Dissertations / Theses on the topic '060205 Marine and Estuarine Ecology (incl. Marine Ichthyology)'

The impact of no-take marine reserves on spiny lobster, Jasus edwardsii, populations and the adjacent lobster fishery was assessed in a study that determined: the response of lobster populations to protection, if lobsters within marine reserves moved out into the surrounding fishery, examined the behavioural characteristic of lobsters that contributed to their recovery and spillover, and contrasted catch characteristics around a north-east New Zealand marine reserve with 2 unprotected sites. Surveys of 4 no-take marine reserves of different ages and 4 unprotected control sites confirmed that J. edwardsii increase in mean size and abundance within protected areas. Total lobster density was estimated to increase by 6.1% per year of protection. The relationship between age of reserve and the density of lobsters above the legal size limit (>100 mm carapace length) was complicated by depth related interactions between reserves, due to seasonal changes in the depth distribution of lobsters and differences in the timing of surveys among locations. However, density increases in legal sized lobsters were greater than those of the overall population. Mean size of protected lobsters increased in a non-linear fashion, reflecting the asymptotic growth characteristics of the species. Mean carapace length of lobsters increased by 11.24 mm after 3 years of protection and only by 16.25 mm after 2l years of protection. Corresponding increases in biomass (kg.500 m-2) and egg production (eggs.500 m-2) were estimated to be 7.4% and 6.6% respectively per year of protection. A tag recapture program indicated that the limited scale of movements and relatively high site fidelity of mature J. edwardsii aided the recovery of lobster populations in protected areas. Of 737 lobsters tagged in and around the Leigh Marine Reserve,212 were subsequently resighted. Seventy percent of resighted lobsters were relocated less than 250 m along the shore from their initial site after a mean period of liberty of 146 (se = 13.42) days. However, seasonal offshore movements took lobsters beyond the seaward boundary of the reserve where they were susceptible to capture. Of the 521 lobsters tagged on inshore reefs within the Leigh Marine Reserve. l.9% were caught over the seaward boundary by commercial fishers, and 14.4% of the 181 lobsters tagged over the seaward boundary were resighted on inshore reefs within the reserve. Movements into or out of the reserve across the longshore boundaries were also recorded for 7 out of the 27 lobsters moving further than 250 m along the shore. Acoustic tracking confirmed that J. edwardsii have a high site fidelity, with tracked lobsters spending a median of 84% of their time at their home site. Twenty one percent of the 26 lobsters fitted with acoustic tags never left their tagging site and, of those that did leave 56% eventually returned. Lobsters moved up to 3.1km away from their home sites but managed to find their way back after periods of 1 to 103 days away. Five lobsters had strong associations with two separate sites and made repeated movements between these alternate home sites. The straight line distance between alternate home sites ranged from 200 m to 1.3 km, and the period between visits to their primary or secondary home sites ranged from 1 to 93 days. Movement activity varied throughout the year, and seasonal patterns differed between males and females. Females displayed one peak in movement activity per year, around the time of larval release in September-October. Males displayed a summer peak centred on January, and a winter peak centred on July. The onset of high movement activity was often accompanied by a shift to deeper water and l0 of the 14 lobsters tracked for over 6 months spent periods away from the inshore reef system. Exposed groups of lobsters were observed aggregating in offshore areas of sand and low lying patch reef during the day. Offshore aggregations were observed over 7 months of the year and lobsters within the aggregations displayed behaviour consistent with the use of mutual defence. The sexual composition of the aggregations reflected seasonal patterns in male and female movement rates. Male J. edwardsii dominated the aggregations in winter and summer; times when peak feeding rates of males held in captivity were also recorded. Females dominated the offshore aggregations in September-October when larvae are released. Seven of the 26 lobsters fitted with acoustic tags moved over the boundaries of the Leigh Marine Reserve and Tawharanui Marine Park during offshore movements. Despite the fact that there is no fishing access to inshore reefs within the Leigh Marine Reserve, no significant difference was detected between the catch per unit effort (kg.trap haul-1) of lobsters caught around the reserve, nearby coastal Leigh or Little Barrier Island. However, catches around the marine reserve contained fewer (P=0.0009) but larger lobsters than at Little Barrier Island. The catch characteristics of lobsters from coastal Leigh were intermediate between the other two sites. As access to inshore reefs around the Leigh Marine Reserve was limited to a small area at either end of the reserve, traps tended to be set in offshore locations and the sexual composition of the total catch around the Leigh Marine Reserve reflected the seasonal movements of males and females into, and out, offshore areas. At coastal Leigh and Little Barrier Island the location of traps was not restricted and greater use was made of coastal fringing reefs. As a result the sexual composition of the catch at these locations did not reflect the movement of various components of the lobster population into and out of specific habitats or locations. Overall, the results of this study suggest that relatively small (~ 5 km2) no-take marine reserves increase lobster biomass and egg production, without adversely affecting catch rates in the surrounding fishery. Marine reserves may therefore represent a viable management tool, which if used in conjunction with other management regimes, could provide a more precautionary approach to the management of the J. edwardsii fishery at minimal cost to the industry.

