes in abundance of Pomacentridae. Page 25

1400 Mean no. of reef fishes per transect 1200 1000 800 600 400 200 2005 2009 0 1 2 3 4 5 6 7 8 Figure 7. Inter-annual variation in the mean abundance (± SE) of demersal reef fishes at each of the 8 survey sites across Ashmore Reef and Cartier Island. Densities of reef fishes were calculated based on a restricted set of families (Acanthuridae, Chaetodontidae, Haemulidae, Labridae, Lethrinidae, Lutjanidae, Mullidae, Pomacanthidae, Pomacentridae, Scaridae, Serranidae and Siganidae) surveyed in both 2005 and 2009. Declines in abundance of reef fishes at Cartier Island between 2005 and 2009 were most pronounced for fishes from the family Pomacentridae, which declined by more then 55% from a mean of 320.7 (± 60.8 SE) individuals per transect down to 140.1 (± 25.6 SE). Three other families, the Labridae, Scaridae and Siganidae, also exhibited significant declines in abundance over this period (Figure 8). For the Signanidae, there was not a single individual counted on transects surveyed at Cartier Reef in 2009, whereas 30 individuals were recorded on similar transects surveyed at the same sites in 2005. Declines in abundance of these reef fishes may be attributable to increased fishing at Cartier Island since 2005, but it is notable that there were no apparent declines in abundance of large piscivores species, including Lethrinidae, Lutjanidae and Serranidae, which are all potential targets of local fishing effort. Moreover, declines were most apparent among the Pomacentridae, which is suggestive of some change in habitat structure rather than fishing pressure, as was shown during rigorous path-analyses undertaken by Wilson et al. (2008) to explain Page 26

declines in abundance of Pomacentridae (and other reef fishes) during habitat degradation in Fiji. 140 120 100 80 60 40 20 0 Acanthuridae Chaetodontidae Labridae Lethrinidae Lutjanidae Mullidae Pomacanthidae Scaridae Serranidae Siganidae Mean no. fishes per transect * 2005 2009 * * Figure 8. Inter-annual variation in the mean abundance (± SE) of demersal reef fishes at Cartier Island. Four families (including Pomacentridae, not shown) exhibited statistically significant declines in abundance between years (T-test, α< 0.05) as indicated by *. Aside from declines in abundance of several families of fishes at Cartier Reef, the spatial and temporal patterns of abundance for demersal reef fishes were fairly consistent between 2005 and 2009. The only significant changes apparent from rigorous parametric analyses (ANOVA, Appendix 1) of individual families were: i) Acanthuridae - There was an interaction between Year, Depth and Site, whereby spatial patterns of abundance are different between years, but there was no overall change in abundance between years. ii) Chaetodontidae - There was significant variation between depth Sites, whereby butterflyfishes are generally more abundant on the reef slope compared to the reef crest. This is contrary to patterns of abundance recorded elsewhere (e.g., Pratchett and Page 27

Berumen 2008), but densities on the reef crest may increase as coral cover continues to recover (discussed later). iii) Pomacentridae There was an interaction between Year, Depth and Site, attributable to declines in abundance of Pomacentridae at sites 1, 2 and 6 (as discussed previously). iv) Scaridae There was an interaction between Year, Depth and Site, attributable to declines in abundance of Scaridae on the reef crest at Cartier, whereas densities were constant elsewhere. v) Serranidae - There was an interaction between Year, Depth and Site, whereby spatial patterns of abundance are different between years, but there was no overall change in abundance between years. 4.1.4 Size spectra analysis for demersal reef fishes Total length was estimated for a total of 13,590 individual fishes across all sites at both Ashmore and Cartier Reef (Table 4). As expected, the reef fish community was dominated by small fishes. More than 90% of all fishes surveyed were less than 25cm total length. even though we did not sample many of the smallest fish species (blennies and gobies). Fishing is expected to further reduce the number of large fishes, thereby leading to a steeper size-spectra. The slope of the size-spectra for all sites combined was -0.23 (Figure 9), which is towards the upper end of slopes recorded among relatively remote islands of Fiji with moderate fishing pressure (Graham et al. 2005). This suggests that there is evidence of fishing impacts in the size structure of the fish communities, but this data will be most useful in comparing to comparable data collected during subsequent surveys at Ashore and Cartier Reefs, as well as in other Commonwealth Marine Reserves around Australia. Page 28

Table 4. Total number of fishes assigned to each size class based on comprehensive surveys of reef fish communities at 8 sites across both Ashmore and Cartier Reef Size Class Frequency Cumulative % 5cm 6558 48.26% 6-10cm 2550 67.02% 11-15cm 1577 78.62% 16-20cm 1090 86.64% 21-25cm 1003 94.03% 26-30cm 239 95.78% 31-35cm 198 97.24% 36-40cm 124 98.15% 41-45cm 168 99.39% 46-50cm 40 99.68% 51-55cm 17 99.81% 56-60cm 16 99.93% >60cm 10 100.00% TOTAL 13590 4.5 4 Log(frequency) 3.5 3 2.5 2 1.5 1 0.5 y = -0.2304x + 2.3454 0-6 -3 0 3 6 Centred size classes Figure 9. Size-spectra relationship for entire fish community surveyed across 8 replicate sites at Ashmore and Cartier Reef. Page 29

4.1.5 Densities of coral reef sharks Only 11 sharks were observed (7 whitetip reef sharks; Triaenodon obesus, and 4 grey reef sharks; Carcharhinus amblyrhynchos) during 24 (3 transects at each of 8 sites) replicate 10,000-m 2 transects conducted along the reef front. This corresponds to an overall density of 0.29 (± 0.13 SE) sharks per hectare for whitetip reef sharks, and 0.17 (± 0.09 SE) sharks per hectare for grey reef sharks. These densities are very similar to those reported by Robbins et al. (2006) for regions of the Great Barrier Reef that are open to fishing (Figure 10). While there is no baseline data on shark densities from Ashmore and Cartier reefs it would be presumed that previous densities would have resembled those of Cocos (Keeling) islands, where both grey reef sharks and whitetip reef sharks are 4-5 time more abundant. This suggests that shark fishing has significantly depleted the shark populations within the vicinity of Ashmore and Cartier Reefs, much as it has throughout most of the Great Barrier Reef (Figure 10). 3 Mean no. sharks per hectare 2.5 2 1.5 1 0.5 whitetip reef sharks grey reef shark 0 Cocos (Keeling) No-Entry (GBR) No-take (GBR) Limitedfishing (GBR) Open- Fishing (GBR) Ashmore & Cartier Figure 10. Densities of reef sharks along reef fronts at Cocos (Keeling) Islands and throughout the Great Barrier Reef (GBR) in different management zones, to compare against overall densities recorded at Ashmore and Cartier Reefs. Data from Cocos (Keeling) and the GBR was extracted from Robbins et al (2006), which used similar survey methods to those which were used at Ashmore and Cartier Reefs. Page 30

