Dissertations / Theses on the topic 'Estuarine hydrology New Zealand'

Coastal lagoon systems are complex and dynamic environments that respond rapidly to the changes of fluvial, marine, climatic and anthropogenic influences. The purpose of this research was to investigate the morphology and dynamics of the New River Lagoon before and after the implementation of engineering outlet management using a methodological framework to analyse active process environments. This information was then used to determine the functional effectiveness of engineering management at reducing the risk of flooding and erosion to the local community and imposing minimal impacts on the environmental integrity of the lagoon system. This investigation used a multidisciplinary approach to investigate the morphology and dynamics of the New River Lagoon in relation to active process environments. Outlet dynamics, lagoon channel structure and adjacent shoreline stability were assessed over a decadal timescale prior to engineering management by analysing temporal aerial photographs. Following engineering management, the hydrology of the lagoon was investigated, along with the relationship between morphological changes to the artificial lagoon outlet and changes in lagoon hydrology, local wave climate and local precipitation levels. Water depth, conductivity and temperature records were used to explain lagoon hydrology and Global Navigation Satellite Surveying (GNSS) and weekly oblique photographs were used to explain and document changes in outlet morphology. Wave and rainfall data were used to explain the balances between marine and fluvial environments and their affects on outlet dynamics. Significant changes in lagoon morphology and dynamics were observed at the New River Lagoon between pre- and post-management periods, with the former considered more stable in terms of outlet migration patterns and hydrodynamics. The lagoon outlet prior to engineering management showed morphological characteristics similar to hapua-type systems, migrating along the coastline and forming shore-parallel outlet channels in response to the dominance of a strong longshore drift of sediment. Current outlet dynamics are restricted by artificial outlet management and typically cycle intermittently between open/closed phases in response to variable levels of rainfall and marine sediment supply; characteristics similar to Intermittently Open/Closed Lagoons (ICOLs) found in areas of Australia and South Africa. Hydrologically, the lagoon is considered to be located on a continuum between hapua and estuaries during pre- and post-management periods due to intermittent tidal influences. However, artificial outlet management has significantly increased the frequency and duration of tidal exchange, which now classifies the New River lagoon closer to an estuarine environment. The artificial lagoon outlet and associated breakwater were effective at flushing high flows of water during the study period. However, the outlet was prone to blockage and migration; two morphological states capable of causing flooding. Currently, the greatest risks to flooding at the lagoon are flash floods, following dry periods where marine sediment has established a solid barrier across the outlet, during which water levels are already elevated. Increases in tidal influences, lower lagoon water levels and an increase in lagoon salinity are a direct result of engineering management intervention. An increase in freshwater flushing through the lagoon outlet and deepened of the outlet channel to below sea level, allows for pronounced tidal influences during outlet opening. Restriction of the lagoon outlet from forming a natural migration outlet channel in the direction of littoral drift has meant the outlet is most often oriented perpendicular to the sea, as appose to at an angle away from the direction of incoming waves and currents, further increasing tidal influences. In order to make sustainable management decisions, future management of the lagoon system must weight-up the effects of a high energy coastline to the integrity of the engineering structure, the impact of the structure on the lagoons environmental integrity and the outlets ability to become unstable and cause a flood risk. The findings of this research have improved the understanding of the New River Lagoon system, and its response to engineering management intervention, while adding to the understanding of river-mouth lagoon systems both nationally and internationally.

The research presented in this thesis was undertaken in order to develop an understanding of the biology of Perna canaliculus sufficient to allow for commercial hatchery based production of Greenshell™ mussel spat. Hatchery production is an alternative to unreliable and inconsistent wild spat collection. In a Perna canaliculus population followed for one year spawning occurred in early spring and late summer. Three quantitative histological measures of gonad maturity utilising image analysis technology and a qualitative classification system were compared. Measuring the relative surface area comprised of gametes on histological sections was found to be the most reliable method. A practical gonad visual index to determine the reproductive condition of adults for the selection of broodstock was developed and found to be highly effective as a means of predicting induced spawning success. Serotonin was not effective for inducing spawning of Perna canaliculus. Temperature shock and the use of stripped gametes was however found to be a reliable spawning induction method. Relative gamete concentration, gamete age, temperature, sperm half life and gamete contact times were all found to have effects on fertilisation success for Perna canaliculus. Sperm concentration and the conditions of sperm aging were particularly important. Fertilisation kinetics of Perna canaliculus gametes modelled using the Vogel-Czihak-Chang-Wolf method suggested that 5% of sperm-egg contacts lead to successful fertilisation. Broodstock management protocols that could be used to condition the adult of Perna canaliculus were investigated in order to enhance and prolong the natural reproductive season. Research suggested that for successful broodstock conditioning animals should already have begun gametogenesis at the time conditioning is commenced. Successful conditioning of Perna canaliculus was achieved at temperatures between l0 and 16°C over a period of about 50 days. A diet ration above 2-3% of the dry meat mass per day is suggested. A trial examining non-algal diet supplements suggest a mixture of yeast and lipid emulsion may have some potential value. Photoperiod manipulation did not effect the reproductive condition of Perna canaliculus. The yield of veliger larvae was significantly enhanced if embryo culture water was treated with 1.0 mg/l EDTA. Veliger yield was not significantly affected at densities below 50 embryos/ml. Perna canaliculus larvae grew most rapidly and survived well at the salinity of 35 ppt. Larvae grew most rapidly when cultured at low densities. Experiments suggest that early larvae can be cultured at 5-10/ml, however late stage larvae grew most rapidly when cultured at l/ml. Perna canaliculus larvae displayed best growth and good survival if fed a mixed flagellate-diatom diet comprising Isochrysis galbana (T-Iso) and Chaetoceros calcitrans. The optimal diet ration, as a function of larval size, increased from about 20 cells/μl Isochrysis galbana (T-Iso) to around 150 cells/μl through the larval development period. Thyroxine between the concentrations of l0-5 and l0-8 M did not have an observable effect on larval developmental rate or eye spot development. Down welling settlement systems were found to be generally successful for Perna canaliculus lanrae. L-DOPA was also demonstrated to enhance the settlement and metamorphosis of Perna canaliculus pediveligers.

Worldwide, estuaries are under increasing pressure from numerous contaminants. There is a need to develop reliable bioassay methodologies to assess the effects of these stressors on estuary health. This thesis aimed to develop and validate toxicity tests in a New Zealand marine harpacticoid copepod species for use in monitoring and evaluating the effects of estuarine pollution. A survey and toxicological assessment of a range of native copepod species resulted in the selection of Quinquelaophonte sp. as the ideal bioassay species. This selection was based on a broad regional distribution, ease of culture and high reproductive rate in the laboratory, sexual dimorphism, and sensitivity to contaminants. To validate the bioassay, spiked sediments were used to expose Quinquelaophonte sp. to three reference compounds representing important categories of estuarine chemical stressors: zinc (a metal), atrazine (a pesticide), and phenanthrene (a polyaromatic hydrocarbon). A method for spiking sediments that Quinquelaophonte sp. inhabit was developed to ensure even contaminant distribution in sediments. Two sediment bioassays using lethal and sublethal endpoints were validated, one acute (96 h) and one chronic (14 d). These assays incorporated both lethal and sublethal endpoints, which included reproductive output and mobility. Acute-to-chronic ratios were calculated for use in environmental risk assessment and to provide insight into the mode of action of the reference contaminants. The chronic sediment bioassay was used to assess sediment quality in three estuaries across New Zealand: Napier, Christchurch and Invercargill. This validated the bioassay for use with naturally-contaminated field sediments with varying mixtures of pollutants and sediment types (coarse sandy to fine silty organic rich sediments). Quinquelaophonte sp. was also tested to assess whether it can be used to characterise multi–generation impacts. After four generations of exposure to zinc, there were changes in acute sensitivity, indicating this species possesses mechanisms for acclimating or adapting to toxic stressors. Sediment bioassays in Quinquelaophonte sp. were successfully developed and validated, offering significant promise as a tool for monitoring effects of pollution in New Zealand estuaries.

