The New Zealand green-lipped mussel, Perna canaliculus, is farmed by an aquaculture industry (> NZ$ 150 million/year) that is dependent on mussel juveniles (spat) collected from unpredictable and unreliable wild sources for more than 80% of its mussel seed requirements. Most wild-caught spat is collected from the surf zone at Ninety Mile Beach, northern New Zealand, where unique environmental conditions cause the accumulation and transport of spat attached to drift algae, which arrive to the shore in great quantities (up to 100 tonnes at once). This study is the first to investigate the ecology of mussels at Ninety Mile Beach throughout their life history, including reproductive behavior, micro-scale settlement patterns on filamentous macroalgae, accumulation and transport of mussel spat to the shore, colonization of the rocky intertidal, and adult population dynamics. Histologic investigation of 4 intertidal and 2 subtidal populations revealed that females and males were well-synchronized throughout their reproductive cycles, with a prolonged spawning season from June to December, when temperatures were lowest and rising. Comparisons of gonad indices and maximum shell length indicated high productivity in certain populations, which likely contribute to the high larval availability of the area. Experiments showed that mussel spat preferentially settled on fine-branching natural and artificial substrata, with correlation evident between mussel shell size and degree of branching. Furthermore, greater numbers of mussels settled on node versus internode areas within natural and artificial substrata. Chemical cues for mussel settlement also were studied using phytogel plates spiked with algal extracts, which were preferred over control plates by mussel larvae/post-larvae in the field, and by hatchery-reared larvae in the laboratory. Three intertidal populations were investigated at different temporal and spatial scales. Mussel concentrations in seawater were higher after spawning for both small mussels (< 0.25 mm) in August, and for larger mussels (> 0.5 mm) in March. Settlement patterns within quadrats cleared of mussels in 2 habitats (adult mussel bed and adjacent areas covered with algae) were studied from July 1999-March 2001. Primary settlement (mussels < 0.5 mm) was found to dominate the algal habitats at the beginning of the spawning season in August, while secondary settlement (mussels > 2.0 mm) was higher in the adult mussel bed late in the spawning season (November-March). Monthly surveys of undisturbed quadrats indicated that a peak in new recruitment coincided with a peak in adult mortality in August. At Scott Point, massive mortality for 2 years in August was followed by a dramatic re-colonization of the empty spaces by juveniles. Settlement patterns of mussels on suspended ropes in the water column were investigated at 3 water depths inside and outside Ahipara Bay during 2 spawning seasons (1999-2000). Mussel settlement was higher for small mussels (< 0.49 mm) in shallower water (2 m water depth) in August, and higher for larger mussels (> 1.0 mm) at greater depths (18 m water depth) in September-December. Mussels found on shallow-water ropes may have settled directly from the plankton, whereas mussels on ropes near the bottom (18 m) may have transferred from macroalgae tumbling on the seafloor. Environmental conditions associated with mussel spat arrival to the beach (spatfall events) were studied by statistical analysis (1990-1998; daily, monthly, inter-annually) of wind speed/direction, tidal range, water temperature, swell height/direction, and records of spatfall events/amounts. Spatfall events/amounts were more abundant during days of strong offshore winds. Swell height in the onshore direction was significantly correlated with spatfall events/amounts. Storm events (wind speeds > 20 m/s) were most frequent between May-August; spatfall events/amounts were more numerous 4 months later (September-October). Years with more storm events (El Niño/La Niña episodes) were associated with significantly higher spatfall events/amounts.