Densities of sharks reported in 2009 are not statistically different from densities reported in 2005 (Kospartov et al. 2006), though the large variance (due to limited replication) in the 2005 estimates limit the ability to detect any meaningful changes in abundance. The current technique (although reasonably well replicated; n = 3 per site) may also suffer the same problems. While densities of sharks recorded using replicate transects are consistent with similar studies conducted elsewhere, it is questionable whether these techniques will provide necessary resolution to detect any further declines in shark populations. Two problems emerge when trying to sample large fishes along visual transects: i) inherently low densities mean that there will nearly always be very large variance in transect-based counts, ii) it is unclear to what extent sharks may actively avoid, or be attracted to, divers in the water, and this may significantly affect estimates of shark densities.. Novel sampling techniques, such as baited video, may overcome issues associated with diver presence and reveal the high diversity of reef-associated sharks (Meekan and Cappo 2004), and thereby provide better methods to monitor sharks assemblages with the Ashmore Reef National Nature Reserve and Cartier Island Marine Reserves. 4.1.6 Sea snakes Only two species of Sea Snake were recorded in the current survey (Olive Sea Snake Aipyurus laevis and Turtle-headed Sea Snake Emydocephalus annulatus) despite 13 species of Sea Snake reported to occur in the Reserves (Wilson and Swan, 2004). The overall density of Sea Snakes recorded across all sites and zones in 2009 was also much lower than that recorded in 2006 (Figure 11). These findings are consistent with other research that reports significant recent declines in the abundance and diversity of Sea Snakes in the Reserves (M. Guinea pers. comm.), though the reason for these declines in unknown. It is important to note that Sea Snakes were only recorded anecdotally on the 2006 and 2009 surveys and on-going dedicated surveys are strongly recommended. Page 31

7 Mean no. of individuals per hectare 6 5 4 3 2 1 0 2006 2009 Figure 11. Comparison of mean density (+SE) of Sea Snakes recorded across all survey sites at Asmore Reef in 2006 (Kospartov et al. 2006) and 2009 (the present study). Page 32

Plate 1. Fishes and reptiles in the Reserves. A). Cymothoid Isopod on Pomacentrus vaiuli B). Neoglyphidodon oxyodon C). Chaetodon punctatofasciatus, D). Pterois volitans lionfish E). Premnas biaculeatus on Entacmea quadricolor, F) Stegastoma fasciatum Leopard Shark G). Pseudoanthias tuka on Tubipora musica H). Rare species of Wobbegong - Orectolobus wardi. I). Aipysurus laevis Olive Sea Snake Page 33

4.2 Commercially important invertebrates 4.2.1 Holothurians Eleven species of holothurian were recorded at Cartier Island and Ashmore Reef during the most recent biological survey in 2009, including one undescribed species (See Plate 2 A & B). Nine species previously reported from within the Reserves were not encountered in the present survey (Figure 12), though sampling during this study was restricted to consolidated reef frameworks. Sampling for this study was intentionally restricted to permanent sites which are mostly sighted in areas of contiguous reef matrix, suitable for surveying reef-associated fauna and flora. Consequently, limited sampling was conducted in sandy areas of the lagoon where many holothurian species are known to reside. Even so, 151 holothurians were counted across the 24 transects, of which the most commonly encountered species were Holuthuria atra (82 individuals) and Pearsonothuria graeffei (29 individuals). Mean densities of holothurians were higher at Ashmore Reef than Cartier Island sites, even when comparing comparable reef habitats (exposed reef crests and slopes). In the shallow reef crest and lagoon habitat, only four species were encountered (Figure 13). At the southern and south-western shallow sites H. atra was recorded in high numbers and was surprisingly absent on all deep transects with the exception of the SW Ashmore site (Figure 13). All eleven species occurred in the deep reef slope and lagoonal habitat, albeit in low numbers. P. graeffei was the most commonly recorded holothurian in the deep habitat but importantly, this species also reached similar densities in the shallow habitat. Two species considered of high market value (H. nobilis and H. fuscogilva) were very rare in the Reserves. Three other species considered of medium market value (Stichopus chloronotus, Thelenota ananas and Actinopyga miliaris) were also recorded in low numbers at only a single deep site with the exception of S. chloronotus, which reached comparatively higher density in the shallow habitat at South Cartier Island. The new unidentified species was recorded in the deep habitat of Ashmore lagoon, but only a single individual was observed. High-density aggregations of H. leucospilota recorded in 2005 and 2006 surveys were not encountered, however the eastern lagoon where this aggregation was recorded, was not surveyed in the present study. H. coluber was recorded in 2006 Page 34

on intertidal lagoon walks but this habitat was not examined in the present survey. An additional seven species were not encountered in the present survey and this is most likely because surveys were conducted at monitoring sites only, enabling only a subset of habitat types to be surveyed. 90 80 70 Total number of individuals 60 50 40 30 20 10 0 H. atra P. graeffei S. chloronotus H. edulis H. nobilis S. hermanni B. argus H. fuscogilva T. ananas A. miliaris Unidentified H. leucospilota T. anax A. mauritiana H. fuscopunctata B. marmorata A. lecanora H. timana H. coluber H. fuscorubra Holothurian species Figure 12. Total number of individuals of each species of holothurian known to exist in the Reserves. Species are presented in order of decreasing abundance. Species with no data were not encountered in the present survey. Page 35