Various aspects of metabolism and physiology were investigated during the ontogeny of yellowtail kingfish (Seriola lalandi), a fish of growing aquaculture importance in both New Zealand and other countries. Incubation experiments between 18-24°C showed that developing eggs and larvae were heavily influenced by temperature. It appeared that at warmer temperatures larvae hatched smaller but grew on the yolk sac, whereas at cooler temperatures larvae grew inside the chorion. Oxygen consumption data supported this, with a negative correlation found between total embryonic oxygen consumption and temperature. A mechanism was proposed to explain the differential effect of temperature on ontogeny and growth. Like other marine fish with pelagic eggs, yellowtail kingfish were found to be heavily reliant on free amino acids as a source of energy. At 23°C the pattern of substrate utilisation in eggs was considerably different from that at 17-21°C, indicating that 23°C exceeded the tolerance for normal development. Inter-individual aggression by large individuals was associated with the development of size heterogeneity in juveniles. Although this aggression also affected the survival of smaller juveniles, it was not the primary agent of much of the mortality that occurs during this phase, as many of these individuals were on a degenerate developmental trajectory. Yellowtail kingfish fingerlings used for ongrowing were robust to the stressors imposed by live transport. The ontogenetic development of metabolic rate from 0.6 mg-2.2 kg did not follow the same scaling exponent as that observed for mammalian models of allometry, and has implications for interspecific studies of mass-dependent metabolism.

The population biology and ecology of scallops in Greater Omaha Bay (a semi-oceanic bay) and Kawau Bay (a estuarine bay) was quantified by observation and experiment. Information was collected to extend the knowledge base on northern New Zealand scallop population dynamics, and for application to potential scallop enhancement in the region. Contagious scallop population organisation was found at all spatial scales examined, ranging from bay wide through to individual bed patchiness, down to the scale of inter-animal distances. Such clumping has strong implications for a range of population processes, including fishing susceptibility and fertilisation success. Monitoring of adults found two main spawning events to occur; in late October and in mid January. Changes in the gonado-somatic index (GSI) were well synchronised between individuals within populations. Subsequent monitoring of spat-fall in artificial collectors documented two main recruitment events, probably the outcomes of the two local spawning events. These spat-fall events occurred on collectors separated by 1Os of km. However, substantial density variations occurred between sites, indicating that local hydrodynamics may have played a significant role in modifying local spat-fall intensities. Smaller spat-fall events were also present between the two major events. The number of spat collected at a number of combinations of site and time were sufficient to support commercial spat catching operations, although problems were encountered with spat detaching at sizes too small to be retained by the collectors. In the 1993/94 summer a large algal bloom event completely eliminated scallop recruitment to collectors for the first three months of that season. Mass mortality events were a major contributor to overall benthic scallop population mortality. Probable causes included intensive scallop harvesting (commercial and recreational), a major storm episode, and a large algal bloom. These effectively eliminated scallop populations from Greater Omaha Bay. The adjacent Kawau Bay was not affected by any of these particular events, but populations there did not survive long after reaching adult sizes. Estimates of M (natural mortality) were higher for all scallop populations than have been previously documented in New Zealand studies. Growth trajectories were reasonably consistent in waters shallower than 19 m, but a progressive decline occurred in both maximal size reached and average growth rates with increasing depth after this point. Food limitation may have been the mechanism involved, which is likely to vary significantly for other locations depending on local environmental conditions. Average time to recruitment to the fishery (100 mm shell width) was three years for the shallower populations. A slight reduction in average size of adults at higher densities was found for some populations, indicating a possible density-dependent effect. Examination of a high density scallop bed found animals to display distinctive substratum preferences over small spatial scales, with higher abundances occurring on coarser materials such as shell gravel, marl and grit. Mud was not favoured as a habitat type. Movements of tagged animals at this location were spatially limited to within the particular habitat patch in which an individual was tagged and released, i.e. at a scale of 1s to 1Os of metres. No animals moved between adjacent patches of similar habitat (100 m scale). A B.A.C.I type experiment was undertaken to assess incidental mortality effects of commercial scallop dredging on undersize scallops, at the spatial scale of beds. Significant negative effects were quantified, with the number of undersize animals