This thesis examines sublethal stress responses in the common New Zealand estuarine bivalve, Austrovenus stutchburyi (cockle). The approach used throughout this thesis is a refinement of the biological indicator approach of Adams (1990), in which biomarker data are collected primarily at the individual and sub-organismal levels, but with additional measurements at the population and community levels. In this research several biochemical and physiological biomarkers are used to assess effects of contaminants on energetics, fecundity and growth of cockles. Adenylate energy charge (AEC) and total adenylate nucleotide pool (TANP) are biomarkers that have previously not been used with A. stutchburyi, and provide new information on energy cycling for this species. RNA concentration has also not previously been used with cockles, and this biomarker is correlated with growth. Glycogen concentration and condition indices are used to indicate reproductive potential and overall health. In order to fully investigate the utility of this comprehensive suite of biomarkers, their performance in laboratory and field situations was tested. Temporal variability in AEC, TANP and glycogen was analysed over two years for two populations of cockles in a northern harbour. The results indicated seasonal patterns for all biomarkers, with AEC reaching a maximum value in spring, TANP being lowest in winter, and glycogen concentration being high over spring and summer. Variability in biomarker response between cockles sampled at low tide and high tide was analysed in a laboratory experiment simulating exposure to air during low tide. Adenylate energy charge was found to be significantly lower in cockles after exposure to air for 4 hours, highlighting the importance of standardised collection protocols. These initial patterns, as well as spatial variability in biomarker response, were further investigated at several sites within a second harbour south of Auckland. There was little among site difference in glycogen concentration, and the data suggested that differences in site characteristics, such as sediment quality and type, were driving the mixed response patterns of AEC, TANP and condition. Because of inherent variability in field conditions, a series of laboratory experiments was then undertaken to assess responses under carefully controlled conditions. Cockles were challenged with PAHs, chlordane and tributyltin at two different doses, and biomarker response (AEC, TANP, glycogen and RNA) measured. One trial examined the effects of a one-off pulse of contaminant, in which sediment containing cockles was dosed at the outset of a 14-day experiment with a high concentration of contaminant. A daily dose of this same concentration of contaminant was supplied to the sediment for 14 days in a second trial to assess effects of a more continuous discharge. There were virtually no significant differences in biomarker response between treatments and controls for either trial, suggesting that the experimental setup may have been causing sublethal stress in some way. Finally, in order to maximise experimental control whilst maintaining environmental realism, a manipulative field experiment was undertaken in which cockles were transplanted from an uncontaminated site to a series of uncontaminated and contaminated sites in one of Auckland's major harbours. Biomarker response (AEC, TANP, glycogen and RNA) was measured in the transplanted and the autochthonous populations two weeks and eight weeks after transplantation. An ability to regulate adenylate nucleotides was detected, as cockles transplanted to contaminated sites had reduced TANP but maintained AEC levels. There were significant differences in glycogen and RNA among sites, with highest levels detected in cockles transplanted to an uncontaminated site. This suite of biomarkers showed great utility for use in environmental quality assessment. It is recommended that an approach such as that used in the Mussel Watch programme in the United States be employed for cockles, in order to monitor estuarine ecosystem health in New Zealand. The transplantation of cockles to estuaries where there are concerns about environmental quality, and the use of TANP, glycogen and RNA concentration to assess sublethal stress, has potential as a sensitive and cost-effective environmental monitoring technique for estuaries in New Zealand.

The eggs and larvae of the New Zealand snapper Pagrus auratus are pelagic with early buoyancy provided by dilute body fluids. The swimbladder begins to develop on the third day after hatch from a dorsal evagination of the gut tube. Communication w1h the gut is lost on about the tenth day following pneumatic inflation at around day eight. At this age the gas gland system appears fully functional and capable of secreting gas. By the age of settlement at around 30 days the swimbladder is a fully functional replica of the adult form except for the lack of a resorbent capillary system which does not develop until later in juvenile life. The swimbladder of the adult is of the euphysoclist form with a dorsally located resorbent oval area and sits high in the pleural cavity. The ventral tunica externa is firmly attached to the connective tissue lining the pleural space. The adult swimbladder displaces 5.6% of the volume of the body and its volume is regulated to provide near neutral buoyancy. The connective tissue integument provides almost no restriction to volume changes brought about by vertical movements of the fish and the swimbladder obeys Boyle's Law for physiological pressure changes. The ability of the connective tissue of the tunica externa to accommodate large tissue strains is due to massive regular crimping of otherwise straight collagen fibrils allowing reversible extensions up to 130%. In all other respects however the tissue structure of the tunica externa is consistent with a tissue providing an active mechanical role. The fibrillar morphology and physicochemical properties of swimbladder collagen is consistent with the vertebrate type I form however there are interesting variations in collagen form distributed throughout the swimbladder. Fibrillar morphology of the highly extensible tunica interna is significantly different to that of the tunica externa and appears to play very little mechanical rote. The extensibilty of the tunica externa appears to be regulated by physiological stress and related to the past history of tissue strain.