Mean no. per hectare 12 10 8 6 4 2 0 H. nobilis (whitmaei) 1 2 3 4 5 6 7 8 140 120 100 80 60 40 20 0 H. atra Crest Slope 1 2 3 4 5 6 7 8 Mean no. per hectare 25 20 15 10 5 0 S. chloronotus 1 2 3 4 5 6 7 8 35 30 25 20 15 10 5 0 B. graeffei 1 2 3 4 5 6 7 8 Mean no. per hectare 30 25 20 15 10 5 0 H. edulis 1 2 3 4 5 6 7 8 12 10 8 6 4 2 0 S. hermanni 1 2 3 4 5 6 7 8 Figure 13. Mean number (±SE) of holothurians per hectare within shallow reef crest or deeper reef slopes at sites across Cartier Island and Ashmore Reef (sites 3-8). All other holothurian species were only recorded on the reef slope. The assemblage of holothurians in the Reserves is spatially and temporally dynamic. In 2005, 16 species of holothurians were recorded at survey sites and two other species were detected outside survey sites. In 2006, 14 species of holothurian were recorded on transects (13 species were present in shallow habitat and 10 present in deep habitat) and again, two additional species were detected in other habitats. In Page 36

the current survey, only 11 species were encountered on transects at survey sites, while there was no sampling of diverse habitats that were considered in 2005. The density of holothurians recorded in 2009 was lower than recorded previously in 2005 and 2006 (Figure 14). The high density of holothurians recorded at survey sites in 2006 was driven largely by the aggregation of H. edulis recorded at the deep East Ashmore site. While a smaller aggregation of the same species was present at the same site in 2005, this species was recorded in far lower density in 2009. When compared in detail with 2006 survey results, there have been marked declines in both the diversity and density of holothurians at both shallow and deep survey sites (Table 6). Overall densities of holothurians are significantly lower now compared to 2005 (ANOVA, Table 5), and much lower than reported in 2006 (Figure 14). For example S. chloronotus was found in relatively high density in 2006 however in the present survey its density has declined to zero at most sites. Further three other species recorded in low density in 2006 (T. anax, H. coluber, H. fuscopunctata) were not detected in present surveys. A substantial increase in the density of H. atra was recorded in the shallow habitat at Southern Ashmore sites and the density of P. graeffei while decreasing at exposed sites, increased in the lagoon. H. nobilis was detected for the first time in both deep and shallow habitats at the East Ashmore site. 70 No. of individuals per hectare 60 50 40 30 20 10 0 2005 2006 2009 Years Figure 14. Mean density of holothurians (+SE) at survey sites in 2005, 2006 and 2009. 2006 data is relevant to Ashmore Reef only. Page 37

Table 5. ANOVA for total abundance of a) holothurians, b) trochus and c) clams, testing for variation between years (2005 and 2009), between depth zones, and among sites at Ashmore Reef and Cartier Island. Count data was log transformed to improve normality. a) Holothurians Source df MS F Sig. Years 1 22.05 105.21 0.00 Site 7 3.23 15.40 0.00 Zone 1 0.43 2.05 0.16 Year * Site 7 2.18 10.41 0.00 Year * Zone 1 0.46 2.20 0.14 Site * Zone 7 1.23 5.89 0.00 Year * Site * Zone 7 0.96 4.57 0.00 b) Trochus Source df MS F Sig. Years 1 23488 5.34 0.05 Site 7 4492.1 0.96 0.53 Zone 1 3378.7 2.30 0.17 Year * Site 7 4440.1 3.64 0.06 Year * Zone 1 2341.9 1.93 0.21 Site * Zone 7 1476.3 1.21 0.40 Year * Site * Zone 7 1218.6 1.55 0.16 c) Clams Source df MS F Sig. Years 1 3.02 9.59 0.00 Site 7 1.41 4.46 0.00 Zone 1 0.60 1.89 0.17 Year * Site 7 0.29 0.94 0.48 Year * Zone 1 0.27 0.84 0.36 Site * Zone 7 0.43 1.37 0.23 Year * Site * Zone 7 0.23 0.72 0.65 Page 38

Table 6. Comparisons of the density (individuals per hectare) of holothurian species on transects between 2006 and 2009. Standard errors are given in brackets. Figures for Cartier Island are not presented because Cartier was not surveyed in 2006. Black cells indicates a decrease in density, grey cells indicates an increase in density. Shallow Habitat Ashmore South Ashmore SW Ashmore East Ashmore North Ash. Lagoon Ash Mid. Lag. Year 2006 2009 2006 2009 2006 2009 2006 2009 2006 2009 2006 2009 H. atra 0 96 16 (16) 56 4 (4) 0 0 0 0 0 4 (4) 0 (29.76) (11.66) S. chloronotus 14 (6) 0 28 (12) 0 2 (2) 2 (2) 0 4 4 (2) 0 0 0 (2.45) T. ananas 2 (2) 0 0 0 0 0 0 0 2 0 4 0 H. edulis 0 0 2 (2) 0 20 (8) 0 6 (2) 0 0 0 14 (2) 0 T. anax 0 0 0 0 0 0 0 0 0 0 2 (2) 0 P. graeffei 28 (4) 0 0 0 8 (4) 0 78 20 0 20 0 20 (10) S. hermannii 0 0 2 (2) 0 0 0 0 0 0 0 6 (2) 0 A. mauritiana 0 0 8 (8) 0 0 0 0 0 0 0 0 0 H. 0 0 0 0 0 0 0 0 4 0 0 0 fuscopunctata B. argus 0 0 0 0 0 0 0 0 0 0 4 0 H. fuscogilva 0 0 0 0 0 0 0 0 0 0 6 (2) 0 A. lecanora 2 (2) 0 0 0 2 0 0 0 0 0 0 0 H. coluber 4 0 0 0 0 0 0 0 0 0 2 (2) 0 H. nobilis 0 0 0 0 0 6 (4) 0 0 0 0 0 0 Page 39

Table 6. continued. Deep Habitat Ashmore South Ashmore SW Ashmore East Ashmore North Ash. Lagoon Ash Mid. Lag. Year 2006 2009 2006 2009 2006 2009 2006 2009 2006 2009 2006 2009 H. atra 0 0 16 (8) 4 2 (2) 0 0 0 0 0 2 (2) 0 (2.45) S. chloronotus 20 0 26 (6) 0 26 0 0 0 2 (2) 0 0 0 (18) T. ananas 4 (2) 0 0 0 4 (4) 2 (2) 0.5 0 0 0 0 0 (0.5) H. edulis 10 (2) 0 46 (26) 2 (2) 110 18 0 0 4 0 10 (2) 2 (2) (10) (6.63) P. graeffei 6 20 2 (2) 0 6 (2) 0 18 26 (4) 2 (2) 20 0 20 (6.32) (14) S. hermannii 0 0 0 0 0 0 0 0 2 (2) 0 10 (6) 6 (4) B. argus 2 (2) 0 2 (2) 0 0 0 0 2 (2) 0 0 8 (4) 0 H. fuscogilva 0 0 0 0 2 (2) 0 0 0 0 2 (2) 2 (2) 2 A. miliaris 0 0 0 0 2 (2) 0 0 0 0 0 0 2 (2) H. coluber 6 (2) 0 12 (4) 0 4 (4) 0 0 0 0 0 0 0 H. nobilis 0 0 0 0 0 2 (2) 0 0 0 0 0 0 Unidentified 0 0 0 0 0 0 0 0 0 2 (2) 0 0 Page 40

