Generalist herbivores profoundly influence the biomass and species composition of macroalgae assemblages. In subtidal ecosystems of temperate latitudes, large invertebrates are usually the most influential herbivores. I tested the prediction that exclusion of invertebrate herbivores would lead to changes in the biomass and species composition of the macroalgae assemblages that are a prominent feature of the reefs in south-western Australia. The most abundant invertebrate herbivores were sea urchins (Heliocidaris erythrogramma, Phyllacanthus irregularis and Centrostephanus tenuispinus), and these occupied different trophic positions. Heliocidaris was present at virtually all reefs surveyed, and was particularly abundant in the Fremantle region. Analyses of stable isotopes and direct observations of gut contents revealed that it was almost exclusively herbivorous, and that it mainly ate foliose brown algae. In contrast, Phyllacanthus and Centrostephanus were omnivorous; while they consumed large proportions of algae, a substantial proportion of the diet of both species was animal tissue. Because Heliocidaris is a generalist herbivore that occurs at high densities, it could exert a large influence on the macroalgae assemblage. This prediction was tested by a series of press experiments. Contrary to the prediction, Heliocidaris exerted a very minor influence on the biomass, and no detectable influence on the species composition, of attached macroalgae. However, it exerted a major influence on the retention of drift macroalgae and seagrass by trapping and feeding on drift. It exerted a particularly strong influence on retention of the kelp Ecklonia radiata. This kelp was not abundant in the attached algae assemblage (when all plots were pooled it ranked 35th in biomass), but was abundant as drift (ranking 1st). Most of the drift Ecklonia was retained by sea urchins, rather than freely drifting.Herbivorous fish may also influence macroalgae assemblages. To compare the effects of sea urchins versus fish on recruiting and adult macroalgae a 13-month exclusion experiment was conducted. There were no detectable effects of sea urchins (mainly Heliocidaris) on either recruiting or adult macroalgae. There were some patterns in the biomass of recruiting algae consistent with an influence by herbivorous fish; however, these patterns were also consistent with the presence of artefacts (shading and reduced water flow) by fish exclusion devices. I began with the prediction that large invertebrate herbivores were a major influence on the macroalgae assemblages of subtidal reefs in south-western Australia. Overall, there was little evidence to support this prediction: within spatial extents of tens of square metres and over periods of 1-2 years, only minor effects were detected. However, it remains plausible that herbivores exert an influence over long time periods across large spatial extents in south-western Australia. I propose that trophic subsidies support the comparatively high densities of Heliocidaris that exist at some reefs. I further propose that these subsidies mediate the effects of sea urchins on the attached macroalgae assemblage, and that they might play an important role in energy and nutrient cycling in these nearshore ecosystems.

[Truncated abstract] The ecological effects of marine protected areas (MPAs) in temperate ecosystems are poorly understood relative to their tropical counterparts. The limited number of rigorous empirical studies supporting existing theoretical models, increasing public awareness of the importance of marine conservation strategies and legislative requirements to review management effectiveness provide further impetus to study temperate MPAs. Investigations should consider confounding effects of natural variability if MPA effects are to be clearly demonstrated. This research helps to address these needs by investigating the short term effects of sanctuary zones (no-take MPAs where fishing is prohibited) and wave exposure at Marmion Marine Park, Western Australia. The three sanctuary zones at Marmion Marine Park are extremely small (0.061 0.279 km2) compared to most reported in the literature. The sanctuary zones are nested within a larger, fished zone (94.95 km2). The sanctuary zones have been protected from fishing since the year 2000. A post-hoc, asymmetrical sampling design was used in this study and involved surveys of fishes, mobile invertebrates and macroalgae at one sanctuary zone and two fished sites (controls) at each of three successive, subtidal reef lines. The three reef lines are exposed to a gradient in wave energy. The size structure and abundance of the heavily exploited Panulirus cygnus (Western Rock Lobster) were positively affected by protection from fishing in sanctuary zones, despite the highly mobile nature of this migratory species. The mean abundance of legal size lobsters was higher in sanctuary zones compared to fished sites during an interannual study (2003, 2005 and 2006). The total abundance of lobsters and the mean abundance of legal size lobsters were higher at inshore and offshore sanctuary zones compared to fished control sites during a 2005/2006 fishing season study. These zoning effects did not vary with the time of survey. ... Furthermore, the abundance of large lobsters in sanctuary zones decreased with the duration of the 2005/2006 fishing season. Similarly, it is likely that sanctuary zones are too small relative to the movement of fishes to adequately protect stocks of some targeted species. The small sanctuary zones at Marmion are unlikely to offer protection to highly mobile species over the long term. And finally, ecological assemblages within each level of wave exposure are distinct. Consequently for each assemblage type, the current reserve design does not include replication of sanctuary zones and does not offer any 'insurance' in the event of isolated impacts affecting a particular zone. This study has identified the benefits and deficiencies of the design and function of small no-take temperate MPAs in Western Australia. An increase in the size and number of sanctuary zones within each wave exposure level will help to address the v shortfalls of the zoning scheme and enhance the conservation benefits of management at Marmion Marine Park. More generally, this study demonstrates that the mobility of the species to be protected from fishing should be considered when designing MPAs. Lessons learned from this work will be beneficial for the future management and conservation of resources in the region and elsewhere.