killed per legal animal harvested estimated at 1.7 and 2.8 : 1, depending on the size frequency structure of the fished bed. Modelling of likely improvements in the number of animals surviving at the end of fishing, given a reduction in the minimum legal size from 100 to 90 mm, indicated improvements of 20 to 41% of the original population remaining after fishing, depending on animal size and assumed dredge efficiencies, A 90 mm MLS has subsequently been adopted by the Coromandel Scallop Fishery. The results from this work provide detailed population based estimates of parameters required for successful management and optimal harvesting strategies of Hauraki Gulf scallop populations. The large variability in parameters such as mortality, and strong abundance correlations with habitat type, has strong implications for such activities. This work also provides essential information for the undertaking of locally based enhancement operations, such as the spatial and temporal magnitude and variability of spat-fall events, and growth rates with respect to habitat features (i.e. depth).

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.

This thesis presents a descriptive and a functional analysis of the ecology of an island host-parasite system consisting of the Polynesian rat, Rattus exulans (Peale) and its gut helminths. The results, which include an historical perspective, are presented in the form of 7 papers or sections. Each of these examines a particular aspect of this host-parasite relationship. A review of the origin and an update of the theorised dispersal of this rat from Southeast Asia to New Zealand is given in the first section of chapter one. Previous theories have derived the New Zealand populations from a line which passed through Micronesia. In accordance with new information from the Lapita cultural assemblage, this rat is now theorised to have accompanied these "Lapita" peoples through the Bismarck Archipelago and Solomon Islands, arriving in the Tonga- Samoa region about 3600-3000 Before Present (B.P.). From here, the Proto- Polynesians then dispersed further east, taking with them the commensal R. exulans, pig, dog, and chicken. This rat is thus thought to have arrived in New Zealand, the most southern and last-settled landmass in Polynesia, in the canoes of the Maori about 1000 years ago. Information on the ecto- and endoparasites of the Polynesian rat from throughout its geographical range is collated and presented in section two. This includes the results of the two surveys (one being part of this thesis) done on the parasites of this rat in New Zealand. All populations of R. exulans sampled in these two surveys came from offshore islands, to which this rat is almost totally confined, and where, on many, it is the only rodent species present. In contrast, most of the populations sampled beyond New Zealand are now sympatric with other rodent species. For the New Zealand populations only, it was also possible to identify those parasites only accidentally associated with this host; these are listed as "transients". In section three, an attempt is made to determine the probable biogeographical origins of parasites recorded from populations of this rat on "exulans only" offshore islands of New Zealand. Such a study was possible only because of the archaeologically documented commensal relationship between rat and Polynesian man. This information, detailed in section one, together with the parasitological data base assembled in section two, provided the material for this analysis. Several "heirloom" species are identified, theorised to have been inherited by this rat during speciation somewhere in Island Southeast Asia. Parasites acquired during dispersal are divided into "old" and "new souvenirs"; the former are thought to have been acquired from sympatric rodent species in Near Oceania sometime prior to 3000 B.P., and the latter from R. rattus, R. norvegicus or Mus musculus introduced in the last 200 years during European settlement in New Zealand. The conclusions further suggest that some at least of the "new souvenir" species have been acquired by R. exulans on "exulans only" offshore islands of New Zealand by cross-transfer from other rodent species which have temporarily gained access to these islands. This theory is examined in more detail in the fourth section, and reports of such accidental colonizations of offshore islands are presented as supporting evidence. In Chapter two, the influence of habitat on the population demography of the host is investigated. Nearly 1000 rats were trapped and necropsied over a 17 month period in three different habitats on Tiritiri Matangi, an "exulans only" island at the entrance to the Auckland harbour. Rank grassland which covers most of this island formed one habitat; a second consisted of forest remnants confined to gullies, and the third consisted of the small, inhabitated, lighthouse station and farmed area at one end of the island. Between-habitat differences were observed in diet, adult longevity, mean weight of immatures, the time of onset of sexual maturation, and annual reproductive output. These results suggested several modifications to existing models of this host's demography in New Zealand. Shelter in particular appears to play an important role in the demography of this species in temperate latitudes. The effects of parasitism on potential fitness parameters