4.2.2 Trochus A total of 38 individual trochus were encountered on transects, which surveyed a total of 10 hectares, representing a mean density of 3.8 (+1.61 SE) individuals per hectare. At the same sites in 2005, almost 14x more trochus were recorded with 528 individual trochus encountered, at a mean density of 28.46 (+8.37 SE) individuals per hectare. Clearly, there has been a significant decline in the abundance of trochus (ANOVA, Table 5B). In 2006, 261 individual trochus were encountered at the same Ashmore Reef sites and the mean density was 39.0 (+17.52 SE) individuals per hectare (Figure 15). The apparent decline in the number of trochus recorded on transects in the present survey is alarming, but these results should be interpreted with caution because trochus are mobile and tend to aggregate so it is possible that aggregations formally present at the survey sites have moved. For example, in 2005 there was a high-density aggregation of trochus on the reef slope at site 5 (on the east side of Ashmore reef), whereas in 2006 the largest aggregation was detected on the reef crest at site 3. In the current survey 92% of trochus individuals were recorded on the reef slope at site 3. It is conceivable, that these aggregations located on different parts of the reef are ostensibly the same individuals. The abundance of trochus has declined from 2005 to 2009, but it is important to recognise that there appears to be considerable temporal variation in these populations. From Ceccarelli et al. (2007) it is apparent that at the reef-wide level trochus mean densities increased from 0.96 (±0.15 SE) individuals per hectare in 1999 to 37.7 (±6.7 SE) individuals per hectare in 2005 (Ceccarelli et al., 2007). In 2009, mean densities are approximately equivalent to densities recorded in 1999. Page 41

60 Mean no. per hectare 50 40 30 20 10 0 2005 2006 2009 Year Figure 15. Mean density of trochus (+SE) at survey sites in 2005, 2006 and 2009. 2006 data is relevant to Ashmore Reef only. The average basal shell width of trochus at survey sites in the current survey was 82.61 (+1.97 SE) (Figure 16). This is substantially larger than the mean basal width recorded in 2005 and 2006 surveys however this result is driven by the lower variability in mean trochus sizes in the current survey due to the absence of juvenile trochus (<55mm) (Figure 17). In both 2005 and 2006 a large proportion of juveniles were recorded it the shallow habitat at survey sites (Ceccarelli et al., 2007) however no juveniles were present in the shallow habitat in the current survey despite thorough searching. As in previous years, there is still a lack of large trochus individuals. While the largest proportion of individual trochus occurs in the medium size category in the current survey, it is important to note that this relates to a comparatively small number of individuals recorded on the reef slope at site 3 (south side of Ashmore Reef) and may represent a single cohort. Page 42

85 Mean basal shell width (mm) 80 75 70 65 60 2005 2006 2009 Figure 16. Mean trochus basal shell width in the Reserves in 2006 and 2009 (2006 data excludes Cartier Island). 40 35 2005 2006 2009 Proportion of individuals (%) 30 25 20 15 10 5 0 <45 46-55 56-65 66-75 76-85 86-95 Size class (mm) Figure 17. Size frequency distribution of trochus recorded on transects in the Reserves in 2006 and 2009 (2006 data does not include Cartier Island). 96-105 106-115 116-125 >126 Page 43

4.2.3 Clams Tridacnid clams were surveyed along the same transects used to survey holothurians and trochus. Five species of clam were counted (Hippopus hippopus, Tridacna maxima, T. crocea, T, squamosa, and T. derasa), but no giant clams (T. gigas) were encountered on transects. The mean density of clams at survey sites was 7.75 (+2.01 SE) individuals per hectare. Ashmore Reef supported a higher density of clams than Cartier Island. Tridacna maxima was the most common species encountered in both shallow and deep habitat, but the distribution of clams was very patchy on transects (as indicated by the large error bars, Figure18). H. hippopus and T. crocea were only recorded on the shallow reef crest or reef top (2-5 metres depth), while T. squamosa and T. derasa were only recorded on the reef slope (8-10 metres depth) Overall densities of tridacnid clams recorded at survey sites in 2009 are significantly lower than were recorded in 2005 for the exact same study sites (ANOVA, Table 5), but also reflect a sustained decline in abundance since 2006 (Figure 19). Declines in abundance are very consistent among sites (even at Cartier Reef). This rate of decline indicates that exploitation of clams continues to occur in the Reserves and/or that clam populations are experiencing elevated rates of mortality due to some other cause (e.g. ocean warming or ocean acidification). Page 44

Mean no. per hectare 25 20 15 10 5 0 T. maxima 1 2 3 4 5 6 7 8 Mean no. per hectare 4.5 4 3.5 3 2.5 2 1.5 1 0.5 0 T. crocea 1 2 3 4 5 6 7 8 Mean no. per hectare Mean no. per hectare 14 12 10 9 8 7 6 5 4 3 2 1 0 8 6 4 2 0 H. hippopus 1 2 3 4 5 6 7 8 T. derasa 1 2 3 4 5 6 7 8 Sites Mean no. per hectare 9 8 7 6 5 4 3 2 1 0 T. squamosa 1 2 3 4 5 6 7 8 Sites Figure 18. Mean (± SE) density of clams on shallow reef crest (white bars) or deeper reef slopes (grey bars) at sites across Cartier Island (sites 1-2) and Ashmore Reef (sites 3-8). Page 45

16 14 Mean no. per hectare 12 10 8 6 4 2 0 2005 2006 2009 Year Figure 19. Mean density of clams (+SE) at survey sites in 2005, 2006 and 2009. 2006 data is relevant to Ashmore Reef only. Page 46

Plate 2. Selection of invertebrates occurring in the Reserves. A & B). Undescribed species of sea cucumber, C) Pearsonothuria graeffei D). Tridacna crocea E). Tridacna maxima F). Hippopus hippopus G). Trochus niloticus H). Panulirus versicolor, I). Colonial Ascidians Page 47