Latitudinal patterns in reef fish assemblages reflect the influence of long-term environmental conditions, evolutionary processes and the recent, short-term influence of fishing. Long-term processes generate the typically common latitudinal patterns in reef fish assemblages, such as decreases in diversity and herbivory towards higher latitudes. These patterns reflect the global gradient in water temperature and the isolation of temperate regions from the tropics. Fishing also influences reef fish assemblages in that it decreases the abundance of large-bodied carnivore species on reefs, often leading to over-exploitation, depletion and in some cases the extirpation of populations. Indirectly, the removal of these large-bodied carnivores can influence the abundance of their prey, leading to an increase in non-target species. This study examines the latitudinal patterns in reef fish assemblages across a unique biogeographic region, the temperate Western Australian coast, and incorporates an investigation of the influence of fishing on the structure of these assemblages. Seven regions across seven degrees of latitude and seven degrees of longitude covering approximately 1500 km of coastline were sampled. Fish assemblages were characterised at each region using diver operated stereo-video transects. At each region, four locations, and within each location, four reefs were surveyed totalling 1344 transects. A significant gradient in water temperature exists with latitude and longitude. Along the Western Australian coast, and in contrast to other regions species diversity of reef fish increased towards higher latitudes and there was no evidence for a decrease in the biomass and abundance of herbivorous reef fish. The presence of the poleward flowing warm water Leeuwin current combined with the absence of major extinction events means the temperate Western Australian coast contrasts with global latitudinal trends in reef fish assemblage structure. The unique biogeographic history of temperate Western Australia has also generated a high degree of endemism among reef fish. Nearly 30 % of the species found along the west coast in this study are endemic to Western Australia, with the narrow range of these species playing an important role in the large scale patterns and spatial vi heterogeneity in reef fish assemblage structure. Furthermore, many of these endemic species are large-bodied carnivores and targeted by fishers. The impact of fishing on the abundance of large-bodied carnivores throughout the Western Australian temperate region is clear both spatially and temporally. The distribution of fishing effort is greatest along the west coast and decreases towards the south following the gradient in SST. Along the west coast, high levels of fishing effort have reduced the biomass and abundance of target carnivores to well below the standing biomass of the south coast where a low level of fishing effort occurs. This reduction in biomass is related to the historical declines in catch per unit effort (CPUE) of many key target species. These target species include endemic species such as Choerodon rubescens, Glaucosoma herbraicum, Epinephilides armatus Nemadactylus valenciennesi and Achoerodus gouldii.

[Truncated abstract] Kelp beds of South-Western Australia have high alpha (within habitat) diversity, through high species turnover at small spatial scales. The E. radiata canopy has a strong negative influence on the diversity of the understorey through intense interspecific competition for light. Literature suggests that when the competitively dominant species such as E. radiata are physically removed, diversity will increase, as less competitive species become more abundant. Apart from disturbance, evidence suggests that reef topography at the 1-10 m vertical scale also has an influence on the structure of the kelp beds, particularly in reference to relative abundance of canopy algae and species richness of the assemblage. In this thesis, I explore the role of algal assemblage recovery from physical disturbance to maintain high diversity. I also investigate the influence of reef structure (in terms of topography at the 1-10 m vertical scale) on assemblage recovery. This thesis provides a valuable functional explanation for the high diversity observed in South-Western algal assemblages. In addition, it explores the influence of reef topography which has received little attention to date . . . Overall, this thesis argues that the high alpha diversity in algal assemblages of South-Western Australia is due to local scale processes including disturbance and assemblage recovery which generate diversity by the creation of species rich gap states and by phase-shifts during the recovery process, creating a mosaic of different patch types. Assemblage recovery is composed of several processes, including survival of juvenile kelp sporophytes and canopy shading, added to macroalgal diversity through spatial and temporal variation in their outcomes. Reef topography contributed to algal diversity by influencing the processes associated with assemblage recovery through alteration of key physical variables including light levels and water motion.