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] Southwestern Australia is a global biodiversity hotspot. The region contains a high number of endemic species, ranging from Gondwanan relicts to more recently evolved plant and animal species. Biogeographic models developed primarily for plants suggest a prominent role of Quaternary climatic fluctuations in the rampant speciation of endemic plants. Those models were not based on explicit spatial analysis of genetic structure, did not estimate divergence dates and may be a poor predictor of patterns in endemic vertebrates. Myobatrachid frogs have featured heavily in the limited investigations of the biogeography of the regions fauna. Myobatrachid frogs are diverse in southwestern Australia, and while we know they have speciated in situ, we know little about the temporal and spatial patterning of speciation events. In order to gain insight into the biogeographic history and potential speciation patterns of Myobatrachid frogs in the southwest I conducted a comparative phylogeography of four frog species spanning three life history strategies. I aimed to: 1) assess the biogeographic history of individual species, 2) determine where patterns of regional diversity exist using a comparative framework, 3) determine whether congruent patterns across species enable the development of explicit biogeographic hypotheses for frogs, and 4) compare patterns of diversity in plants with the models I developed for frogs. I conducted fine-scale intraspecific phylogeographies on four species. ... Geocrinia leai: deep divergences, coincident with late Miocene arid onset, divide this species into western and southeast coastal lineages, with a third only found within the Shannon-Gardner River catchments. Phylogeographic history within each lineage has been shaped by climatic fluctuations from the Pliocene through to the present. Arenophryne shows the first evidence of geological activity in speciation of a Shark Bay endemic. Divergence patterns between the High Rainfall and Southeast Coastal Provinces within C. georgiana are consistent with patterns between Litoria moorei and L. cyclorhynchus and plant biogeographic regions. Subdivision between drainage systems along the southern coast (in M. nichollsi, G. leai and the G. rosea species complex) reflect the relative importance of distinct catchments as refuges during arid maxima, similarly the northern Darling Escarpment is identified as a potential refugium (C. georgiana and G. leai). Divergences in Myobatrachid frogs are far older than those inferred for plants with the late Miocene apparently an important time for speciation of southwestern frogs. Speciation of Myobatrachids broadly relates to the onset of aridity in Australia in the late Miocene, with the exception of earlier/contemporaneous geological activity in Arenophryne. The origins of subsequent intraspecific phylogeographic structure are coincident with subsequent climatic fluctuations and correlated landscape evolution. Divergence within frogs in the forest system may be far older than the Pleistocene models developed for plants because of the heavy reliance on wet systems by relictual frog species persisting in the southwestern corner of Australia.

A field-based project was undertaken to develop and test a mechanism which would allow for the correlation of the health of vegetation surrounding playa lakes in south-west Australia with the natural variation in salinity and waterlogging that occurs spatially and temporally in natural systems. The study was designed to determine threshold ranges of vegetation communities using moderately extensive data over short temporal periods which will guide the design of potential engineering solutions that manipulate hydrological regimes to ultimately conserve and protect native vegetation. A pair of playa lake ecosystems, surrounded by primary production land, was modelled with hydro-geological data collected from March 2006 to March 2007. The data was used to determine the hydroperiods of vegetation communities fringing playa lakes and provide insight into the areas and species that are most affected by extreme rainfall events which are hypothesised to have a significant, rapid deleterious effect on the ecosystems. The methodology was multi-faceted and included; a detailed topographical survey; vegetation surveys; hydrological and hydro-geological monitoring over a 12 month period. 4 The hydro-geological data and vegetation data was linked with the topographical survey at a high resolution for spatial analysis in a Geographic Information System (GIS) to determine the degree of waterlogging experienced by vegetation communities over the monitoring period. The study has found that the spatial and temporal variability of hydroperiods has been reduced by rising groundwater levels, a result of extensive clearing of native vegetation. Consequently populations are becoming extinct locally resulting in a shift in community composition. Extreme summer rainfall events also have a significant impact on the health of vegetation communities by increasing the duration of waterlogging over an annual cycle and in some areas expanding the littoral zone. Vegetation is most degraded at lower positions in the landscape where communities are becoming less diverse and dominated by salt tolerant halophytic species as a result of altered hydrological regimes. Some species appear to be able to tolerate groundwater depths of less than 2.0 m from the surface, however there are thresholds related to the duration at which groundwater is maintained at this depth. Potential engineering solutions include groundwater pumping and diverting water through drains to maintain sustainable hydroperiods for vegetation in areas with conservation value. The effectiveness and efficiency of the engineering solutions can be maximised by quantifying thresholds for vegetation that include sustainable durations of waterlogging. The study has quantified tolerance ranges to salinity and waterlogging with data collected over 12 months but species may be experiencing a transition period where they have 5 sustained irreversible damage that will result in their eventual mortality. With long-term monitoring, the methodology developed and tested in the study can be used to quantify the long-term tolerance ranges that are important for the application of conservation approaches that include engineering solutions.