e.g. reproduction, and adult mortality/survival, are examined in chapter three. Based on the results obtained in chapter two, a number of hypotheses were developed, and the predictions arising from these were tested. Few significant results were obtained; these revealed habitat and some sexual interactions with the level of infection, at certain times of the year. However, no causal relationship could be established between these effects and host reproduction or mortality. It is concluded that the helminth parasites of this rat on this island have little or no effect on these host parameters, and support the suggestion that these species constitute a depauperate and well-adapted rodent parasite fauna. The last chapter presents the results of an analysis of the effects of habitat, season, host age, and sex on the distribution and abundance of the helminths of this rat on this island. Together, the graphs and the statistical analyses demonstrate that habitat has the most important influence, significantly affecting all 7 species; this effect is of greater magnitude than the other 3 variables on 5/7 of these species. Season and age also have important effects, while sex had no apparent influence. Explanations for the observed patterns are sought in known aspects of the biology of the host in the three habitats described in chapter two, and in the life cycles of the parasites. In total, this thesis provides a comprehensive account of the ecology of the Polynesian rat and its helminth parasites on Tiritiri Matangi Island. It also identifies gaps in the existing data base, formulates certain hypotheses, and makes a number of predictions all of which will hopefully stimulate further interest in this rat and its parasites.

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.

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.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris.
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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 population dynamics of juvenile snapper, Pagrus auratus, were investigated in the Hauraki Gulf, north-eastern New Zealand, between 1982 and 1990. Attention focused on age and growth, temporal and spatial variation in abundance, and recruitment. Daily increment formation was validated in the sagittae of snapper up to about 160 days old. Increment width varied with time of year, and snapper age, and increments were not resolvable with a light microscope during winter. Increment counts inside a prominent metamorphic mark showed that larval duration was 18-32 days, and was inversely related to water temperature. Spawning dates were back-calculated from increment counts in settled juveniles, and ranged from September to March with a peak in November-January. The onset of spawning was temperature dependent. Fast-growing snapper had smaller sagittae than slow-growing snapper, indicating an uncoupling of otolith and somatic growth. Snapper gonads differentiated first as ovaries during the second year of life, and then some juveniles changed sex to become males during their third year. Sex change occurred before maturity, so snapper are functionally gonochoristic. Growth was slow during the larval phase, but increased rapidly after metamorphosis to about 0.6-0.9 mm.day-1. From the first winter, growth followed a well-defined annual cycle, with little or no growth during winter, and linear growth of 0.16-0.43 mm.day-1 during spring-autumn for 0+/1+ and 1+/2+ snapper. Snapper grew faster at higher temperatures. Trawl catch rates were affected by numerous gear and environmental factors, but probably provided reasonable estimates of snapper relative abundance. Recommendations are made for improving snapper trawl survey procedures. There was a strong annual abundance cycle in the Kawau region, peaking in spring, and declining to a minimum in winter. Snapper were patchily distributed at a spatial scale of 1-2 km, probably because of preference for specific micro-habitats. Year class strength of 1+ snapper varied 17-fold over seven years, and was strongly positively correlated with autumn sea surface temperature during the 0+ year. The strengths of the 1991 and 1992 year classes are predicted to be below average, and extremely weak, respectively.

This thesis develops a quantitative cladistic approach to panbiogeography. Algorithms for constructing and comparing area cladograms are developed and implemented in a computer program. Examples of the use of this software are described. The principle results of this thesis are: (1) The description of algorithms for implementing Nelson and Platnick's (1981) methods for constructing area cladograms. These algorithms have been incorporated into a computer program. (2) Zandee and Roos' (1987) methods based on "component-compatibility" are shown to be flawed. (3) Recent criticisms of Nelson and Platnick's methods by E. O. Wiley are rebutted. (4) A quantitative reanalysis of Hafner and Nadler's (1988) allozyme data for gophers and their parasitic lice illustrates the utility of information on timing of speciation events in interpreting apparent incongruence between host and parasite cladograms. In addition the thesis contains a survey of some current themes in biogeography, a reply to criticisms of my earlier work on track analysis, and an application of bootstrap and consensus methods to place confidence limits on estimates of cladograms.