The characterisation of the universal features of intertidal zonation on rocky coasts (Stephenson and Stephenson 1949; 1952; 1954; 1961) has stimulated many attempts t o explain the factors responsible for the observed patterns of distribution. Initial investigations which were essentially confined to the effects of a single factor upon different species suggested that ecological position was often correlated with physiological response. Recent studies have indicated that the subtidal distributions of algae show characteristic patterns (Kitching 1941 ; Bergquist 1960; Kain 1960; 1971; Morgans 1961 ; McLean 1962; Schwenke 1966; Neushul 1967; Clark and Neushul 1967; Larkum et al.1967; John 1971). However, there have been relatively few attempts to examine in detail and subsequently integrate the physiological response to environmental factors of major belt-demarcating algae of the sublittoral . The four New Zealand species of Carpophyllum are inhabitants of the uppermost sublittoral and the sublittoral fringe (Bergquist 1960; Dromgoole 1965). This particular study was undertaken in an attempt to elucidate the subtle differences in response which determine the distribution limits characteristic of each species. There is little information on the biology of Carpophyllum with the exception of some anatomical and embryological work (Delf 1939; Dawson 1940; Naylor 1954) and an earlier investigation of C. maschalocarpum (Dromgoole 1965). Thus to provide a basis for physiological experiments preliminary studies were directed to the following aspects: ( i ) a brief review of the morphology, anatomy and taxonomy of the genus, ( ii ) growth of sporelings in laboratory culture using various seawater media, ( iii ) definition of the geographical and vertical limits of the four species and a general study of their ecology with emphasis on population distributions, periodicitiy of reproduction and plant composition in relation to environment. The physiological response of algae to environmental factors has been examined by previous workers at the protoplasmic level using the criterion of resistance (e.g. Biebl 1956, 1962; Kanwisher 1957); at the metabolic level by measurement of photosynthesis and respiration (e.g. Chapman 1961n) ; and at the level of the whole plant by growth rates in laboratory cultures (e.g. Kain 1965) or of selected individuals in the field (e.g. Klugh and Martin, 1927). Attempts to culture Carpophyllum were not entirely successful. An earlier investigation indicated that the growth rates of Carpophyllum in situ are difficult to assess (Dromgoole 1965) and hence the metabolic approach, which does allow some integration of response to several factors by means of carbon balance calculations (e.g. Brown and Johnson 1964), has been used extensively in this study. The metabolic activity of large brown algae varies considerably with age and part of plant (Clendenning and Sargent 1957a, b; Chapman 1961a). To eliminate sampling problems in Carpophyllum a cuvette allowing continuous long-term monitoring of oxygen exchange of a single piece of material was developed. This laboratory apparatus has shown that the photosynthesis and respiration of the various organs is sensitive to environmental changes in pH, C02 supply, oxygen tension, light , water flow, dehydration and temperature. The nature and possible causes of the response t o each factor were examined in detail as this was considered essential to any interpretation of their ecological significance. Finally, the information obtained from these gas exchange measurements has been integrated by means of metabolic balance calculations and a descriptive synthesis of field and laboratory results has provided a general picture of the biology of these plants.