Bauxite mining is a major activity in the jarrah (Eucalyptus marginata Donn ex Sm.) forest of south-western Australia. After mining, poor tree growth can occur in some areas. This thesis aimed to determine whether soil constraints, including reduced depth and compaction, were responsible for poor tree growth at low-quality restored bauxite mines. In particular, this study determined the response of jarrah root morphology, leaf-scale physiology and growth/development to soil constraints at two contrasting (low-quality and high-quality) restored bauxite-mine sites. Jarrah root excavations at a low-quality restored site revealed that deep-ripping equipment failed to penetrate the cemented lateritic subsoil, causing coarse roots to be restricted to the top 0.5 m of the soil profile, resulting in fewer and smaller jarrah trees. An adjacent area within the same mine pit (high-quality site) had a kaolinitic clay subsoil, which coarse roots were able to penetrate to the average ripping depth of 1.5 m. Impenetrable subsoil prevented development of taproots at the low-quality site, with trees instead producing multiple lateral and sinker roots. Trees in riplines, made by deep-ripping, at the high-quality site accessed the subsoil via a major taproot, while those on crests developed large lateral and sinker roots. Bauxite mining is a major activity in the jarrah (Eucalyptus marginata Donn ex Sm.) forest of south-western Australia. After mining, poor tree growth can occur in some areas. This thesis aimed to determine whether soil constraints, including reduced depth and compaction, were responsible for poor tree growth at low-quality restored bauxite mines. In particular, this study determined the response of jarrah root morphology, leaf-scale physiology and growth/development to soil constraints at two contrasting (low-quality and high-quality) restored bauxite-mine sites. Jarrah root excavations at a low-quality restored site revealed that deep-ripping equipment failed to penetrate the cemented lateritic subsoil, causing coarse roots to be restricted to the top 0.5 m of the soil profile, resulting in fewer and smaller jarrah trees. An adjacent area within the same mine pit (high-quality site) had a kaolinitic clay subsoil, which coarse roots were able to penetrate to the average ripping depth of 1.5 m. Impenetrable subsoil prevented development of taproots at the low-quality site, with trees instead producing multiple lateral and sinker roots. Trees in riplines, made by deep-ripping, at the high-quality site accessed the subsoil via a major taproot, while those on crests developed large lateral and sinker roots.