4.3 Habitat structure 4.3.1 Hard coral cover Mean cover of hard (scleractinian) corals across the 8 sites surveyed at Cartier Island and Ashmore Reef was 26.25% (±1.5 SE), ranging from 18.2 (±2.8 SE) at site 8 in the Ashmore lagoon, up to 31.3% (±4.0 SE) at site 3 on the south-west corner of Ashmore Reef. Coral cover varied significantly among sites and between depth zones (ANOVA, Table 7), but there was no consistent pattern of depth variation among sites (Figure 20). At site 1 on the south side of Cartier Island, coral cover was the highest on the reef slope due to a high abundance of Isopora colonies. In contrast, coral cover was higher on the reef crest at site 2 (on the north side of Cartier), where there was high cover of corals from the Family Pocilloporidae. Table 7. ANOVA for hard coral cover, testing for differences between depth zones and among sites at Ashmore Reef and Cartier Island. Proportional cover of corals was arcsin(sqrt(x)) transformed to improve normality Source df MS F Sig. Site 7 0.03 3.37 0.01 Zone 1 0.01 0.45 0.51 Site * Zone 7 0.03 2.53 0.03 Error 32 0.01 Coral cover recorded in 2009 at Cartier Island and Ashmore reef was much higher than has been recorded during the two previous surveys conducted in 1999 (Skewes et al. 1999) and 2005 (Kospartov et al. 2006). At Ashmore Reef, reef-wide cover of hard (scleractinian) corals is now 29.4% (±1.8 SE), representing a 3-fold increase in percentage cover since 2005, and more than 6-fold increase since 1999 (Figure 21). Area cover of soft corals has also increased significantly over the same period up from 1.42% (±0.7 SE) in 1995 to 8.3% (±1.4 SE) in 2009. Cover of both hard and soft corals has increased steadily at Cartier Island since 1999, but started from a higher base level and has not experienced the same rate of increase (Figure 21). Page 48

50 45 40 Crest Slope Coral Cover (%) 35 30 25 20 15 10 5 0 1 2 3 4 5 6 7 8 Sites Figure 20. Mean percent scleractinian coral cover (± SE) in each depth zone (shallow reef crest or reef top, versus deeper reef slope) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). 35 30 25 Ashmore Reef Cartier Island Coral cover (%) 20 15 10 5 0 1999 2005 2009 Figure 21. Temporal variation mean (± SE) cover of hard and soft corals at Cartier Island and Ashmore Reef, based on comparisons between this study and comparable surveys conducted in by Skewes et al (1999) and Kospartov et al (2006). Page 49

Shallow reef habitat (3-5m depth) 2005 2009 50 Mean hard coral cover (+SE) 45 40 35 30 25 20 15 10 5 0 Cartier South Cartier North Ashmore South Ashmore SW Ashmore East Ashmore North Ashmore lagoon Ashmore middle lagoon Deep reef habitat (8-10m depth) 2005 2009 45 Mean hard coral cover (+SE) 40 35 30 25 20 15 10 5 0 Cartier South Cartier North Ashmore South Ashmore SW Ashmore East Ashmore North Ashmore Lagoon Ashmore middle lagoon Figure 22. Temporal comparison of hard coral cover for i) the reef crest and ii) the reef slope, comparing coral cover recorded in 2009 to comparable data from surveys undertaken by Kospartov et al (2006). Sustained increases in coral cover since 1999 are suggestive of coral recovery in the aftermath of the 1998 coral bleaching events. Coral cover typically takes 5-10 years to Page 50

recover following major disturbances (e.g., Halford et al. 2004), but this will depend on the local abundance of corals and availability of brood stock in the aftermath of the disturbance. In 2005, there was a general absence of new recruits and large colonies and also a high proportion of dead coral (Kospartov et al, 2006). Whilst there is still a lack of large colonies, it is evident that 2006/2007 were successful years for coral recruitment especially within the families Acroporidae and Pocilliporidae. 4.3.2 Coral composition The relative abundance of different coral genera varied significantly between depth zones and among sites at Ashmore Reef and Cartier Island (Figure 23, Table 8), but there were no consistent differences between zones. The reef crest communities at site 2 (at Cartier Island) were among the most unique, characterised by very high cover of Stylophora. Elsewhere, coral communities tended to be dominated by Acropora and/ or Seriatopora. Variation in coral composition may occur due to stochastic variation in recruitment patterns, but may also reflect differences in the successional stages of recovery at different sites. Ongoing monitoring of community structure is critical to test for potential changes due to differential susceptibility to major disturbances. Table 8. MANOVA for community structure of hard corals (based on the 10 most abundant genera), testing for differences between depth zones and among sites at Ashmore Reef and Cartier Island. Proportional cover of corals was arcsine(square-root(x)) transformed to improve normality. Effect Value F Hypothesis df Error df Sig. Site 3.982 3.82 70.0 203.0 0.00 Zone 0.665 4.56 10.0 23.0 0.01 Site * Zone 3.195 2.43 70.0 203.0 0.00 Page 51

8 Axis 2 19.4% 6-S Stylophora Isopora 1-S Pocillopora 1-C Montipora 5-S Goniastrea 4-C 6-C Acropora Axis 1 2-C 5-C Porites 36.7% -8 4-S Goniopora Favites 8 8-C 2-S 7-C 8-S 3-C 7-S 3-S Seriatopora -8 Figure 23. CDA of community structure for hard corals, comparing the shallow reef crest (open circles), versus deeper reef slope (grey circles) across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). The influence of dominant coral genera on community structure are indicated by structural vectors. 4.3.3 Benthic composition The predominate substrate encountered within the 8 permanent survey sites is consolidated carbonate pavement. Where there are no live corals, the substrate is generally occupied by turf algae (Table 9), which is typical of offshore coral reef habitats (Wismer et al. 2009), but particularly at shallow exposed sites (Figure 24, Table 10). Calcareous algae made up a large proportion of the shallow benthic community at the south and southwest Ashmore sites. North Cartier Island (site 2) is distinguished from Page 52

other sites surveyed in the Reserves by both the high cover of non-scleractinian coral (12%) in the shallow habitat, and the high percent cover of soft coral (53%) in deep habitat. Table 9. Mean percent cover (± SE) of major benthic categories at Cartier Island and Ashmore Reef. Cartier Island Ashmore Reef Turf Algae 33.1 (± 6.9) 22 (± 3) Hard coral 25.6 (± 2.8) 29.4 (± 1.8) Soft Coral 12.4 (± 6.2) 8.3 (± 1.4) Coralline Algae 6.1 (± 1.1) 7.1 (± 1.1) Halimeda 5.0 (± 1.6) 2.7 (± 0.5) Sponge 1.0 (± 0.4) 4.9 (± 0.8) Macroinvertebrates 0.1 (± 0.1) 0.9 (± 0.3) Table 10. MANOVA for community structure of coral reef benthos, comparing dominant coral genera and non-coral benthos, testing for differences between depth zones and among sites at Ashmore Reef and Cartier Island. Proportional cover of all categories was arcsin(sqrt(x)) transformed to improve normality. Effect Value F Hypothesis df Error df Sig. Site 5.74 5.93 119 154 0.000 Zone 0.93 12.14 17 16 0.001 Site * Zone 4.80 2.82 119 154 0.000 Page 53