Interactions among large brown macroalgae, sea urchins, and fishes were investigated in northeastern New Zealand during the period 1988 - 1993. The Cape Rodney to Okakari Point Marine Reserve was the site of many of these investigations. The patterns of abundance of large brown macroalgae and urchins down depth gradients over a wide geographic range were compared with those reported from earlier studies, and 3 major trends were identified. First, the fucoid alga Carpophyllum flexuosum now occurs at many sites which are exposed to wave action, in contrast to earlier studies. This alga occurred most abundantly on urchin-grazed coralline flat areas. Second, at four sites in the Marine Reserve, the densities of the echinometrid urchin Evechinus chloroticus decreased with increasing depth, rather than reaching maximal densities at mid-depths, as had previously been described. Finally, at sites of decreased exposure to wave action, the coralline flats habitat did not occur at all, and dense stands of. C. flexuosum occurred, in conjunction with the ubiquitous laminarian alga, Ecklonia radiata. Following the discovery of this new algal component to exposed rocky reefs, a more detailed study of its population characteristics was initiated. The population size structure of C. flexuosum on coralline flat areas was markedly different from that of the same species in sites sheltered from wave action. These differences occurred at both offshore islands and sites near Leigh, suggesting that it was a general pattern. C. flexuosum plants on coralline flats were smaller than those from sheltered sites, and had a greater number of smaller laminae, heavier stipes, and a greater degree of branching. There was some evidence of temporal change in the morphology of C. flexuosum from coralline flats. Comparisons between a site with C. flexuosum and a site with coralline flats suggested that the activity of fish was 75% lower in the vegetated than in the unvegetated site, and the feeding rate in the vegetated site was less than 50% that in the unvegetated site. I speculate that future effects on fish activity of the invasion of C. flexuosum into a habitat which previously lacked macroalgal vegetation may depend on changes in the morphology of plants. An investigation of many aspects of the biology of E. chloroticus in different habitats was undertaken. Analysis of the body dimensions of E. chloroticus suggested that this species was relatively tall compared to other echinometrids (average ratio of test height: test diameter = 0.54), Comparisons among habitats with differing amounts of vegetation revealed only small differences in the relationship between test diameter and test height. Small E. chloroticus (<40 mm test diameter) lived in crevices, while larger individuals grazed freely over the substratum. In vegetated habitats, the crevice-dwelling habit was maintained at test diameters about l0 mm greater than in unvegetated habitats. Very small (<20 mm test diameter) E. chloroticus frequently covered themselves with shell. Population size structures of E. chloroticus within the Cape Rodney to Okakari Point Marine Reserve were bimodal; other localities had unimodal populations. Modal sizes varied among localities, with smallest modes (50-60 mm TD) being found at Inner Hauraki Gulf sites, and largest modes at the offshore Mokohinau Islands (70-80 mm TD). Habitat did not predictably affect population size structure. A bimodal population structure was maintained at Waterfall Reef rock flats throughout the 5-year study period. Gonad size showed seasonal fluctuations at several sites, being greatest in summer. There were few consistent differences in gonad size between biological habitats. Gonad colour varied among sites and habitats, with orange gonads generally being more prevalent in vegetated habitats, and black gonads being represented more in unvegetated habitats. Smaller urchins had greater proportions of orange gonads, while larger urchins had greater proportions of brown and black gonads. Although highly variable among individual urchins, movement of E. chloroticus was greater at unvegetated sites (0.7 m per 5 days) than at vegetated sites (0.4 m per 5 days), in the Marine Reserve. Feeding of E. chloroticus was studied at a number of sites in the Marine Reserve. Urchins frequently consumed drift algae, particularly E. radiata. C. flexuosum was consumed at less than half the rate of other macroalgae in several laboratory feeding experiments, and was chosen least frequently in a field assay of feeding preferences among 8 species of macroalgae. Boosting densities of E. chloroticus in stands of E. radiata to 60 m-2 led to destructive grazing of plants over a 2 month period - at lower densities, the urchins dispersed. Densities of C. flexuosum were effectively unchanged when urchin densities were increased to these elevated levels. As a result of these observations I speculate that feeding preferences of E. chloroticus may have a role in allowing C. flexuosum to survive on coralline flats. In a laboratory experiment, urchins from a feeding aggregation did not graze algae at higher rates than individuals from outside aggregations. Diets of both E. radiata and C. flexuosum consistently produced similar gonad volumes in urchins held in the laboratory, although gonad volumes produced were low. A preliminary experiment suggested that C. flexuosum from exposed sites was consumed at lower rates than C. flexuosum from sites which were sheltered from wave action. These differences in palatability are mirrored in the formation of stable borders between coralline flats and C. flexuosum of the sheltered morphology, and the ability of C. flexuosum of the exposed morphology to survive in the coralline flats habitat. The fish fauna of the Cape Rodney to Okakari Point Marine Reserve was shown to be different from that of a nearby area. A number of species were more abundant within the Marine Reserve. Subsequent surveys showed that there were differences in abundances of 3 large carnivorous fishes among sites within the Marine Reserve, and that population size structure and the distance within which divers could approach one species, (Pagrus auratus), clearly varied between areas within the Marine Reserve. Mean standard length of P. auratus in the central marine reserve was 40% larger than that of P. auratus outside the central marine reserve, and the average minimum approach distance was 70% less in the central marine reserve. Feeding of fish by humans in the central part of the Marine Reserve was suggested to be the main cause of the differences in responses to divers. Population size structure of, and crevice occupancy by, E. chloroticus, clearly differed between the Marine Reserve and an adjacent area, with bimodal population size structures and a 10 mm greater size of crevice occupancy occurring in the Marine Reserve. The implications of these findings for extrapolating from experiments done in one area to other areas are discussed. The major biological components of rocky reef habitats identified in this study were broadly similar to those identified in previous studies in northeastern New Zealand, and have parallels in overseas studies. Long term changes to the flora of rocky reefs in northeastern New Zealand have occurred, and appear to persist by a mechanism which had previously been discounted. Similar processes to those observed in overseas studies appear to maintain habitats (consistent recruitment of algae or urchins to habitats which they dominate), or cause them to change from one habitat state to another (e.g. grazing outbreaks by urchins). However, the predictability of the persistence of these habitats at a particular site appears to be low. Further, the precise mechanisms whereby habitats may change from one to another may also be unpredictable. I argue that there is little scope for general statements concerning the spatial and temporal occurrence, or mode, of habitat transitions on temperate subtidal reefs. This study emphasises the value of repeated descriptions of patterns of abundance, and highlights problems of extrapolation and generalisation in marine ecology. Insufficient information exists at present to comment adequately on the persistence of subtidal habitat types. This may in part stem from the types of information which have been collected in the past. Methodological problems with the use of quadrats to sample densities of organisms in areas of differing topography are therefore addressed. In conclusion, it is suggested that sampling protocols which incorporate a variety of information, gathered over as wide an area, and as intensively as possible, should be used in future research of this type.