Alternative grazing systems and pasture types for wool production in the south west of Western Australia were analysed using bio-economic modelling techniques in order to determine their relative productivity and profitability. After reviewing the experimental and modelling literature on perennial pastures and grazing systems, seven case studies of farmers were conducted in order to investigate the practical application of innovative grazing systems and use of perennial pastures. Together these case studies provided information for identifying relevant variables and for calibrating the modelling work which followed. The core of the work lies in a bio-economic model for investigating the comparative value of the three grazing systems and two pasture families mentioned above. A baseline scenario using currently available and reliable scientific data provides baseline results, after which a number of sensitivity analyses provide further insights using variations of four key parameters: persistence, heterogeneity, water soluble carbohydrates, and increased losses. Results show that perennial pastures are in the studied region more profitable than annual pastures. Under current baseline conditions, continuous grazing with perennial pastures is the most profitable enterprise, but this superiority is not robust under parameter variations defined by other scenarios. The more robust solution in terms of enterprise profitability is cell grazing with perennial pastures. The results indicate that intensive grazing systems such as cell grazing have the potential to substantially increase the profitability of grazing operations on perennial pasture. This result is an encouraging one in light of its implications for water uptake and salinity control. It means that economics and land care can go hand in hand, rather than be competitive. It is to be noted that it is the choice of the grazing system in combination with the pasture species, rather then the pasture species itself, that allows for such complementarity between economics and sustainable land use. This research shows that if farmers adopt practices such as cell grazing they may be able to increase the area that they can profitably plant to perennial pasture thus reducing the impacts of dryland salinity. This finding is consistent with the findings of the case studies where the farmers perceived that, provided grazing was planned, increasing the intensity of their grazing management and the perenniallity of their pastures would result in an increase in the profitability of their grazing operation. As a result this research helps to bridge a gap which has existed in this area of research, between the results of scientific research and those reported in practice.

[Truncated abstract] Land clearing is known to increase runoff, and in many dryland landscapes is also associated with rising saline watertables, causing increased stream salinity and degrading riparian vegetation. The limited understanding of how river morphology responds to these changes and the potential for vegetation-based strategies to offer river management options under these conditions, has prompted this research. In southwestern Australia the severity of salinity and recent nature of land clearing provides an appropriate setting to investigate river response. A data-based, multidisciplinary methodology was applied to determine how land clearing and landscape salinisation has altered landscape sensitivity through changes in erosive potential, system connectivity and material threshold mechanisms, and how these affect patterns of river response. The study investigated the responses of morphologically similar reaches across fifty two study sites in the Kent River and Dalyup River catchments, in the south coastal rivers region of Western Australia. Land clearing was found to have significantly altered the hydrologic regime and erosive potential in both frequency and magnitude, with flow becoming more perennial, and increased annual discharge, flood peaks and bankfull flow frequency. While sediment transport rates have also increased since land clearing, they remain low on a global scale. Human response to a reduced rainfall regime and related water security pressures has caused large hillslope areas to be decoupled from the main channels by bank and farm dam construction, and have reduced downstream transmission of change. ... By contrast, steeper-sloped mid-catchment areas with minimal vegetation degradation caused by salinity are associated with higher erosive potential. A more erosive response is observed in these reaches where floodplains have been cleared for agricultural purposes. A conceptual model of vegetation growth across the salinity gradient observed in the study catchments was developed, and applied to selected river styles to assess the potential that vegetation-based strategies offer for river management. This work identifies the unsuitability of river restoration strategies, but the potential for river restoration or remediation in a saline landscape. Hydraulic modelling demonstrated that river rehabilitation strategies such as improving the vegetation condition of the riparian buffer using native or commercial species on areas elevated above saline flow can stabilise reaches. For river styles in wide and flat valleys, there is limited potential for vegetation-based river rehabilitation under the current salinity gradient. Field observation and modelling suggest that river remediation may offer geomorphic management options in salt-affected reaches through channelisation to lower watertables, and further research on this is warranted. This work found a consistent response for river styles across the two study catchments. Based on the understanding of river response and the potential for vegetation-based river management for each style, this research offers a regional-scale tool for river management in a saline landscape.