12 Axis 2 28.1% Axis 1 31.9% 1-C 1-S 3-C 4-S 4-C Turf Rubble Seriatopora Isopora Nepthea Milleopora 5-C -12 Halimeda Montipora 6-S 12 6-C Clavularina Pocillopora 8-S Sponge 2-C CCA Heliopora Sand 3-S 5-S 7-C Acropora 7-S 8-C 2-S -12 Figure 24. CDA of community structure for all coral reef benthos, comparing the relative abundance of major coral genera and non-coral benthos across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8). Centroids are labelled with the site number followed by either C (reef crest) or S (reef slope). The influence of dominant coral genera and non-coral benthos on community structure are indicated by structural vectors. Percentage cover of fleshy (macro) algae was very low at both Cartier Island and Ashmore Reef, typically occupying <10% of reef habitats. The only sites with substantial amounts of fleshy algae were the reef crests at sites 3 and 4 on the south side of Ashmore (Figure 25). This finding is consistent with Kospartov et al (2006) which recorded that macroalgae occupied <10% of the total survey area, even though coral cover was much lower than recorded now. As reported in 2005 surveys, the calcareous green alga Halimeda spp. reaches higher densities at Cartier Island than Ashmore Reef. However at Cartier, reef-wide mean cover has dropped by 3.3% but remained relatively constant (2.8% & 2.7%) at Ashmore. Halimeda is an important member of the Reserves reef system because it contributes significant amounts of aragonitic calcium carbonate to reefal sediments and together with coralline algae is important to reef building (Stoddart, 1969). It is possible that the higher Halimeda biomass at Cartier Island reflects localized periodic Page 54

upwellings of nutrient rich water that stimulates productivity (see Andrews and Gentien 1982). 100% 80% 60% 40% 20% 0% 1 - Crest 1 - Slope 2- Crest 2- Slope 3- Crest 3- Slope 4 - Crest 4 - Slope 5 - Crest Median Percent Benthic Cover 5 - Slope 6 - Crest 6 - Slope 7 - Crest 7 - Slope 8 - Crest 8 - Slope Scleractinian coral Non-scleractinian coral Soft coral Sponge Turf Algae Coralline Algae Halimeda Other Algae Macroinvertebrates Abiotic Figure 25. Proportional composition of major habitat categories within each depth zone across 8 sites at Cartier Island (sites 1 & 2) and Ashmore Reef (sites 3-8) Soft coral cover (Order Alcyonacea) was an important component of the benthic cover at some sites at Cartier and Ashmore Reefs, where it accounted for >20% and up to 50% of benthic cover. Cover of soft coral was highest on the reef slope at site 2 (north Cartier Island) but was completely absent from transects conducted at the South Cartier site (Figure 25). At Ashmore Reef, soft coral was more prevalent on the reef slope and was most abundant at site 7 in Ashmore lagoon (Figure 25). Thirteen types of soft coral were recorded on point-intercept transects. At Cartier Island, Clavularia was the dominant soft coral taxon, whilst at Ashmore Reef Isis hippuris was the most commonly recorded taxon (Figure 26). Briarium and Sinularia were recorded from Cartier Island only and Klyxum and Pinnigorgia were recorded from Ashmore Reef only. Ten taxa of soft coral recorded during 2005 surveys were not encountered in the current survey. Some taxa were observed off transects, e.g. Xenia. Page 55

12 10 Cartier Island Ashmore Reef Mean cover (%) 8 6 4 2 0 Acanthogorgia Briarium Capnella Clavularina Melithaeidae Isis Juncella Klyxum Lobophytym Nepthea Pinnigorgia Sarcophytum Sinularia Figure 26. Mean percent cover (± SE) of different genera of soft corals at Cartier Island versus Ashmore Reef. Data was pooled among depth zones and across replicate sites at each reef in the Reserves 4.3.4 Coral diversity One hundred and eighty-six species of Scleractinian (zooxanthellate hermatypic hard coral) from 14 families and 51 genera were recorded in the Reserves in the present survey (See Appendix 1). Non-scleractinian corals including octocorals (blue coral/organ pipe coral) and hydrozoans (fire coral) were also recorded. Twenty-four scleractinian species were recorded from the reserves for the first time (Table 11) and two of these species are recorded from Western Australia for the first time. Twelve species were rerecorded for the first time since 1997 surveys by Griffith (1997). An additional 24 species previously recorded in the Reserves during 2006 surveys (Kospartov et al. 2006) were not detected in the present survey (Table 12). Rather than indicating local extinctions, it is probable that species recorded in 2006 but not the in present survey still occur in the reserves however the intensive belt transect methodology deployed in the current survey prevented the detection of rare species or those occurring outside the 2-5m and 8-10m habitat zones examined here. It is also possible that some observer/identification bias has occurred between surveys conducted by different benthic specialists, particularly within Page 56

genera such as Montipora however without the collection of skeletal samples the extent to which this has occurred is difficult to quantify Table 11. New coral records from Ashmore Reef and Cartier Island Marine Reserves. Asterix indicates species recorded from Western Australia for the first time. Genera Species Genera Species Acanthastrea lordhowensis Favites stylifera Acropora grandis Favia rotumana Acropora microclados Leptastrea purpurea Acropora micropthalma Leptoseris yabei Acropora secale Montipora aequituberculata Acropora spicifera Montipora calcarea Acropora willisae Montipora incrassata Astreopora listeri Montipora stellata Echinophyllia orpheensis Platygyra acuta Favia veroni Platygyra verweyi Favia maritima* Psammocora obtusangula* Favia speciosa Psammocora superficialis Table 12. Species recorded in Kospartov et al. (2006) but not in the current survey. Genera Species Genera Species Acanthastrea hillae Montastrea annuligera Acropora anthocercis Montipora caliculata Acropora subglabra Montipora efflorescens Acropora yongei Montipora nodosa Favites flexuosa Montipora venosa Fungia danai Mycedium elephantotus Goniastrea favulus Mycedium mancaoi Goniopora norfolkensis Oxypora glabra Goniopora pendulus Pavona clavus Leptoseris mycetoseroides Pavona minuta Lobophyllia flabelliformis Physogyra lichtensteini Lobophyllia hataii Sandalolitha robusta The number of species recorded in the present survey is substantially less than the 251 recorded to occur in the Reserves in 1997 by Griffith (1997). However, the methodologies employed during this survey were not intended to ascertain reef-wide levels of biodiversity, rather sampling was focussed on providing intensive within habitat/site assessment of coral biodiversity. To better establish reef-wide levels of biodiversity sampling would need to be conducted across a wide range of different habitat-types. Nevertheless, when the additional new species recorded in the present survey are added Page 57