The scope of the present work is the systematic revision of the Demospongiae of the N.Z. region, here defined as including North and South Is. and all outlying islands as far north as Three Kings and South to Auckland and Cambell Is. The Kermadec Is. are not considered as part of the N.Z. region, but the sponges recorded from these islands are revised in the sytematic account. At present, 243 species of Demospongiae are recorded for this region, these belonging to 124 genera and 35 families. Of this total 49 species have been described as new and forty-six species are recorded as new to the fauna in this work.

The humpback whale was almost driven to extinction by commercial whaling in the Southern Ocean. Little is known about the degree of interchange among the remaining Southern Hemisphere populations. This thesis aimed to assess the connectivity among breeding grounds, feeding areas and migratory corridors of humpback whales using mitochondrial and nuclear DNA markers. The population structure of humpback whale populations in breeding grounds across the South Pacific and eastern Indian oceans was investigated, with an interest in the origins of whales in eastern Polynesia, using an extensive collection of mitochondrial DNA (mtDNA) sequences (n = 1,112; 470 base pairs in length). Samples were obtained from living whales at six breeding grounds: New Caledonia, Tonga, Cook Islands, French Polynesia (Society Islands), Colombia and western Australia. We found significant differentiation, at both the haplotype and nucleotide level, among the six breeding grounds (FST = 0.033; ΦST = 0.022) and for most pair-wise comparisons. The differentiation of the eastern Polynesia humpback whales is consistent with the hypothesis of a relic subpopulation, rather than vagrancy or colonization from known neighbouring breeding grounds. Regardless of their origin, it seems probable that islands of eastern Polynesia are now the primary breeding grounds for humpback whales feeding in the management Area VI (170°W – 120°W) of the Antarctic, as defined by the International Whaling Commission. A population of humpback whales migrates along the western South American coast, with breeding grounds mainly off Colombia and Ecuador and feeding areas off the western coast of the Antarctic Peninsula and in the channels and fjords ofsouthern Chile. We analysed the genetic relationship between humpback whales from these two summer feeding areas of the eastern South Pacific population to assess the potential heterogeneity in the migratory pattern of the population. We compared mitochondrial DNA control region sequences from 132 whales from the Antarctic Peninsula and 52 whales from the Magellan Strait areas. An AMOVA showed significant differences between the two feeding areas (FST = 0.180; ΦST = 0.169). A phylogenetic analysis showed both areas are represented in the AE clade that is only found in the Southern Hemisphere in the Colombian breeding ground. Genetic and previous demographic data (based on photo-identification) strongly suggest that both feeding areas are related to the same breeding ground but that heterogeneity exists among the feeding areas of this population, similar to that observed in the North Pacific and North Atlantic populations of humpback whales.Humpback whales migrating through eastern Australia and New Zealand have been linked with those breeding off northeastern Australia, New Caledonia, Fiji and Tonga, forming a single stock (Breeding Stock E). We investigated the relationship between the New Caledonian and Tongan breeding grounds, based on interchange of individual whales (genetically identified) and population genetic differentiation (mitochondrial DNA control region sequences and nuclear DNA microsatellites). We found significantly higher recapture probabilities within each breeding ground compared to the recapture probability between them using genetic identification, and significant differences at the population level in the FST and ΦST for mitochondrial and nuclear markers. These analyses suggest differentiation among the Breeding Stock E, supporting a proposed sub-stock division for New Caledonia (E2) and Tonga (E3). Historically, humpback whales off New Zealand coasts were caught during their migratory journeys between Antarctic feeding areas and tropical breeding grounds in the South Pacific. Here we investigated the genetic diversity of New Zealand humpback whales, comparing mitochondrial DNA control region sequence data with that from breeding grounds across the South Pacific (New Caledonia, Tonga, Cook Islands, French Polynesia and Colombia) and eastern Indian (western Australia) Oceans. We analyzed 30 samples collected around New Zealand, revealing 20 haplotypes. All haplotypes were found in New Caledonia and some were also found in other breeding grounds. New Zealand humpback whale haplotype diversity and nucleotide diversity were similar to those from the compared breeding grounds, but were significantly different at haplotype level from the Cook Islands, French Polynesia and Colombia breeding grounds. We found significant differences at haplotype level with the same three locations when a pair-wise AMOVA was performed. Three breeding grounds (western Australia, New Caledonia and Tonga) did not show significant differences at either nucleotide or haplotype levels. This genetic evidence and the available demographic data suggest a closer relationship of the New Zealand stock with New Caledonia and to a lesser extent with Tongan whales, supporting New Zealand as a primary migratory corridor for the humpback whales breeding in these western Pacific Islands.