[Truncated abstract] Spatial structuring of genetic variation is commonly observed in plant species due to limited dispersal and local adaptation. Intraspecific genetic variation has significant implications for ecological restoration because the source of seed or plants influences patterns of gene flow, and may affect performance if there is adaptive divergence among source populations. This study assessed quantitative trait variation, local adaptation and molecular variation within three common, widespread, long-lived forest tree species from south-western Australia to understand the distribution of intraspecific genetic variation and predict the consequences of seed transfer for restoration. The geographic distribution of quantitative trait variation of jarrah Eucalyptus marginata was assessed through measurement of 15-year-old trees grown in a provenance trial. Survival of trees from the northern jarrah forest was significantly higher than that of trees from southern jarrah forest provenances, where mean annual rainfall is much higher, but stem diameter at breast height (d.b.h.) of southern jarrah forest trees was greater, implying faster growth. D.b.h. of trees from within the northern jarrah forest also exhibited a positive relationship with mean annual rainfall, with maximum d.b.h. observed in trees from provenances in the high rainfall zone. These patterns may reflect selection for faster growth under high rainfall conditions or environmentally-induced parental effects. The percentage of trees bearing buds and flowers varied among latitudinal divisions. ... Neither genetic variation within nor among populations of any species could explain variation of emergence and establishment in reciprocal transplant trials. Collectively, the findings of this study suggest structuring of genetic variation in these species at a broad, rather than a very local, scale. This is expected for widespread, long-lived species, where extensive gene flow and temporal variation are likely to favour high within, relative to among, population genetic variation. However, there is evidence that the source of seed may have a significant influence on the success of restoration of these species, whether as a result of genetic variation among populations or due to other factors affecting seed quality. These results highlight the importance of integrating studies of molecular and adaptive trait variation when seeking to understand the causes and consequences of genetic variation within plant species and contribute to the development of seed sourcing practices for improved restoration success.

[Truncated abstract] The southwest of Western Australia is an intraplate area classified as a stable continental region. It comprises predominantly Archaean and Proterozoic geology and has generally subdued topography. The region currently experiences significant seismicity in the Southwest Seismic Zone (SWSZ), which is one of the most seismically active areas in Australia and is thought to represent the highest seismic hazard of the region. In recent years, numerous scarps, potentially related to large palaeoearthquakes have been recognised not only within the SWSZ, but also in a broader region of the southwest of Australia. Palaeoseismological investigations of two of these scarps, the Dumbleyung and the Lort River scarps, confirm their association with surface-rupturing palaeoearthquakes and indicate events with likely maximum magnitudes of ~Mw 7.0 on faults of low to medium slip rates. Two trenches across the Dumbleyung Fault scarp revealed a thrust fault in alluvial sediments with two associated earthquakes in the last ca 24-60 ka. A possible Holocene age was recognised for the last recorded earthquake event exposed in these trenches. Two trenches across the Lort River Scarp show that this feature results from thrust faulting in the weathered gneissic country rock. These trenches exposed evidence of two events in the last ca 35 ka, with a likely late Pleistocene age for the last earthquake. On both sites, the earthquakes are interpreted as associated with the last phase of fault activity, which was likely been preceded by a long period of quiescence. Assessment of the earthquake hazard associated with large earthquakes at the Dumbleyung and Lort River Faults resulted in calculated peak ground accelerations of up to 2 g in the near-fault fields. Such earthquakes would significantly affect nearby towns such as Dumbleyung, Wagin, Katanning, and Esperance, but they are unlikely to cause any significant damage in Perth. The palaeoseismological investigations show that the earthquake activity in the southwest of Western Australia is not only confined to the SWSZ, as it has been considered in previous assessments of the seismic hazard, but that there is also potential for strong earthquakes across much of the region. The seismicity in the southwest of Western Australia appears to be transient and migratory. This is suggested by the lack of local relief associated with places of current seismicity and fault scarps, the widespread distribution of the fault scarps across the region, the increase in seismicity in the SWSZ following strong recent events, and the apparent long periods of earthquake recurrence at fault sites. Accordingly, the current seismicity in the SWSZ is inferred to be transient and probably associated with stress changes produced by the recent earthquakes. '...' This uplift could be associated with dynamic topography effects resulting from processes along the plate margins. The uplift is probably enhanced by a flexural response of the lithosphere to local differential loads and density contrast along the southern margin, a mechanism that may also help explain the occurrence of some earthquake activity. The results from this study, complemented by additional palaeoseismological studies must be included in future probabilistic assessments of the seismic hazard of the southwest of Western Australia.