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 management of New Zealand’s freshwater resources has come under increasing pressure from different industrial and environmental stakeholders. Land use change and the pressure it can put on water resources has been a significant issue regarding resource management in New Zealand. A significant mechanism driving land use change has been the growth of forestry, dairy farming, and other agricultural industries. Improvements in agricultural and forestry science and irrigation techniques have allowed new, previously less arable areas of New Zealand to be subject to land use change, such as the conversion of tussock grassland to pasture in steep, mountainous regions in the South Island. Studies regarding the effects of land use change in such catchments, especially with focus on flood hydrology, appear to be limited, despite the importance of managing catchment headwaters to minimise flood risk downstream. The TopNet model was used in this research project to evaluate the potential effects of land use change on flood hydrology in mountain catchments. It is a semi-distributed continuous rainfall-runoff model developed by the National Institute of Water and Atmospheric Research (NIWA). It has been widely used in New Zealand, and applications have included modelling water yield and the effect of climate change in catchment networks. However, it was not developed specifically for predicting flood flows. Hence, testing the model for flood peak prediction in mountainous catchments was also performed, and may show that TopNet can be a useful tool in resource management in New Zealand. The Ahuriri and Pelorus River catchments were used in this investigation. Both are steep catchments located in the South Island. The Ahuriri River catchment, in the Waitaki Basin on the eastern side of the Southern Alps, is a semi-arid catchment dominated by tussock grassland. The surrounding catchments are heavily influenced by infrastructure for hydroelectric power (HEP) generation and more recently irrigation for dairy farming. The Pelorus River catchment is located at the northern end of the South Island. It is primarily covered in native forest, but adjacent catchments are subject to agricultural and forestry development. The ability of the TopNet model for each catchment to predict flood flows were tested using a selection of historical flood events. Rainfall input to the model was at a daily timestep from the virtual climate station network (VCSN), and the method of disaggregating the daily estimate into an hourly rainfall series to be used by the model was found to have a significant influence on flood prediction. Where an accurate historical rainfall record was provided from a rainfall gauge station within the catchments, the disaggregation of the daily rainfall estimate based on the station data produced a significantly more accurate flood prediction when compared to predictions made using a stochastic disaggregation of the daily rainfall estimate. The TopNet models were modified to reflect land use change scenarios: the conversion of tussock grassland to pasture and the afforestation of tussock in the Ahuriri River catchment, and the conversion of forested land to pasture and the harvest of plantation forestry in the Pelorus River catchment. Following a past study into modelling the effects of land use change using TopNet, three key model parameters were modified to reflect each land use scenario: saturated hydraulic conductivity KS, canopy storage capacity, and the canopy enhancement factor. Past studies suggested a wide range of suitable values for KS, although also acknowledged that KS depends heavily on the specific catchment characteristics. A sensitivity analysis showed that KS had a significant influence on flood peak prediction in TopNet. It is recommended that further investigation be conducted into suitable values for KS. TopNet appeared to predict the effect of land use change on flood magnitude in mountainous catchments conservatively. Past studies of land use change suggested that the effect on flood flows should be significant, whereas TopNet generally predicted small changes in flood peaks for the scenarios in each catchment. However, this may suggest that the topography, geology, and soil properties of steep catchments are more important to flood hydrology than land cover. Further investigation into the effect of such catchment characteristics is recommended. Nevertheless, TopNet was shown to have the potential to be a useful tool for evaluating and managing the effects of land use change on the flood hydrology of mountainous catchments in New Zealand.

In the Heretaunga Plains area, New Zealand, parts of the low lying land adjacent to the Awanui Stream are flooded annually. The purpose of the study was to find out if the flooding water trapped in the field gets sealed off from infiltrating the soils in any way (and hence is unavailable to replenish the stream flow). What would be the effects on stream base flow if pumping of the flooding water would occur direct to the stream after wet periods and heavy rains? The method of this project was to investigate the infiltration, soil type and ground water conditions in the field. The infiltration was investigated with the help of a double ring infiltration test, a disc permeameter that measures hydraulic conductivity, and pvc-pipes with core samples were saturated for an extended period of time to find out if there was any kind of seal forming during saturated conditions. The soil in field was sampled and a soil fraction test was performed. The potential evaporation was measured with an evaporation pan and calculated with data from a climate station in field. With flow records from the outgoing drain, potential evaporation and precipitation data a rough water balance model could be created. The results showed that there is no seal formed in the top part of the soil profile preventing the water from infiltrating. The flooding water is the result of a rising groundwater table, on top of a thick clay layer seven meters down in the ground. Once the flooding water has drained and evaporated away there is nothing wrong with the infiltration rate in field. There are very fine particles of silt and clay in the top soil that decreases the infiltration rate and can cause a separation of the ground water and the water above land surface. When the project was finished two recommendations could be given to the landowner to solve the problem with the flooding. The recommendations were to either re-level the field to get the surface water to runoff towards the drains instead of being trapped in the current low parts of the field. Or to dig drains from Horonui Drain and Cambell Drain into the field's low parts and in that way drain the flooding water away.
I området Heretaunga Plain, Nya Zeeland, översvämmas årligen delar av det låglänta området kring floden Awanui Stream. Syftet med den här studien var att ta reda på om översvämningsvattnet i fält hindras från infiltration i jorden på något sätt (och kan där med inte bidra till basflödet till floden). Vad skulle effekterna på basflödet i floden bli om översvämningsvattnet pumpades direkt ut i floden efter våtare perioder och större regn? Metoden för att svara på detta var att undersöka infiltrationen, jordtyperna och grundvattenförhållandena i fält. Infiltrationen undersöktes med hjälp av dubbelring infiltrationstest, en s.k. disc permeameter användes för att undersöka den hydrauliska konduktiviteten och PVC-rör med borrkärnor ställdes under vattenmättadeförhållanden en längre tid för att ta reda på om infiltrationen då skulle förändras. Jorden i fält provtogs och ett kornstorlekstest utfördes. Den potentiella avdunstningen mättes med en evaporationspanna och beräknades med data från en klimatstation i fält. Med flödesdata från diket med utgående vatten, potentiell avdunstning och nederbördsdata kunde en grov uppskattning av vattenbalansen i fält göras. Resultaten visade att det inte bildas någon hinna som hindrar infiltrationen av vatten i den övre delen av jordprofilen. Översvämningen är ett resultat av en stigande grundvattenyta, som stiger från ett tjockt lager av lera 7 meter ner i marken. När vattnet har dräneras och avdunstat bort är det ingenting som hindrar infiltrationen i fält. Det är dock väldigt fina partiklar av silt och lera i den översta torvjorden som minskar infiltrationshastigheten och kan orsaka en separation av grundvatten över och under markytan. När projektet var avslutat kunde två rekommendationer ges till landägaren om hur man kan lösa problemet med översvämningen. Rekommendationerna var att antingen skulle landägaren kunna göra om marknivån i fält för att få ytvattnet att rinna av mot dikena istället för att vara fast i de lägre partierna av fältet. Eller att gräva diken in i fältet från Horonui Drain och Cambell Drain in till de lägre översvämmade områdena i fält för att dränera bort översvämningsvattnet.

The New Zealand (NZ) sea lion Phocarctos hookeri is the only pinniped endemic to NZ with a population of approximately 12,000 individuals. Its breeding range is currently restricted to NZ sub-Antarctic islands, and it has failed to recolonise its pristine distribution around the NZ main islands despite its protection since 1881. The current hypothesis is that the population growth of this pinniped is limited by the distribution of suitable prey on the Auckland Islands (50°30'S, 166°E) shelf, and by the direct and indirect pressure exerted by the arrow squid Nototodarus sloani fishery. However, this hypothesis has not been fully tested to date as there has been limited information on the diet of the NZ sea lion and their potential prey. The objective of this thesis is to analyse the diet of NZ sea lions over several years with particular emphasis on the most reproductively important segment of the population: lactating females. This thesis provides the first quantification by percentage mass of the diet of NZ sea lion using a combination of stomach content analysis, qualitative fatty acid (FA) analysis, and quantitative FA signature analysis (QFASA). Stomach contents and blubber FAs were analysed from 121 individuals incidentally caught (by-caught) in the southern arrow squid fishery from the years 1997 to 2006. The blubber FAs of 78 freeranging lactating females captured at Enderby Island, Auckland Islands, were also examined during January and February of 2000 to 2005. Data obtained from both stomach analysis and QFASA indicate that arrow squid, rattails Macrouridae, hoki Macruronus novaezelandiae and red cod Pseudophycis bachus are key prey species for NZ sea lions in the Auckland Islands region. Because these prey species live mostly at depths greater than 200 m, lactating females must undertake long foraging trips and dive regularly to greater depths than other sea lion species. Data from QFASA indicates that this foraging pattern is conducted over an extended period through the summer and autumn. The daily food requirement of a lactating female was estimated by a simple energetic model to be greater than 20% of its body mass. During years of low arrow squid recruitment such as 1999 and 2001, the amounts of squid required by the NZ sea lion population may have been similar to the amount harvested by the fishery, suggesting that resource competition is likely to occur between the arrow squid fishery and NZ sea lions in years of low squid abundance. Half of the fishing activity of the southern squid fishery occurs in the north of the Auckland Islands shelf where NZ sea lions forage, leading to incidental captures every year. This research emphasises that management of the NZ sea lion must not only consider the direct interactions with the arrow squid fishery, but also the likelihood of food resource competition between the fishery and NZ sea lions.