This thesis examined the relative importance of natural and human influences to the population and assemblage dynamics of reef fishes in northeastern New Zealand. In particular, how different reef fishes responded to the implementation of no-take and partial marine reserve protection, and physical factors responsible for spatial differences in fish abundance. Included were data from prior to the establishment of a no-take marine reserve, multiple fished reference locations, biannual sampling and the use of two independent methods to provide quantitative estimates of fish abundance and size. This combination of factors is rare in studies of marine reserves was an important strategy leading to an improved understanding of the mechanisms structuring fish communities. Responses of the reef fish assemblage to changes in fishing mortality were examined at the Poor Knights Islands Marine Reserve. Full no-take marine reserve protection was implemented on the 1st Oct 1998 but for the prior 17 years, the Poor Knights Reserve comprised only two small no-take zones and allowed recreational fishing in the rest of the reserve. Following implementation of no-take marine reserve status the reef fish community changed rapidly; there were no obvious changes at either reference location. Species targeted by fishers, such as Pagrus auratus (snapper) and Caprodon longimanus (pink maomao), responded most strongly to protection. An increase in the density of some non-targeted species can probably be attributed to climatic effects, rather than a reduction in fishing pressure. A decline in the abundance of several species at the Poor Knights may have been a result of natural mortality, or competitive or predatory interactions with snapper. Along with human influences (fishing), physical variables are important in determining the distribution and abundance of reef fish. Four locations (two mainland and two island) were surveyed in northeastern New Zealand to determine spatial patterns for seven labrid species, one of the most abundant and widespread taxa of reef fish in New Zealand. The underlying mechanisms were then explored through an examination of the relationship between swimming ability (as examined through pectoral fin morphology), exposure and depth. Each of the four locations consistently displayed distinct labrid assemblages, likely due to the influence of the East Auckland Current. Regardless of location, there was a consistent depthrelated trend for most labrids and a trend for some species to be associated with certain levels of wave exposure. By analogy with tropical labrid assemblages, it was expected that there would be a clear relationship between pectoral fin aspect ratio and depth and/or exposure. However, this relationship was not strongly evident suggesting that wave exposure may not be as important for labrids on northeastern New Zealand reefs as hypothesised for tropical coral reef systems. The response of snapper, an important recreational and commercial finfish, was investigated following the cessation of all fishing at the Poor Knights. The rate of response of snapper to protection was rapid, in areas that had previously been partially protected as well as in those that had been fully protected from fishing, with the overall density of legal sized fish increasing by 7.4 times over 4 years, likely a result of recolonisation rather than recruitment. The 818% increase in snapper biomass has the potential to enhance areas outside or within the reserve through the export of biomass (eggs and/or larvae and adults) - the daily batch fecundity was 11 to 18 times higher at the Poor Knights compared to the reference locations. The effects of partial protection on reef fish were further examined at the Mimiwhangata Marine Park, an area where recreational fishing is permitted but all commercial fishing has been prohibited for 18 years. Snapper showed no difference in abundance or size between the Mimiwhangata Marine Park and adjacent control areas, with the density of snapper most similar to fished reference locations. The lack of any recovery by snapper within the Marine Park, despite the exclusion of commercial fishers and restrictions on recreational fishing, and results from the Poor Knights, indicates that partial fishing regulations are ineffective as conservation tools for protecting targeted species or for fish communities in general (i.e. through reduction in by-catch). Results from this study provide evidence that recreational fishing has significant impacts on reef fishes.