to the pre-existing Reserve species list, the overall biodiversity at Ashmore Reef and Cartier Island is estimated to be 275 species A recent survey of Scott Reef conducted by the West Australian Museum reported 306 species (Gilmore et al., 2008), and 278 species were recorded from the Bonaparte Archipelago (Kimberley coastline - Richards et. al. unpublished) (Table 13). Coral biodiversity decreases with increasing latitude along the West Australian coastline. Hence the current estimate of 275 species is regionally appropriate and in this context; Ashmore and Cartier Reefs are important reservoirs of regional coral biodiversity. The Reserves are optimally placed to receive warm water from the West Central Pacific Ocean via the Indonesian-flow through current (Wyrtki, 1987) which joins with the Leewin Current in the East Pilbara region and flows southward along the West Australian coastline. Table 13. Regional comparison of scleractinian coral biodiversity. West Australian location Reference Species Richness Ashmore Reef This study 275 Scott Reef Gilmore et al., 2008 306 Bonaparte Archipelago Z. Richards et al. unpub. 278 Dampier Archipelago Veron, 2004 217 Barrow Island Veron, 2004 208 Ningaloo Reef Veron, 2004 209 Houtman Abrolhos Is. Veron, 2004 192 Rowley Shoals Veron, 2004 187 Shark Bay Veron, 2004 81 Geraldton Region Veron, 2004 14 Rottnest Island Veron, 2004 19 The mean site species richness of scleractinian corals is slightly higher at Ashmore Reef than Cartier Island and higher in the deep habitat at both locations (Figure 27). Higher species richness on the slope than the reef crest is commonly observed due to the high disturbance regime in shallows from extreme hydrodynamic forces (Cornell and Karlson, 1996). Biodiversity is similar between locations at Cartier Island whereas at Ashmore Reef there are clear directional trends. In particular, the north Ashmore site has the highest coral biodiversity, followed by Ashmore South site (Figure 27). Site biodiversity is lowest at the south-west Ashmore site and also comparatively low at both lagoon locations. A larger amount of error is associated with the mean species richness at the Ashmore middle lagoon site due to the large amount of sand recorded on one of the transects. Page 58

Mean Scleractinian Species Richness (+SE) 70 60 50 40 30 20 10 0 Cartier South Cartier North Ashmore South Ashmore Southwest Ashmore East Ashmore North Ashmore West Lagoon Shallow Deep Ashmore Middle Lagoon Figure 27. Mean scleractinian species richness at the eight Reserve sites showing the deep sites have higher coral biodiversity than shallow sites. Overall, 9397 hard coral colonies were counted across the 48 belt transects. The species with the largest number of colonies recorded on transects was Seriatopora hystrix (10.6%, n = 1003 colonies). By ranking species according to their summed abundance, we describe 35 species (18.8% of the hard coral assemblage) as being key species within the reserves because their total colony count is within 75% of that of S. hystrix (listed in Table 14). These key species are critical for reef building and are the primary contributors to the observed level of coral cover (see next section). It is important to note however that a large proportion of the S. hystrix colonies at Ashmore Reef were juveniles (<3 years old) that appear to have established since the 2003 bleaching event. Eight species of common Acropora corals appear on the list of key species confirming Acropora as one of the most important genera of corals in the context of reef building. Again, a large proportion of the Acropora colonies recorded were juveniles of approximately two years of age. Species with particularly high numbers of juvenile recruits include A. cerealis, A. microphthalma, A. nana, A. millepora and A. acuminata. It is important to note however that species belonging to 14 different genera appear on the list so numerous types of coral are functionally important for reef-building within the Reserves. Octocoral (Heliopora coerulea i.e. blue coral) and Hydrozoans (Millepora spp. i.e. fire coral) also are important contributors to reef growth in the Reserves. Isopora palifera is a particularly Page 59

important microhabitat building coral forming solid vertical upgrowths on the exposed reef fronts. The largest proportion of coral species are rare within the reserves (41.4% of the assemblage, n = 77) meaning their sum of abundance is only 10% or less of that recorded for S. hystrix. Amongst those species classified here as rare are Favia maritima and Psammocora obtusangula (i.e. the two new species records for Western Australia), Lithophyllon undulatum (a species whose Australian range is restricted to WA and NT), and Lobophyllia robusta (Ashmore Reef is the western-most limit of this species). Six colonies of Tubipora musica (organ pipe coral) were recorded on transects however additional colonies were observed off transects. The remaining 39.8% (n=74) of species recorded in the Reserves reach intermediate local abundance. Page 60

Table 14. Ranked list of key hard coral species that occur within the Reserves. Key species are classified as those species with a total sum of abundance 75% or more of the most abundant species S. hystrix of which 1003 colonies were recorded on transects. All corals are scleractinian unless stated. Genus Species 1 Seriatopora hystrix 2 Isopora brueggemanni 3 Acropora austera 4 Acropora millepora 5 Isopora palifera 6 Porites cylindrica 7 Acropora cerealis 8 Pocillopora verrucosa 9 Heliopora coerulea (Octocoral) 10 Symphyllia radians 11 Seriatopora aculeata 12 Porites lutea 13 Goniastrea retiformis 14 Porites lichen 15 Montipora turgescens 16 Favites abdita 17 Acropora nasuta 18 Cyphastrea microphthalma 19 Pavona varians 20 Acropora digitifera 21 Acropora gemmifera 22 Montipora undata 23 Pocillopora damicornis 24 Porites rus 25 Montipora peltiformis 26 Galaxea fascicularis 27 Pocillopora meandrina 28 Millepora branching spp. (Hydrozoa) 29 Goniopora lobata 30 Porites nigrescens 31 Acropora cytherea 32 Acropora intermedia 33 Goniastrea pectinata 34 Millepora encrusting spp. (Hydrozoa) 35 Echinopora lamellosa Page 61

Plate 3. Selection of hard coral occurring in the Reserves. A). Acropora cytherea B). Coscinarea columna C). Favia maritima (new species record for WA). D). Merulina scabricula E). close up of plating Acropora species F). Lobophyllia hemprichii G). Goniastrea aspera (above) and Pachyseris speciosa H). Three genera, Porites, Pocillopora and Isopora commonly occur together in-situ in the Reserves. Page 62

Plate 4. Soft coral and sea fans occurring within the Reserves. A). Sinularia. B). Isis (centre) and Junceella. C). Antipatharian (black coral). D). Klyxum. E). Melithaeid Fan. Page 63