Growth, development and behaviour were examined in artificially reared larval Pagrus auratus and Forsterygion varium, from the time of hatching. Yolk-sac larval P.auratus hatched at a small size (2.00mm SL), without functional eyes, mouth or digestive tract, and for three days spent long periods at rest. Growth was initially rapid but slowed by 3 days as yolk reserves neared depletion. By days 4-5, the mouth had opened, eyes were functional, yolk was depleted, and a rudimentary gut had formed. Larvae were now able to maintain a horizontal swimming mode and were actively searching for and attacking prey. First feeding was observed in some larvae. Growth was retarded during the transition from endogenous to exogenous nutrition and then increased as feeding proficiency improved. Yolk-sac F.varium hatched at a larger size (4.78mm SL), with functional eyes and jaws. Larvae were able to maintain a horizontal swimming mode from hatching. First feeding was observed from the first day after hatching. F.varium larvae grew steadily from the time of hatching. Ocular morphology was examined in larval, juvenile and adult P.auratus and F.varium. There was a 96 fold increase in eye size, from 0.23mm diameter in a 4 day old larval P.auratus (3.4mm SL) to a maximum diameter of 22mm in an adult of 333mm body length. F.varium displayed a 26 fold increase in eye size, from 0.28mm diameter in the smallest larva (5.00mm SL) to a maximum eye diameter of 7.2mm in a 11gmm long adult. Larval fish had pure cone retinae, however putative rod precursor cells were present from hatching in F.varium and from 18 days in P.auratus. Juvenile and adult fish had duplex retinae with cones arranged in a square mosaic in which 4 twin cones surround a central single cone. Hypertrophy of cone ellipsoids with increasing eye size, resulted in maintenance of a closely packed array in fishes of all sizes. The appearance of retinomotor movements was coincident with the development of a duplex retina in both species. Theoretical spatial acuity (calculated as a function of cone spacing and focal length of the lens) was poor in the smallest larval fish (2° 1' and 1° 8' minimum separable angle in 4 and 1 day old P.auratus and F.varium respectively) but improved to asymptotic values in adults (3'- 4', and 9' in P.auratus and F.varium respectively). Behavioural acuity (determined using the optokinetic response) of 4 day old larval P.auratus (37° 30') and 1 day old F.varium (29°) was very much lower than histological estimates. Behavioural acuity improved to 8° 8' in 16 day old P.auratus and 4° 18' in 14 day old F.varium, but did not attain theoretical estimates for fish of that size (55' and 54'). A rudimentary retractor lentis muscle was first apparent in larval fish 1 week after hatching, and was coincident with the formation of a posterior lental space. Presumably larval fish eyes were incapable of accomodative lens movements until this time. A relative measure of Matthiessen's ratio (distance from lens centre to boundary of the pigmented retinal epithelium/lens radius) measured histologically, decreased from 4.2 and 2.7 in 3 day old P.auratus and newly hatched F.varium, to 2.2 and 2.3 in larvae 22 and 16 days of age respectively. This suggests that growth of the retina and lens were not symmetrical in the eyes of very small larval fish. If Matthiessen's ratio holds for little eyes, then they will initially be strongly myopic. This may account in part for the mismatch between behavioural and theoretical acuity. Perceptive distances of first feeding larval P.auratus and F.varium, estimated for prey items equal in dimensions to maximum jaw widths, were very small (0.2mm and 0.4mm for prey 0.15mm and 0.2mm in size respectively), but increased with increasing body size to 2.1mm and 4.0mm for prey 0.3mm in size, at 16 and 14 days of age respectively. These data have implications for larval feeding in the wild.

Light microscopy, low ionic strength solution culture and image analysis methods were used to make detailed measurements on root hair populations of different genotypes of white clover (Trifolium repens L.) and ryegrass (Lolium perenne L.). A model of root hair population structure was developed and validated that will facilitate research on root hairs of these species. Diagrams were drawn of the root hair length and frequency on entire root systems. The distributions of root hairs on these diagrams often differed from textbook diagrams of root hairs because root hair length and frequency varied considerably along the root axis. The key issue examined was the response at species, population and genotype levels of root hair populations perturbed by aluminium and phosphate, and the implications of these responses for our understanding of the strategies adopted by plants growing in stressful environments. Demographic growth analysis gave the best understanding of the mechanisms of root hair population response to genetic variability, resource depletion and environmental perturbation. Root hair length seemed to be controlled by the individual root hair. However the number of root hairs appeared to be controlled by the root. Therefore it is the root that controls the distribution of the hairs on the root, and how this distribution is modified by perturbation. Root hair populations were shown to have strategies that were similar to their shoot system growth strategies-guerrilla for clover, phalangeal for ryegrass. The root and root hair systems, and shoot systems also demonstrated similar characteristics when the r and K strategy model was applied. At an ecosystem level, clover and ryegrass occupied the same orthogonal in the CSR (competitive-stress-ruderal) model. Therefore at a larger scale, these plants are able to coexist, but they do this by having different strategies at a species level.