The decline of coral reefs is well documented, yet a detailed understanding of the processes involved in the establishment, persistence, and ecology of the coral-dinoflagellate associations still remains largely unknown. The advent of molecular techniques has resulted in significant advances in understanding the molecular diversity present of symbiotic dinoflagellates from the genus Symbiodinium, but information concerning the functional, ecological, and biogeographical significance of this expanding symbiont diversity remains limited. This thesis therefore used molecular methodologies to uncover Symbiodinium diversity in Stylophora pistillata, Pocillopora damicornis, and Seriatopora hystrix at ecological scales, in response to thermal stress, and to long-term environmental shifts. In addition, all the molecular methods currently used in Symbiodinium research are critically reviewed to provide an important baseline for future studies. The application of ITS2-DGGE coupled with the integration of alternate speciation concepts and analyses showed great merit in assessing Symbiodinium diversity in S. pistillata, P. damicornis, and S. hystrix along a depth gradient (3 m to 18 m) at Heron Island on the Great Barrier Reef (Australia), and emphasizes that sampling regimes should focus on the role of symbionts within their functional habitat. S. pistillata associates with symbionts C78 or C35/a in shallow areas and C79 in the deep, but also harbors a generalist type C8/a that can be found at all depths. P. damicornis harbors C42/a in shallow areas while C33/a is generally found in deeper reef zones, although it is occasionally observed in the shallows. On the other hand, S. hystrix only harbors a single symbiont (C3/t) at all depths. The data from Chapter 2 therefore shows that closely related symbionts within a single clade can diverge rapidly under influence of ecological differentiation whereby each symbiont represents a separately evolving lineage that occupies a specific ecological niche. As such, closely related symbionts are likely to have evolved specializations that optimize performance within their environmental range. Previous studies have sought to explain the bleaching susceptibility of scleractinian corals as a function of the presence or absence of six major clades of Symbiodinium. In chapter 3 it is shown that sub-cladal types of clade C in S. pistillata differ in their response to thermal stress, and these differences are as large as those previously reported between different clades. Molecular (ITS2-DGGE) data is integrated with physiological measurements (PAM fluorometry, host protein, symbiont cell density) to investigate the response to stress (bleaching) and is directly related to fine-scale differences in symbiont-types. This suggests that the cladal distinction of Symbiodinium is insufficient to explain the highly variable responses commonly seen in reef-building corals. Furthermore, the results highlight that shifts in symbiont community within a host population are due to differential mortality rather than the uptake of novel symbionts. It therefore appears that changes in the thermal tolerance of corals by acquiring novel more resistant Symbiodinium to meet the challenges of global warming may be restricted, and as such cannot be expected to prevent large-scale reef degradation. Whilst most Symbiodinium cladal studies have focused on bleaching, Chapter 4 combines molecular (ITS2-DGGE) and physiological analyses (PAM fluorometry) to assess the flexibility of the coral–symbiont assemblages in S. pistillata, P. damicornis, and S. hystrix when faced with long-term shifts in key environmental conditions. To test this, a 32 month reciprocal transplant experiment was set-up on Heron Island, whereby corals were transplanted to a new light environment, i.e. shallow to deep, or deep to shallow. Although some host-symbiont combinations were able to shuffle sub-cladal symbiont types, almost all colonies reverted back to their original type within 7 to 12 months. Interestingly, transplanted colonies showed a broad acclimatory response by adjusting their physiological responses to those of the control colonies at the transplanted depth. However, those that persisted with sub-optimal symbiont types suffered disproportionate rates of mortality at the onset of additional stress (bleaching). This suggests that, despite their large acclimatory capacity, the holobiont was likely living at the limits of its tolerance range. As such, it appears that coral species cannot readily form a novel symbiotic unit by changing their symbiotic partner in response to prolonged periods of change, and it is therefore unlikely that they will be able to adjust their symbionts in an attempt to cope with changing global conditions. Finally, Chapter 5 reviews the different DNA markers (18S, 28S, ITS1, ITS2, cp23S) and