The potential impact of sea level rise on Lake Ellesmere - Te Wiahora and the subsequent effect on the efficiency and performance of the L2 Drainage network was investigated in relation to the operation of the L2 Drainage scheme. Lake Ellesmere is currently manually opened for drainage to the sea when the lake levels reach 1.05 m above mean sea level (asl) in summer and 1.13 m asl in winter. With a rise in sea level, the lake opening levels for both summer and winter would have to increase in order to maintain the current hydraulic gradient. Higher lake levels would impact drainage schemes such as the L2 drainage network. An integral research approach was used to study this potential impact, including fieldwork, analysis of data, hydrologic and hydraulic modelling. Both the hydrologic and hydraulic response of the L2 catchment and river were reproduced with reasonable accuracy by the use of computational models. Simulations of 2, 10 and 20 year annual recurrence intervals (ARI) rainstorm events coupled with higher lake levels show increase flooding along the length of the river. An increase in the lake opening levels, coupled with south-easterly wind was shown to have increased the degree of flooding on adjacent farmlands, but only a 3.50 per cent increase of water level (for all conditions simulated) 3.5 km upstream of the L2 River. The study clearly shows that weed growth within the L2 River plays an important part in controlling the water level within the channel. Results show it was responsible for an observed water level rise of 0.30 m from the winter to summer season. The combined use of hydraulic and hydrological models provides an effective tool to study future impacts on the drainage efficiency and performance of the L2 drainage scheme and other similar systems. The potential for both models to be used as a predictive tool for improving the operation of the L2 scheme and Lake Ellesmere was only limited by the difficulty in estimating model parameters especially for the hydrologic model.

En 2004 et 2007, neuf structures d'échappements de fluides (SEF), constituées de volcans de boue (VdB), d'évents de gaz (GS, gas seeps en anglais) et/ou de sources, ont été échantillonnées dans la partie émergée du Bassin de la Côte Est (BCE) de l'île nord de la Nouvelle-Zélande.L'étude granulométrique indique que la boue émise par les VdB, les roches encaissantes et les niveaux de décollement voisins sont composés d'argiles et de silts en majorité. L'étude de la fraction argileuse et de la roche totale par diffraction des rayons X (DRX) a révélé de nombreuses similitudes. Les volcans de boue, les roches encaissantes et les niveaux de décollement présentent ainsi le même assemblage minéralogique, à savoir smectite, illite, chlorite, kaolinite, quartz et feldspaths. Les proportions sont variables d'un échantillon à un autre mais le couple smectite-illite est toujours majoritaire.L'étude géochimique de la fraction solide indique que les échantillons sont riches en Si02, pauvres en Fe2O3, MgO, MnO et en alcalins, à quelques exceptions près. La composition en éléments majeurs s'organise entre un pôle argileux alcalin et un pôle carbonaté. Les spectres de terres rares sont similaires et caractéristiques des argiles ; Ils présentent également un faible degré de fractionnement, lié à la formation des carbonates. Ce sont donc les mêmes minéraux qui contrôlent la chimie des échantillons.L'étude géochimique de la phase liquide montre que l'eau impliquée dans les volcans de boue est d'origine marine essentiellement, et des réactions eau/roche similaires, notamment l'altération de smectite en illite. Cette étude a permis aussi d'obtenir une estimation de la température d'équilibre, comprise entre 60 et 110°C, impliquant une profondeur d'origine de 2 à 3 km, voire plus.L'étude géophysique indique qu'à l'aplomb des VdB et des deux sources chaudes étudiés, la croûte continentale a sensiblement la même épaisseur et que la profondeur de la croûte océanique en subduction avoisine les 20 km. A cette profondeur, la fusion de la péridotite n'est pas possible et la fusion résultante de la croûte continentale, responsable du volcanisme d'arc, non plus. Le gradient géothermique mesuré à TePuia est donc influencé par un autre phénomène, mais la modélisation de la lithosphère ne nous a pas permis de trouver lequel.Ces différentes études mettent en évidence des caractéristiques géochimiques, pétrographiques et minéralogiques communes aux volcans de boue de Nouvelle-Zélande. Les fluides impliqués dans ces structures proviendraient donc d'un même niveau source, recouvert du même assemblage sédimentaire. L'étude géophysique ne nous apporte aucune information à ce sujet mais permet cependant d'établir avec certitude que le régime thermique est le même du Nord de Hawke's Bay au Sud du BCE ; la région de TePuia est un cas particulier, peut-être influencée par le complexe volcanique de Matakaoa
In 2004 and 2007, nine areas of fluids escapes structures (FES) with mud volcanoes (MVs), gas seeps (GSs) and springs, were sampled in the East Coast Basin (ECB) emerged part of New Zealand's north island.The grain size study indicates that the mud emitted by MVs, like surrounding rocks and decollement layers in the vicinity, is mainly composed of clays and silts. Clay fraction and whole rock XRD study revealed many similarities. Mud volcanoes, surrounding rocks and decollement layers have exactly the same mineral assemblage, i.e. smectite/illite, chlorite, kaolinite, quartz and feldspars. The proportions vary from one sample to another but the couple smectite/illite is always majority.The geochemical study of the solid fraction indicates that the samples are rich in Si02, low in Fe2O3, MgO, MnO and alkaline, with a few exceptions. The major element composition is organized between a pole and a pole clay alkaline carbonate. The REE patterns are similar and characteristics of clays They also have a low degree of fractionation, due to the formation of carbonates. So these are the same minerals that control the chemistry of samples.The liquid phase geochemical study shows that water involved in the MVs is mainly of marine origin, that water/rock reactions are similar, including weathering of illite in smectite, allowed us to obtain an estimate of the water equilibrium temperature between 60 and 110°C, implying an origin depth of 2-3 km.The geophysical study indicates that directly above the MVs and the two hot springs studied, the continental crust has substantially the same thickness and the depth of the subducting oceanic crust is around 20 km. At this depth, the melting of the peridotite is not possible and the resulting fusion of continental crust, responsible of arc volcanism, neither. The geothermal gradient measured at TePuia is influenced by another phenomenon, but the modeling of the lithosphere does not allow us to find which one.These studies show geochemical, petrographical and mineralogical characteristics common to mud volcanoes in New Zealand. Fluids involved in these structures therefore come from the same parent bed, covered with the same sedimentary package. The geophysical study gives us no information about it but nevertheless allows us to establish with certainty that the thermal regime is the same from Northern Hawke's Bay to the south of the ECB; TePuia region is a special case, perhaps influenced by the Matakaoa volcanic complex