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The doctoral studies described in this thesis involve the phenotypic characterization of the tremor rat, an animal model of Canavan disease, and a proof of principle gene transfer study in this model. The phenotype of the tremor rat is examined at the genetic, molecular, cellular, neurochemical, physical and behavioural levels, and tremor mutants are described within the context of Canavan disease. Tremor mutants appear to share many phenotypes with both human patients and to the knock-out mouse model. The deletion of aspartoacylase results in a total loss of the capacity to metabolize N-acetyl-aspartate to acetate and aspartate in brain, leading to elevations in brain N-acetyl-aspartate levels, changes in cell and tissue morphology, and physical and behavioural deficits including mild akinesia and loss of normal motor coordination and balance. Parallel to this work was the development of a gene transfer approach to treat Canavan disease, involving Adeno-associated virus mediated delivery of aspartoacylase to the mammalian central nervous system. Gene transfer was undertaken in tremor rat mutants, and analysis was made of gene expression and function as well as the effect of aspartoacylase expression on improving the phenotypic deficits observed in mutant animals. Gene expression was observed at the RNA and protein level, with recombinant protein observed in cell soma and processes. Although not significant the data suggested a trend of decreased NAA levels after aspartoacylase transfer in comparison to animals injected with a vector encoding green fluorescent protein. Improvement was noted in the rotorod phenotype with mutant animals receiving aspartoacylase gene transfer performing better at tests of balance and coordinated locomotion than animals receiving a control vector. The study provided evidence that Adeno-associated virus mediated aspartoacylase gene transfer to the brain improves some of the deficits in tremor mutants, and supports the rationale of human gene transfer for Canavan disease.
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Previous studies indicated the marine pyridoacridone alkaloid ascididemin possessed a unique biological profile. Investigation of synthetic routes to ascididemin led to the discovery that ascididemin precursors possessed a wide range of biological activities. One precursor possessed hollow fiber in vivo antitumoral activity and continuing in vivo studies at the NCI, using subcutaneous xenograft assays, are in progress. A crystal structure of a precursor indicates that these tetracyclic heterocycles are planar, suggesting intercalation as a mechanism of antitumoral action. Ascididemin was synthesized by two novel ring E forming reactions. The superior methodology was also useful in the preparation of analogues, such as kuanoniamine A. Ascididemin possessed promising hollow fiber in vivo antitumoral activity but was poorly active in a subcutaneous xenograft study. Ascididemin was incapable of exerting antitumoral activity at a distance and further analogues were prepared to address this problem. Ten analogues were prepared, with all the non-bromine containing analogues selected for in vivo evaluation at the NCI. Two ring A analogues were prepared by a thennew synthetic route, including the antiviral natural product 11-hydroxyascididemin. 11-Methoxyascididemin was selected for hollow fiber evaluation. Two bromine containing ring D analogues were prepared, including the antifungal natural product 2-bromoleptoclinidinone. A crystal structure on 2-bromoleptoclinidinone was the first determined on a pyridoacridone alkaloid and the molecule was planar, further supporting an intercalative mechanism of action. Due to non-selective antitumoral cytotoxicity, ring D analogues are not useful antitumoral agents. Six carbon-based ring E analogues were prepared by novel methodology. All 6-substituted analogues assessed were selected for in vivo antitumoral evaluation. Hollow fiber antitumoral activity decreased with bulk of the substituent. 6-Methylascididemin has been selected for subcutaneous xenograft studies. The 5-substituted analogue prepared gave the best in vitro antitumoral profile of all alkaloids in this study and has been selected for in vivo evaluation. Ring E substituted N-8-deaza-ascididemin analogues possessed no antitumoral activity, highlighting the importance of the 1,10-phenanthroline-like bay region of ascididemin in antitumoral activity. Another four structurally novel, quinoid containing alkaloids have been selected tor in vivo evaluation. While ascididemin was the only compound capable of topoisomerase IIα cleavable complex stabilization, related alkaloids possessed a similar level of inhibitory action against this enzyme. This further supports intercalation as the dominant mechanism of action for