Salsola australis is an introduced weed of crop and pasture systems in the Western Australian broad acre cropping and pasture region (wheat-belt). This thesis investigated the classification, biology and ecology of the genus Salsola in southwest Australia, as well as modelling the effectiveness of possible weed control practices. Prior to this research, S. tragus was the only recognised species of the Salsola genus within Australia. However, genetic analysis revealed that four genetically distinct putative taxa of the genus Salsola were found in southwest Australia, none of which were S. tragus. The taxa that is the most prevalent agricultural weed was classified as S. australis, but the other three putative taxa could not be matched to recognised species. All four taxa were diploid (2n = 18), as opposed to tetraploid (2n = 36) S. tragus. Within the agricultural system of southwest Australia, S. australis plants established throughout the year, although the majority of seed production occurred in late summer and autumn. Total seed production (138-7734 seeds per plant) and seed viability (7.6-62.8%) of S. australis were lower than that reported for other agricultural weed species of the Salsola genus. Seed dispersal occurred when the senesced plants broke free of their root system to become mobile. Wind driven plants travelled and shed seed over distances of 1.6 to 1247.2 m. Movement of approximately half the plants was restricted to less than 100 m by entanglement with other S. australis plants within the stand. Some seed was retained on the senesced plants, but the germinability of this seed fell to less than 2% in the two month period following plant senescence (i.e. a decline of 79%). Once seed shed into the soil seed bank, anywhere from 32.3 to 80.7% of the viable seeds germinated in the year following seed production, with the rest remaining dormant or degrading. A model of the life cycle of S. australis based on the population ecology data indicated that the dormant seed bank had very little effect on annual seedling recruitment, but seed dispersal from neighbouring populations had a large impact on population growth rate. Therefore, the most successful weed control measures were those that restricted seed dispersal from neighbouring populations, or those that were applied to all populations in the region rather than to a single population. Weed control techniques applied to a single population, without reducing seed dispersal, could not reduce population size.

Field measurements and numerical modelling of the shallow coastal waters offshore in south-western Australia were used to describe changes in the water column's vertical structure and the biological response on temporal scales of the order of hours and days. A cycle of chlorophyll a concentration, primary production, and photosystem II function on a diel timescale, which was related to changes in the solar irradiance and thermal structure, was identified. The diel cycle included (1) vertically well-mixed (or weakly linear) conditions in density and chlorophyll a early in the morning, resulting from vertical mixing through penetrative overnight convection; (2) depleted chlorophyll a concentration in the surface layer during the middle of the day due to photoinhibition; (3) an increased chlorophyll a concentration in the bottom layer by late afternoon due to optimum light conditions; and (4) the formation of a chlorophyll a break point (CBP) at the thermocline, which migrated downwards with the deepening surface mixed layer. On a longer timescale (days), moored acoustic instruments were used to derive echo level (EL), which approximated suspended particulate matter (SPM). Wind events ultimately controlled SPM, a conclusion based on (1) elevated EL during high windgenerated turbulence and bed shear stress, (2) positive time-lagged correlations between wind speed and EL at three field sites with different exposures to wave action, and (3) significant negative correlations between wind speed and depth-differentiated echo level (d(EL)/dz) at all sites. Sea breezes produced a similar response in EL through the water column to a small storm event, and wind-driven SPM resuspension resulted in a reduction in the sub-surface light climate (kd). Near-bed dissolved oxygen concentrations varied in accord with elevated wind speeds, EL and kd, highlighting a possible suppression of photosynthesis. One-dimensional modelling revealed that wind stirring was most often the dominant process in these waters. It was found that for a brief period during thermal stratification there was shear production of turbulent instabilities that migrated from the thermocline to the surface and the seabed. Convective cooling was not able to mix the water column entirely overnight without the addition of wind, and minimum wind speeds were determined for this complete vertical mixing. Bottom-generated turbulence was limited to a small region above the bed, and was deemed insignificant compared with mixing generated at the surface. Minimum wind speeds required for de-stratification and prevention of stratification were determined for summer, autumn and winter. A hypothetical desalination outfall was simulated for all seasons and it was concluded that positioning of the discharge at middepth was preferable compared to at the seabed. The results of this thesis advance the current knowledge of coastal biophysical oceanography and provide new insights into the temporal dynamics of the coastal water column of south-western Australia.