Waterfowl are known to be capable of influencing wetland ecology in a number of ways, sometimes to the detriment of other species that also inhabit this type of environment. Western Golden Bay including Farewell Spit is one of the largest areas of intertidal sand flat habitat in New Zealand and supports a wide array of species including internationally important populations of bar-tailed godwits (Limosa lapponica) and red knot (Calidris canutus). These species, particularly red knot, have declined in number over the last the 25 years at this site. Another numerous species at this site, the black swan (Cygnus atratus), has been suggested as a possible contributor to the observed decline in wader numbers through their impact on the habitat. This thesis presents the findings of a research project on the role of black swans in the tidal seagrass (Zostera muelleri) ecosystem in western Golden Bay carried out between October 2007 and October 2008. In an effort create a clear picture of what role the black swans play in this environment the project focused on four major aspects of swan-ecosystem interactions. The first of these looked at the activity patterns of black swan. This showed the swans’ activity is largely dictated by the tidal cycle with foraging occurring during the intertidal period when the seagrass is accessible while roosting is mostly confined to around high and low tides. The second part of the project explored the influence black swans have on the tidal seagrass landscape through their foraging habits. This showed that while swan foraging occurs across the tide flats it is concentrated on denser patches, on both small (meters) and large (hectares) scales. Experimental grubbings showed that the grubbing activity of swans is capable of forming and expanding bare sand patches within seagrass beds and that these bare patches can persist for at least two months. The third part of the project focused on the direct impacts of swan foraging on the seagrass and associated benthic invertebrates. Exclusion plots showed that at some sites swan foraging can significantly reduce Zostera biomass and invertebrate biodiversity. The final aspect examined was the role of swan in biomass and nutrient cycling. A faecal deposition survey showed swans consume 23.40 g DW ha-1 day-1 of Zostera. The average intake rate was 27.25 g DW ha-1 day-1. Nutrient analysis of seagrass 4 showed that shoot material has significantly higher N, P, Ca and fibre than rhizome and that rhizome has significantly more soluble carbohydrates than shoots. On the basis of the swans’ direct and/or indirect influences on Zostera muelleri beds and the associated invertebrate fauna, swans could arguably be considered to be a major ecosystem engineer in the intertidal sandflats of Golden Bay.

Orca (Orcinus orca), also known as killer whales, are more widely recognised than other marine mammals. Although they have been reported from all oceans of the world, including the seas around New Zealand, information above anecdotal notes exists for only a few places. Orca are an apex marine predator that exhibits cultural differences in diet, vocalisations, and behaviour, between and within populations. This study was established to determine baseline information on New Zealand orca and to provide recommendations for future management and conservation. The conservation status of orca worldwide is poorly known, although two populations of the Pacific North West Coast of North America have recently been classified as ‘Threatened’ and ‘Vulnerable’. Photo identification was used to determine the population size, distribution around New Zealand waters, as well as range use and association among individuals. The total New Zealand orca population is small (range 65-167 animals, with 115 calculated alive in 1997). Resighting rates were high, with 75 % (n = 88) of the animals seen on more than two occasions. The mean number of sightings for the 117 photo-identified animals was 5.4, the mode was one sighting, and the median 9 – 10 sightings. One orca was photographed over a 20 year period. Population structure, frequency of association with others, and other social behaviours were used to determine population demographics. The New Zealand orca population appears to be made up of at least three sub-populations based on geographic distribution (North-Island-only, South- Island-only and North+South-Island sub-populations). Preliminary mtDNA analysis supports the hypothesis that some New Zealand orca do not mix. The mean Association Indices within the North-Island-only and South-Island-only sub-populations are significantly greater than within the North+South-Island sub-population. Those animals sharing food had higher Association Indices than those who did not share food. Sex ratios appear similar within each sub-population and calves were present in each, suggesting all sub-populations are breeding. Feeding behaviour was observed to assess habitat use and differences between foraging strategies and prey preferences. Twenty four different species of prey have been recorded in the New Zealand orca diet. Of these, ten have not been recorded elsewhere. The prey consists of four types; rays (the most common food type), sharks, fin-fish and cetaceans (pinnipeds have not been identified as a prey source). Foraging strategies were different for each prey type, with benthic foraging for rays in shallow waters the most diverse strategy used in New Zealand. Food sharing was observed for all prey types. One of the three proposed New Zealand subpopulations appears to be generalist or opportunistic foragers, feeding on all four prey types, another sub-population slightly less so, feeding on three prey types, and the third sub-population appears to be a more specialist forager, only recorded taking one prey type (cetaceans). Potential threats to orca, in addition to small population size, such as bioaccumulation of toxic chemicals, oil spills, boat strikes and shootings are considered and recommendations for conservation and future management are offered. Whether the three sub-divisions within the New Zealand orca population are reproductively isolated and hence require separate management, and whether there is further sub-division within the proposed North+South-Island sub-population, requires further study including genetic analysis. Some level of ongoing monitoring is recommended to ensure that the population of New Zealand orca does not decline. In addition, records of stranding locations and details of strandings are appended. Twenty-four live strandings occurred, involving 63 killer whales, of which 17 animals were successfully refloated and two of these resighted. One was seen after three years (nine resightings) and the other after four months (10 resightings). Refloating stranded orca is recommended.

This thesis is a study of the large scale flows of water and heat which give rise to the geothermal fields in the Taupo Volcanic Zone (TVZ), New Zealand. To carry out this study, a super-critical equation of state module has been developed for the geothermal simulator TOUGH2, which can describe the flow of water at the conditions expected deep in the TVZ. The code is used to simulate the behaviour of a range of idealised TVZ models in 2D and 3D settings. Hydrothermal plumes which remain stable for periods comparable to the lifetime of the TVZ can occur when there is a contrast between the high permeability of the inner TVZ 'infill' region and the lower permeability exterior region. In this case, downflows of cool surface fluid in the inner TVZ 'sweep' the geothermal heat across the TVZ at depth to the permeability barrier, where the heated fluid ascends to the surface in discrete plumes. This behaviour occurs in 2D models, where separate plumes form at each side of the high permeability infill region, and also in 3D models of caldera-like structures, where perhaps four hot plumes can form around the perimeter of the caldera. This notion is then applied to the complete TVZ hydrological system, where a permeable ‘envelope’ is defined by the location of the Taupo Fault Belt and the currently known volcanic centres in the TVZ. The permeability within this envelope varies spatially according to the geothermal heat flux, and the region outside has relatively low permeability. The spatial variation of the geothermal heat flux is obtained by summing the measured heat flows from the geothermal fields for a number of areas across the TVZ. In this model, the geothermal fields form about the boundary of the envelope, as in the TVZ, and bear a striking resemblance to the actual TVZ geothermal fields. Finally, a new simulation code, NaCl-TOUGH2, is developed to provide a tool for future modelling involving the commonest chemical species in the TVZ - salt. The code incorporates the complete phase diagram for salt-water mixtures and involves liquid, vapour and solid phases over a wide range of temperatures, pressures and salt concentrations. The code is used to solve a number of simple geothermal and mathematical problems.

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 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.