screening methods (RFLP, LICOR, SSCP, DGGE, cloning-sequencing) currently applied to uncovering Symbiodinium diversity. Current rDNA markers are used to identify ancient or more recent evolutionary lineages and separate symbionts into broad groups such as clades, as well as uncovering fine-scale differences between ecologically different sub-cladal types. The 18S and 28S rDNA in combination with RFLP are appropriate for studies that focus on large groupings at the cladal level and may uncover broad biogeographical. However, studies on the ecology or physiology of host-symbiont associations clearly benefit from the capacity to detect the full level of variability present within a community (e.g. 28S-SSCP, ITS2-DGGE). Despite the suitability of the rDNA, it is an imperative that sequence information is combined with ecological data in order to accurately predict how each hostsymbiont combinations responds as a unit that is optimized to function within the range of its distribution. Symbiont types present in individual hosts are shown to be distinct cohesive groups that are not interchangeable on an ecological, functional and evolutionary scale. In summary, this thesis expands on the current knowledge of the role of Symbiodinium on coral reefs and introduces a number of novel concepts. It is imperative that effort and resources continue to be channelled to combine genetic and ecological studies on Symbiodinium, as they appear to be an important factor driving responses of their host. Although diversity assessments would benefit from the development of a single-copy molecular marker, it is important to continue utilizing current methodologies to increase our knowledge of coral-symbiont diversity if we are to understand and manage coral reefs in the short-term as environmental conditions continue to change.

Estuarine ecosystems are under enormous stress due to rapid coastal developments and climate change. Proper management of these important ecosystems requires a good understanding of their key processes. In this thesis, riparian groundwater-surface water interaction is explored for an aquifer-estuary system primarily by a series of numerical experiments. The work focuses on riparian-scale groundwater flow and salinization. The overall aim of the study was to extend our understanding of aquifer-estuary exchange, which is currently centered on the lower marine estuarine reach, to middle estuaries (i.e., the estuary reach that has variable salinity). The numerical experiments were guided by previous studies and observations made from an exploratory field investigation conducted in and next to Sandy Creek, a macro-tidal estuary incised in the alluvial aquifer of the Pioneer Valley, North-eastern Australia (Longitude 49.11°, Latitude -21.27°). The following observations were made from the field investigation: Sandy Creek estuary experiences a variable salinity regime in its mid reaches that consists of periods of 1) freshwater flushing due to up catchment-derived flooding, 2) persistent freshwater conditions for at least 2 months following the flooding, 3) tidal salinity fluctuations and 4) constant near-seawater salinity; laterally extensive and disconnected aquitards were found to occur at the field site; Sandy Creek had an essentially ‘vertical’ bank slope. Numerical simulations were conducted using the finite element modeling code FEFLOW for saturated unsaturated, variable-density groundwater flow and solute transport, to examine the influence of the following factors on aquifer-estuary exchange: a tidally varying estuarine salinity and hydraulic head, a seasonal freshwater flush (i.e., estuary with freshwater and an elevated stage due to an up catchment sourced flood), near estuary aquitard layers, lateral asymmetry (about the estuary centerline) in hydraulic conductivity and regional hydraulic gradients. The simulations neglected seepage face development after numerical experiments showed that for a vertical bank estuary interacting with a sandy loam aquifer, seepage face effects on groundwater flow and associated salinity distribution were minimal. The following observations were drawn from the range of numerical experiments considered. Tidal salinity fluctuations in the estuary (varying between 0 and 1 - i.e., using a relative salinity scale where a salinity of 1 is seawater) produced flow paths and residence times that were distinctly different to the constant seawater salinity case. While the constant average 0.5 salinity case and the corresponding tidally-varying salinity case (i.e., salinity varying between 0 and 1) produced somewhat comparable results in terms of RUC and RLC (RUC represents groundwater discharge to the estuary that originated from recharge to the estuary bank and RLC groundwater discharge to the estuary that originated from recharge through the estuary bed), whereas flow