Percentage cover of scleractinian corals recorded across all transects was unrelated to species richness of corals on the same transects (Figure 28), which has important implications for management because it demonstrates that percent coral cover estimates alone do not adequately represent coral biodiversity or reef condition. Essentially this is because in coral communities it is commonly observed that a small number of species can dominate the community and obtain a high level of cover. In such situations, the monopolizing species (e.g. thickets of branching Acropora) are often clonal hence, even though there is a high level of coral cover, there is a low level of species and genetic variability within the community making it vulnerable to density dependent processes. For example, high host density is a major factor driving disease prevalence and transmission in animals (Altizer and Augistine, 1997; Rudolf and Antonics, 2005), especially under thermal stress (Bruno et al, 2007). High coral cover reduces the distance between neighbouring coral colonies (Connell, 2004) and thus between infected and healthy hosts, increasing the potential for horizontal disease transmission between corals in close proximity. It is important therefore that both coral cover estimates and coral biodiversity estimates are collected in tandem in standardized and replicated ways. 80 70 Species richness 60 50 40 30 20 10 0 0 20 40 Coral cover (%) 60 Figure 28. Regression of hard coral cover against species richness of scleractinian corals on each individual transect (n = 48). No significant relationship exists between these two variables (Regression analysis, r 2 = 0.03, df = 45, p=0.28). Page 64

4.4 Coral health 4.4.1 Coral predators Densities of two major invertebrate corallivores, Drupella snails and Crown-of- Thorns Starfish (Acanthaster planci) were very low at Ashmore Reef and Cartier Island. Drupella sp. were detected on 9 species of coral (A. acuminata, A. austera, A. intermedia, A. nasuta, A. subulata, A. verweyi, P. eudoxyi, P. verrucosa, S. hystrix) across 3 sites at Ashmore Reef (3, 4 and 6), and were most abundant at site 3. No A. planci were counted on transects, though solitary individuals were observed at the sites 3 and 6. There was also evidence of feeding scars, presumably caused A. planci on 2 species of coral at Ashmore Reef (A. digitifera and A. subulata) and 3 species at Cartier Island (Astreopora myriopthalma, Montipora peltiformis and Pocillopora verrucosa). Most massive and encrusting Porites colonies also had numerous distinct feeding scars (Plate 5C) at both exposed and lagoonal Ashmore Reef sites, caused by coral-feeding fishes (Cole et al. 2009). 4.4.2 Coral disease Prevalence of coral disease on belt transects was very low at Cartier Island and Ashmore Reef. No coral disease was recorded at Cartier Island, but one instance of a tumor was observed on A. microcladosi at site 1, and one colony of Porites lutea exhibited a pigmentation response at site 2. At Ashmore Reef, only 11 isolated cases of coral disease were observed across all 36 transects. At the southern Ashmore site, black band disease was observed on A. myriopthalma and Galaxea fascicularis. Also at this site, white syndrome was observed on Porites lichen and Echinopora mammiformis. Tumors were observed on M. peltiformis. There were also a variety of pigmentation responses on corals that appeared to be in response to abrasive impacts due to the large amount of rubble at this site. At the east Ashmore site, P. cylindrica was observed with black band disease and various white, pink and yellow pigmentation responses were observed on Montipora folveolata and Porites lutea. At the north Ashmore site, white syndrome was observed on A.austera, A. gemmifera and Montipora aequituberculata. At the Ashmore lagoon site, white syndrome was observed on Acropora intermedia, Acropora tenuis and Fungia repanda. Page 65

Plate 5. Selection of degraded reef shots. A). White band disease transmitted between Acropora colonies. B). A recently dead Acropora colony. C). Fish feeding scars on Porites lutea. D). White band disease advancing up the branches of Isopora palifera. E). Compound ascidian overgrowing a dead coral. F). Acropora rubble dominates the southern exposed reef site. G). Filamentous algae growing on rubble at the Southern exposed site. Page 66

5 Conclusions 5.3 Biogeography Ashmore Reef National Nature Reserve and Cartier Island Marine Reserve are evolutionary significant biodiversity hotspots. The reasons for this are 2-fold. Firstly, the Reserves lie at the edge of the continental shelf in the Timor Sea directly in the path of the fast westward surface flowing South Equatorial Current (10 S - 15 S) that introduces low salinity North Pacific water into the Indian Ocean (Wyrtki, 1987). However this is not the only current influencing the region. The Indonesian through-flow current is augmented by outflows from the Indonesian Seas (Godfrey, 1996) and Anticyclonic eddies (100-150km diameter) associated with the South Java Current and the Eastern Gyral Current (Sprintall et al., 2002) drive recirculation in the vicinity of the Reserves (Feng et al. 2005) (Figure 29). This unique amalgamation of currents with mixed origins creates unique opportunities for diversification. The second reason why Ashmore and Cartier are evolutionarily significant hotspots is that these reefs are thought to have persisted during glacial maxima when sea levels were more than 100m below present levels. Paleoclimatic events during the Pleistocene epoch led to an unprecedented level of speciation (Hewitt, 2000) due to the cyclic emergence and transgression of Australia s continental shelf that led to population bottlenecks during lowered sea stands and population expansions at times of high sea level. In the Timor Shelf region, sea level fluctuations caused the Reserves to become increasingly isolated. Recent research on Sea Snakes shows that in the Ashmore Reef region Aipysurus laevis (olive sea snakes) are genetically distinct and more genetically diverse than populations from the GBR and Gulf of Carpentaria (Lukoschek et al., 2007b). Such traits make the Ashmore Reef region of great importance for conservation. Page 67

Figure 29. Major current systems in the southeast Indian Ocean and ocean basins around western Australia (from Domingues et al., 2007). 5.2 Benthic communities Data presented here shows that coral cover has increased in the Reserves since the 2005 marine survey. The benthic communities are recovering well from the 1998 and 2003 bleaching events. An important finding of the current survey is that a large number of juvenile corals (2-3years old) were recorded. In 2005, there was a general absence of new recruits (Kospartov et al, 2006). Hence it is apparent that 2006/2007 was successful years for coral recruitment especially within the families Acroporidae and Pocilliporidae. The finding of 186 species of Scleractinian (zooxanthellate hermatypic hard coral) from 14 families and 51 genera on belt transects is important because it confirms that this methodology is sufficient to detect a significant proportion of the 275 species of coral that are predicted to occur in the Reserves. However it is important to reiterate that the current coral biodiversity methodology did not enable a full Reserve wide assessment of coral biodiversity moreover it provided an intensive within habitat/site assessment of coral biodiversity. Nevertheless, these results confirm that Ashmore and Cartier Reefs are important reservoirs of regional coral biodiversity. Page 68