Common dolphins (genus Delphinus) are poorly understood within New Zealand waters. Prior to this study, most information relating to the taxonomy, population structure, diet and pollutant loads of this genus relied upon untested assumptions. Furthermore, factors affecting the occurrence, demographics and habitat use of common dolphins in the Hauraki Gulf remained unknown. This lack of empirical data has resulted in the inadequate recognition and management of New Zealand Delphinus. Inappropriately classified by the New Zealand Threat Classification System, the anthropogenic impacts that affect this genus have clearly been overlooked. The present study examines behaviour of common dolphins in the Hauraki Gulf and details analyses undertaken on tissue samples collected from around New Zealand. Results detailed here challenge many of the untested assumptions about this genus within New Zealand waters. The taxonomy of New Zealand common dolphins was assessed using 92 samples analysed for 577 base pairs (bps) of the mtDNA control region (D-loop). New Zealand samples were compared with 177 published sequences from eight other populations from around the world. New Zealand Delphinus exhibited a high genetic variability, sharing haplotypes with both short- (D. delphis) and long-beaked (D. capensis) populations. Indeed, the New Zealand population showed significant genetic differentiation when compared with most other populations world-wide. Furthermore, intrapopulation analyses revealed significant genetic differentiation between Hauraki Gulf individuals and other common dolphins sampled within New Zealand waters. Results suggest habitat choice and site fidelity may play a role in shaping the fragmented population structure of New Zealand Delphinus. Data relating to the occurrence and demographics of common dolphins in the Hauraki Gulf region were collected during boat-based surveys between February 2002 and January 2005. In total, 719 independent encounters, involving one to > 300 common dolphins were recorded. Dolphin presence was significantly affected by month, latitude and depth. Group size varied significantly by month, season, depth, sea surface temperature (SST) and latitude, and was highly skewed towards smaller groups comprising fewer than 50 animals. Calves were observed throughout the year but were most prevalent in the austral summer months of December and January. Group composition was significantly affected by month, season, depth and SST. The yearround occurrence and social organisation of Delphinus in Hauraki Gulf waters suggest this region is an important nursery and potential calving area. The effects of diel, season, depth, sea surface temperature, and group size and composition on dolphin behaviour were investigated using activity budgets. Foraging and social were the most and least frequently observed behaviours, respectively. A correlation between group size and behaviour was evident, although behaviour did not vary with the composition of dolphin groups. Resting, milling and socialising animals were more frequently observed in smaller groups. Foraging behaviour was prevalent in both small and large groups, suggesting foraging plasticity exists within this population. Behaviour differed between single- and multi-species groups, with foraging more frequent in mixed-species aggregations, indicating the primary mechanism for association is likely prey-related. Stomach contents analysed for forty-two stranded and eleven commercially by-caught individuals collected from around North Island, New Zealand between 1997 and 2006, revealed arrow squid (Nototodarus spp.), jack mackerel (Trachurus spp.) and anchovy (Engraulis australis) as the most prevalent prey. Stranded individuals and dolphins bycaught within neritic waters fed on both neritic and oceanic prey. Moreover, a mixed prey composition was evident in the diet of common dolphins by-caught in oceanic waters, suggesting inshore/offshore movements of New Zealand Delphinus on a diel basis. Additionally, prey differences were also evident in the stomach contents of common dolphins sampled from within the Hauraki Gulf. Trace elements, polychlorinated biphenyls (PCBs) and organochlorine (OC) pesticide levels were determined in five stranded and fourteen by-caught Delphinus sampled from around New Zealand between 1999 and 2005. Generally, levels of trace elements were low. However, concentrations of OC pesticides were similar in range to those previously reported for Hector’s (Cephalorhyncus hectori) and common bottlenose dolphins (Tursiops truncatus). Organochlorine pesticides dieldrin, hexachlorobenzene (HCB), o,p’-DDT and p,p’-DDE were present at the highest concentrations. Markov chain models were used to assess the impact of tourism activities on Delphinus within the Hauraki Gulf. Foraging and resting bouts were significantly disrupted by boat interactions. Both the duration of bouts and the time spent in these two behavioural states decreased during boat interactions. Additionally, foraging dolphins took significantly longer to return to their initial behavioural state in the presence of a tour boat. Impacts identified are similar to those previously reported for the common bottlenose dolphin, a coastal species typically considered to be more susceptible to cumulative anthropogenic impacts. Data presented here reveal the nature and apparent susceptibility of New Zealand common dolphins to human-induced impacts, namely fisheries by-catch, pollution and tourism. This in conjunction with taxonomic uncertainty, lack of abundance estimates and the year-round use of inshore waters for feeding, clearly warrants immediate attention from managers. Furthermore, the current threat classification of New Zealand Delphinus should be reconsidered in light of population uncertainties, and in view of the susceptibly to human-induced impacts revealed by the present study.

Bottlenose dolphins (Tursiops truncatus) are frequently brought into contact with humans, due to their coastal habitat use. Over the last decade there has been considerable growth in the commercial dolphin-based tourism industry. This growth exposes coastal populations to boats and swimmers. New Zealand has allowed commercial operations offering swimming with wild dolphins since 1989. Little is known about the effects of boats and swimmers on dolphin behaviour. The present study examines a population of bottlenose dolphins that utilise the Bay of Islands as part of their range along the northeastern coast of New Zealand, and their behavioural response to commercial swim-with-dolphin operations. Data were collected from an independent research boat and the commercial dolphinwatching boats from December 1996 to February 2000. Photo-identification showed a closed population of 446 (95% C.I. 418-487) dolphins, with an 81% resight rate of the 378 catalogued individuals. Group size ranged from 2 – 50 dolphins, with 80% of groups (n = 160) containing 2 - 20 dolphins. The number of groups with calves present increased from 32% (n = 17) in 1997, to 63% (n = 47) in 1999. This could be explained by the increased number of neonates born; from four in 1997, to nine in 1999. Photo-identification in areas outside the Bay of Islands showed that individuals ranged minimum distances of 82 km north, and 388 km south of the Bay of Islands. All photographs taken outside the Bay of Islands were matched to known animals, suggesting that the majority of the northeastern coastal population is seen in the Bay. With the next nearest population of bottlenose dolphins approximately 1,000 km south, these dolphins probably form an isolated population ranging along the east coast of the northeastern North Island. Habitat use by the dolphins was examined using Geographic Positioning System (GPS) points simultaneously linked to behavioural states. In total, 31 groups were followed, and 847 GPS points were recorded. Position of initial encounter was recorded for 138 groups of dolphins. There was a significant correlation between water depth and sea-surface temperature, with dolphins found in deeper waters in summer when water temperature was highest, and in shallow waters in winter when the water temperature was lowest. Only one behavioural state, slow travel, was significantly different by season. Although all behaviours were observed in all zones, dolphins had preferential habitat use throughout the four zones within the Bay. To determine the level of impact on dolphin behaviour due to boat traffic, focal-group follows using a scan sample methodology were conducted from an independent research boat. A CATMOD analysis was used to determine dolphin behaviour by season, number of boats, and group size. Dolphin behaviour differed by boat number; in particular, resting behaviour decreased as boat number increased and milling behaviour increased as boat number increased. Behaviour differed when the research boat was the only boat present. Closer examination of boat type, i.e., permitted dolphin watching boats, non-permitted tour boats, and recreational boats, found a difference in dolphin behaviour in the presence of the permitted boats when compared to the other types. Dolphins rested less and engaged in more milling behaviour when the permitted boats were present. Responses to swim attempts from the commercial boats were compared from 1994 - 1995 to 1997 - 1998. In total, 255 groups were encountered of which 36% (n = 93) were exposed to at least one swim attempt. Successful swims (i.e., where at least one dolphin remained within 5 m of at least one swimmer) decreased from 48% in 1994 - 1995 to 34% in 1997 - 1998 and avoidance responses increased from 22% to 31%. Dolphin response varied according to swimmer placement from the boats. The ‘in path’ placement had the highest level of avoidance. Only ‘line abreast’ placement resulted in a decrease in avoidance. Based on the photo-identification sighting records, it was estimated that an average dolphin was exposed to 31 swim attempts per year. This suggests that individual dolphins have, with cumulative experience, become sensitised to swim attempts. If a swim attempt was successful, on average, it involved 19% of the group. Juveniles were more likely to interact with swimmers than adults. The present study suggests that the wide-ranging population of bottlenose dolphins that frequents the Bay of Islands is exposed to levels of tourism which can affect the dolphins behaviour. In particular, the permitted boats’ presence results in decreased resting behaviour by the dolphins. The apparent sensitisation of this population to swim attempts, and the relatively small number of individual dolphins that interact with swimmers, are grounds for concern about the long-term impact of interactions. Ongoing monitoring of this populations’ response to swimmers and boats, combined with a precautionary approach to management of boats and swimmers, are recommended.