paths and the total salt mass in the aquifer differed. Freshwater flushing simulations indicated that the near-estuary aquifer responds rapidly to a 2-day ‘wet season’ flushing event with a short-lived freshwater lens created through freshening of the hyporheic zone. Annual cycling of the seasonal flushing led to significant disruption of the estuary water circulation in the aquifer thereby impacting on residence times, transport pathways, and RUC and RLC, and acting to potentially remobilize groundwater and contaminants previously trapped in continuous and semi-continuous re-circulation cells. Although groundwater flow paths determined using tide-averaged velocity vectors were representative of flow paths from transient tidally driven flow vector field, residence times calculated from the two flow fields were markedly different. The influence of riparian scale aquitards and lateral asymmetry (about the estuary centreline) in hydraulic gradients and hydraulic conductivity on groundwater flow and associated salinity distribution was also found to be sensitive to estuarine salinity conditions. The results indicate that observations made about aquifer-estuary interaction in the lower estuary may not be directly applicable to the middle estuary. According to the simulations, tidal salinity variations in the estuary are important factors that affect hyporheic-riparian salt transport processes and that the use of a time averaged estuarine salinity as an approximation to variable salinity conditions is unsuitable for the accurate prediction of the near-estuary dynamics in middle estuaries. This study was based on a two dimensional representation of the riparian scale interaction and it is clear that future research needs to focus on the three-dimensionality of the aquifer-estuary system, incorporating spatially and temporally varying flow and transport characteristics. That is, many estuaries are tortuous and the aquifer geology spatially complex such that assumptions required for the two-dimensional section will most likely restrict application to the field. The tidal dynamics in the middle estuary is also expected to generate three dimensional aspects to the aquifer-estuary interaction. Thus further investigation that explicitly models the hydrodynamics and salt transport in the estuary and estuarine morphology is required to refine the insight provided by the simple conceptual model adopted in this study.

‘Infaunal haloes’ of either decreasing or increasing abundances of individual soft-sediment species with distance from reefs have been suggested to be caused by reef-associated predators. A large-scale mensurative experiment was used to investigate the distribution of two size classes of macrofauna with distance from the reef edge across three locations in northeastern New Zealand. The role of reef-associated predators, the snapper (Pagrus auratus Sparidae) and rock lobster (Jasus edwardsii Palinuridae), was investigated using established marine reserves at each location. Consistent patterns were found in a few large-bodied fauna. The hermit crab Pagurus novizelandiae occurred more frequently near the reef edge, whilst the heart urchin Echinocardium cordatum and bivalve Dosinia subrosea were more abundant further away from the reef. Dosinia subrosea and another bivalve, Myadora striata, exhibited lower biomass at sites with higher densities of snapper and rock lobster. In contrast, small-bodied macrofauna showed no consistent patterns with distance from the reef or among sites with different predator populations. It was hypothesised that predation was driving the distribution of large bivalves. An experiment was done to investigate this model using D. subrosea. Equal densities of this bivalve were established in plots either with or without cages at sites either inside or outside of reserves. Significant predation was detected, but only inside reserves. Much of this mortality could be specifically attributed to predation by large rock lobsters, given the distinctive marks on the valves of dead D. subrosea. Inside reserves, predators are not only more abundant but also larger. It was hypothesised that different size classes of predators would result in different levels of predation. Laboratory feeding experiments were used to investigate this model. Lobsters of all sizes chose D. subrosea over the heavier shelled D. anus. Small lobsters chose to prey on small D. subrosea and large lobsters more frequently chose larger prey. The distributions of these two bivalve species at protected (large predators) and fished sites (small predators) reflected the feeding choices observed in the laboratory. Results suggested that rock lobster populations are capable, where their size structure is not truncated by fishing pressure, of controlling population-level dynamics of bivalve communities adjacent to reefs.