The Chilean oyster, Tiostrea chilensis, is a commercially important species that is native to New Zealand and the Pacific Coast of South America. The description of the variability in life history characteristics among populations of the Chilean oyster is fundamental to understanding its biology and may help in solving some of the problems encountered in culturing this species. Research presented in this thesis describes some aspects of the reproductive biology of the Chilean oyster from four populations, mainly in northern New Zealand, and compares the results with previous studies from elsewhere. Similar patterns of gametogenesis were found among three study populations at Manukau Harbour, Hauraki Gulf and Foveaux Strait. Oysters were protandrous, maturing firstly as males and later also producing ova. In all three populations the majority of the contents of all the gonads were male reproductive products. There was no evidence that the sexuality of oysters alternated rhythmically as has been reported in other species of larviparous oysters. For spawning females, the often concurrent release of ripe sperm indicated the possible presence of self fertilisation. In samples of oysters examined from Foveaux strait the sexuality of oysters was found to change markedly with size. This suggested that the infection of oysters by the parasite Bonamia may not be related to their sexuality as was previously thought. At two northern populations (Hauraki Gulf and Manukau Harbour) larvae were produced from young, small oysters, and a much larger proportion of the population was brooding larvae each year than has been reported elsewhere. In both populations, larvae were being brooded, released and were settling at all times of the year, unlike other populations. The mean fertility of the Manukau Harbour oysters was the highest so far reported for any population of this species. The size of larvae in all three northern populations were smaller than has been reported for all other locations in New Zealand and chile and is thought to be related to differences in water temperatures. Overall, the results highlight the importance of investigations into populations of molluscs across their geographical range for revealing variation in life history characteristics which may be of benefit for aquaculture.
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The tellinid bivalve, Macomona liliana, is important to the structure and organisation of intertidal sandflat communities in Manukau Harbour. This thesis reports on features of the reproductive, larval supply and recruitment biology of Macomona liliana in relation to environmental factors in the harbour. Macomona liliana is gonochoric. In a mid-tide population sexual maturity occurred in animals ≥ 22 mm (shell length). Spawning is asynchronous and protracted from late November to March throughout the harbour and timing of the reproductive cycle is associated with seasonal changes in environmental variables: temperature, salinity and seasonal production of phytoplankton and benthic microalgae. A visual gonad index was useful for establishing the main periods of spawning activity. Favourable habitats are at mid-tide on the large exposed sandflats characterised by well sorted fine sands. Less favourable habitats are in sheltered bays characterised by moderate-poorly sorted sands. A delay in the onset of gametogenesis in small compared to large adults (July-August of. May-June) indicates size and/or age dependent resource allocation to growth and reproduction. Adult size classes are evenly represented in favourable habitats whereas in less favourable habitats size classes are dominated by small adults. Favourable habitats have an equal sex ratio or are biased towards females whereas in less favourable habitats the converse is true. Early life-history stages are described and techniques employed to facilitate their identification in plankton and sediment samples. A spatial Taylor's Power Plot (slope, b = 1.31) demonstrates thorough mixing of larvae in the main channels. Spatial autocorrelation models confirm that densities of larvae are higher to the south of Karore Bank than to the north. The recruitment period is December to early March but varies between successive years. Physical transport processes, post-settlement migration and high levels of mortality in Boccardia syrtis tube-mats dominate recruitment patterns in the high energy environments. Larval supply and active habitat selection by settling larvae may, however, be significant determinants of population structure in sheltered bays. Generalisations are made on the effect of habitat quality on the reproduction and recruitment biology of the Manukau Harbour metapopulation.

Theoretical research has demonstrated that ecological interactions in sympatry or parapatry can generate disruptive selection that in concert with assortative mating can lead to speciation. However, empirical examples are few and restricted to terrestrial and lacustrine systems. New Zealand triplefin fishes (Family Tripterygiidae) are an ideal model system to study speciation in the sea, as they conform to the criteria of an adaptive radiation, being philopatric, speciose and abundant, and having largely sympatric distributions. This thesis investigates two key aspects of the New Zealand triplefin radiation: 1) which ecological traits are under selection?; and 2) which traits are potentially available for the development of assortative mating? Habitat use was identified as a possible key trait for selection and investigated in detail in this thesis. Habitat use of the majority of New Zealand triplefin species was censused quantitatively throughout most of their latitudinal range and analysed using novel statistical methods. Analyses showed that habitat use was highly divergent between species and thus diversification in habitat may have been a major component in the evolution of this clade. The phylogenetic analysis of habitat characters confirmed that there has been rapid evolution in habitat use among species. Habitat selection at settlement was highly species-specific, indicating that interspecific differences in adult habitat use may be the outcome of active habitat choice established at settlement. These species-specific habitat associations showed no evidence for geographic variation in habitat use. Laboratory trials and field observations of the sister-species pair Ruanoho decemdigitatus and R. whero showed that competition was linked with body size, with R. decemdigitatus being the larger and consequently dominant species. The second part of this thesis investigated which traits may have contributed to prezygotic isolation, and thus to assortative mating. Little evidence was found for divergence in breeding season or male colour patterns. However, divergence in habitat affected breeding habitat choice, as triplefins court and mate in the same territory as that occupied year round. This suggests that assortative mating in New Zealand triplefin species could be the by-product of adaptation to habitat resources. Body size affected mate choice and time at first maturity in the Ruanoho sister-species pair, suggesting that size is important in the maintenance of reproductive isolation in these species. Differences in body size may have also lead to assortative mating in other New Zealand triplefin sister-species pairs, as all sister-species pairs differ in maximum body size. The findings of this thesis invoke a strong role for ecologically-based selection in speciation, and support the hypothesis that adaptation to habitat has been a major factor in speciation in this system.
This PhD was funded by the New Zealand Royal Society (Marsden Fund 02-UOA-005 to Kendall Clements), the Tertiary Education Commission (Top Achiever Doctoral Scholarship), and the University of Auckland (University of Auckland Doctoral Scholarship.

Lakes resulting from open pit mining may be potential water resources or potential environmental problems, depending on their water quality. As the global abundance of pit mines and pit lakes increases, there is increasing pressure on the mining industry to create pit lakes that have environmental, social, and/or economical utility. This thesis uses an interdisciplinary approach involving mineralogy, physical limnology, and geochemistry to predict and improve the water quality of a proposed pit lake at the Martha gold mine, New Zealand. A mineral quantification method developed for this study measured the distributions and concentrations of wall rock minerals, and identified 8 relatively homogeneous wall rock regions, called mineral associations. Acid-base accounting using calcite and pyrite quantities identified 3 associations with acid-generating potential. Three physical limnology tools (relative depth, wedderburn number, and numerical modeling with DYRESM), predicted that the upper 2/3 of the lake will circulate annually during the winter turnover period, whereas the lower 1/3 will remain permanently isolated. Permanent stratification resulted from density differences between groundwater and river water inputs during lake filling, plus lake morphology. The geochemical model used the distribution of mineral associations to characterize the composition of pit wall runoff, and used the limnologic prediction to define the mixing frequency, mixing depth, and layer volumes. Initial modeling with the geochemical program PHREEQC indicated the lake will have a pH of 5, and Cu and Zn concentrations that exceed aquatic life protection guidelines. Sensitivity analyses showed that subaqueous water-rock reactions did not have a significant affect on lake pH, suggesting these reactions are less important geochemical factors in pyrite-bearing pit lakes. Surface adsorption onto ferrihydrite reduced concentrations of As, Pb, and Cu, suggesting these reactions are important geochemical factors in pit lakes. By covering the acid-generating mineral associations, lake pH increased above 6.5, allowing for future recreational use. Concentrations of Cu complied with aquatic life protection guidelines, however, Zn concentrations remained above these guidelines. This study demonstrates the value of interdisciplinary pit lake predictions in the design of closure plans for open pit mines. Such studies improve the ability of mining companies to sustainably develop mineral resources.

The Participatory Irrigation Management approach was introduced into Cambodia in 2000, which was called the Participatory Irrigation Management and Development (PIMD). The goal of PIMD is to establish Farmer Water User Communities (FWUCs) to take over the management of irrigation schemes in their district in order to improve the performance of irrigation schemes and farmers’ livelihoods. The implementation of FWUCs has resulted in both failure and success. Several studies have identified factors that influence the failure of FWUCs, but little research has focused on their success. By employing a single embedded case study approach, this research selected the most successful scheme in Cambodia to identify factors that influenced the success of the FWUC in irrigation management. The findings of this research could provide concrete assistance to the government, donors, and non-governmental organisations in improving the performance of less successful FWUCs in Cambodia. The result of this research showed that the success of the O-treing FWUC was influenced by five internal and two external factors. The internal factors were: 1) the level of local participation, 2) the governance and management of the scheme, 3) the value of the benefits that flow from the irrigation scheme, 4) the quality of the irrigation infrastructure, and 5) the characteristics of the farmer members within the scheme. The external factors were: 1) the level of external support provided to the scheme, and 2) market access. The success of the FWUC required farmer participation and this participation was enhanced when farmers obtained benefits from it. This research also found that access to markets was critical to make the benefits that flowed from the irrigation scheme more profitable to farmers, leading to farmer participation. Similarly, it was also important to make sure that the irrigation infrastructure was of a high quality to ensure the delivery of an adequate and timely supply of water to farmers so that they could grow crops that provided them with the benefits. This required external support from the Ministry of Water Resources and Meteorology, NGOs, and local authorities to help rehabilitate the scheme. External support was also critical for enhancing the governance and management of the scheme through assistance with the formation process, provision of financial resources, capacity building, rule enforcement, and conflict resolution. The governance and management of the scheme, in particular the leadership capacity of the FWUC was another critical factor because it ensured the maintenance and development of the irrigation infrastructure, the timely and adequate supply of water to farmers, farmers’ trust and respect for leaders, and farmer participation. Finally, the success of the FWUC could not be viewed independently from farmer characteristics within the scheme. Farmers tended to participate in irrigation management when they had a history of self-organisation, when they were relatively homogenous, and when they were dependent upon farming for their livelihoods. This research suggests that the successful implementation of FWUCs requires a focus on the seven factors and the interactions that occur between these factors. Irrigation stakeholders such as the Ministry of Water Resources and Meteorology, donors, NGOs, local authorities, local leaders, and farmers should work together to enhance these factors in order to ensure the success of FWUCs.

The last decade has been a period of great expansion and land use intensification for the New Zealand dairy farming industry with a 44% increase in national dairy cow numbers. Intensive dairy farming is now considered to be a major contributor to the deterioration in the quality of surface and ground water resources in some regions of New Zealand. Previous research has demonstrated intensive dairy farming is responsible for accelerated contamination of wateways by nutrients, suspended solids, pathogenic organisms and faecal material. A number of common dairy farming practices increase the risk of nutrient leaching. In particular, farm dairy effluent (FDE) has been implicated as a major contributor to the degradation of water quality. With the introduction of the Resource Management Act in 1991, the preferred treatment for FDE shifted away from traditional two-pond systems to land application. However, on most farms, irrigation of FDE has occurred on a daily basis, often without regard for soil moisture status. Therefore, it has been commonplace for partially treated effluent to drain through and/or runoff soils and contaminate fresh water bodies. The objectives of this thesis were to design and implement a sustainable land application system for FDE on difficult to manage, mole and pipe drained soils, and to assess the impacts of FDE application, urea application and cattle grazing events on nutrient losses via artificial drainage and surface runoff from dairy cattle grazed pasture. To meet these objectives a research field site was established on Massey University's No.4 Dairy farm near Palmerston North. The soil type was Tokomaru silt loam, a Fragiaqualf with poor natural drainage. Eight experimental plots (each 40 x 40 m) were established with two treatments. Four of the plots represented standard farm practice including grazing and fertiliser regimes. Another four plots were subjected to the same farm practices but without the fertiliser application and they were also irrigated with FDE. Each plot had an isolated mole and pipe drainage system. Four surface runoff plots (each 5 m x 10 m) were established as subplots (two on the fertilised plots and two on the plots irrigated with FDE) in the final year of the study. Plots were instrumented to allow the continuous monitoring of drainage and surface runoff and the collection of water samples for nutrient analyses. An application of 25 mm of FDE to a soil with limited soil water deficit - simulating a 'daily' irrigation regime - resulted in considerable drainage of partially treated FDE. Approximately 70% of the applied FDE left the experimental plots with 10 mm of drainage and 8 mm of surface runoff. The resulting concentrations of N and P in drainage and runoff were approximately 45% and 80% of the original concentrations in the applied FDE, respectively. From this single irrigation event, a total of 12.1 kg N ha-1 and 1.9 kg P ha-1 was lost to surface water representing 45% of expected annual N loss and 100% of expected annual P loss. An improved system for applying farm dairy effluent to land called 'deferred irrigation' was successfully developed and implemented at the research site. Deferred irrigation involves the storage of effluent in a two-pond system during periods of small soil moisture deficits and the scheduling of irrigation at times of suitable soil water deficits. Deferred irrigation of FDE all but eliminated direct drainage losses with on average <1 % of the volume of effluent and nutrients applied leaving the experimental plots. Adopting an approach of applying 'little and often' resulted in no drainage and, therefore, zero direct loss of nutrients applied. A modelling exercise, using the APSlM simulation model, was conducted to study the feasibility of practising deferred irrigation at the farm scale on No 4 Dairy farm. Using climate data for the past 30 years, this simulation exercise demonstrated that applying small application depths of FDE, such as 15 mm or less, provided the ability to schedule irrigations earlier in spring and decreased the required effluent storage capacity. A travelling irrigator, commonly used to apply FDE (a rotating irrigator), was found to have 2-3 fold differences in application depth and increased the risk of generating FDE contaminated drainage. New irrigator technology (an oscillating travelling irrigator) provided a more uniform application pattern allowing greater confidence that an irrigation depth less than the soil water deficit could be applied. This allowed a greater volume to be irrigated, whilst avoiding direct drainage of FDE when the soil moisture deficit is low in early spring and late autumn. A recommendation arising from this work is that during this period of low soil water deficits, all irrigators should be set to travel at their fastest speed (lowest application depth) to minimise the potential for direct drainage of partially treated FDE and associated nutrient losses. The average concentrations of N and P in both 2002 and 2003 winter mole and pipe drainage water from grazed dairy pastures were all well above the levels required to prevent aquatic weed growth in fresh water bodies. Total N losses from plots representing standard farm practice were 28 kg N ha-1 and 34 kg N ha-1 for 2003 and 2004, respectively. Total P losses in 2003 and 2004 were 0.35 kg P ha-1 and 0.7 kg P ha-1, respectively. Surface runoff was measured in 2003 and contributed a further 3.0 kg N ha-1and 0.6 kg P ha-1. A number of common dairy farm practices immediately increased the losses of N and P in the artificial drainage water. Recent grazing events increased NO3--N and DIP concentrations in drainage by approximately 5 mg litre-1 and 0.1 mg litre-1, respectively. The duration between the grazing and drainage events influenced the form of N loss due to a likely urine contribution when grazing and drainage coincide, but had little impact on the total quantity of N lost. Nitrogen loss from an early spring application of urea in 2002 was minimal, whilst a mid June application in 2003 resulted in an increased loss of NO3--N throughout 80 mm of cumulative drainage suggesting that careful timing of urea applications in winter is required to prevent unnecessary N leaching. Storage and deferred irrigation of FDE during the lactation season caused no real increase in either the total-N concentrations or total N losses in the winter drainage water of 2002 and 2003. In contrast, land application of FDE using the deferred irrigation system resulted in a gradual increase in total P losses over the 2002 and 2003 winter drainage seasons. However, this increase represents less than 4% of the P applied in FDE during the lactation season. An assessment of likely losses of nutrients at a whole-farm scale suggests that it is standard dairy farming practice (particularly intensive cattle grazing) that is responsible for the great majority of N and P loss at a farm scale. When expressed as a proportion of whole-farm losses, only a very small quantity of N is lost under an improved land treatment technique for FDE such as deferred irrigation. The management of FDE plays a greater role in the likely P loss at a farm scale with a 5% contribution to wholefarm P losses from deferred irrigation.