pyridoacridone alkaloids. Ecological roles of four natural pyridoacridone alkaloids were assessed. Alkaloids were species specific antifeedant agents against important consumers. These alkaloids may have a long term detrimental effect on predator physiology, due to the well established ability of these alkaloids to interfere with cell proliferation. Ascididemin elicited avoidance responses in numerous marine species. Ascididemin has no antifouling activity against macrofoulers. Microbiological assessment of ascididemin, 11-hydroxyascididemin and 2-bromoleptoclinidinone indicated that modification of the ascididemin chromophore leads to the directing of antimicrobial activity towards a different phyla of parasites. Pyridoacridone alkaloids may be part of a non-antibody based immune system. All studies point to pyridoacridone alkaloids enhancing the eventual reproductive success of the organism. Biological and chemical evaluation of 29 New Zealand ascidians has been performed. Significant biological activity was detected in ten ascidians. Novel metabolites isolated were 2-(3'-bromo-4'-hydroxyphenol)ethanamine (Cnemidocarpa bicomuta) and 1,3-dimethylguanine (unidentified ascidian). Known metabolites isolated were 1,3-dimethylisoguanine (Cnemidocarpa bicomuta) and rubrolides A, B and C (unidentified ascidian). The survey highlighted the importance of overexpressed purine bases in ascidian metabolism. No physiological roles for these overexpressed purines are as yet apparent. Our study of NZ ascidians has led to the isolation of many compounds previously isolated from sponges. The widespread distribution of such metabolites gives credence to the theory that common metabolite-generating genes are present in both phyla, due to the evolutionary success of these genes. Two optically active 9-(5-S-methyl-5-sulfinyl-lyxofuranosyl)-9H-purin-6-amine (lyxosyl-MTAS) nucleosides were isolated from the nudibranch Doriopsis flabellifera. This is the first report of any lyxosyl-MTAS nucleoside as either a natural or synthetic product.

Broadcast spawning marine invertebrates have been widely used as model organisms to study processes of evolution. One of these is the study of various life history stages associated with reproduction. Fertilization ecology in broadcast spawning marine organisms, i.e. the process by which sperm and egg fusion occurs once released into the ocean, has been the subject of intensive study for roughly the last 20 years, and represents thus a recent field in ecological sciences. This growth in interest was sparked by studies that showed spawning events may take place predominantly under sperm limiting conditions. More recent findings however, suggest that the occurrence of sperm competition, and the risk of polyspermy (multiple sperm entry in to the egg, which is lethal in echinoderms) can also occur during reproductive events in marine invertebrates. This has also been predicted on theoretical grounds. Even though polyspermy has been observed previously, particularly during aquaculture studies, evidence to assess the occurrence of polyspermy in situ, and the conditions under which it occurs is lacking. Simulated field studies in Evechinus chloroticus as well as laboratory studies in E. chloroticus and Coscinasterias muricata found high levels of polyspermy, even under the sperm limiting conditions that are naturally found in the field in other marine broadcast spawners. Furthermore, laboratory results in both Evechinus and Coscinasterias showed that polyspermy is most likely to increase when sperm concentrations are increased. In addition, even though increasing sperm concentrations increases monospermy to a certain extent, an increase in gamete contact times generates similar levels of monospermy. Results from these studies confirmed the mathematical model predicting some of these events. The timing of gamete release to achieve maximum fertilization success (monospermy) in a broadcast spawner is thought to be under strong selective pressures, because reproductive success is directly related to fitness. The spawning patterns in the sea urchin E. chloroticus observed in this study demonstrated that E. chloroticus spawns under varying environmental and ecological conditions. Interestingly, it appeared that highly synchronous and widespread spawning was found to occur when highly turbulent conditions existed. This may reduce the potential for polyspermy that may exist during mass spawnings under shallow and calm conditions. The demonstration of polyspermy and the confirmation of the mathematical model, suggest that polyspermy is a common and frequent occurrence during broadcast spawning events. Thus polyspermy represents an evolutionary force that may shape the evolution of reproductive phenomena at levels ranging from the gamete to the population.

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.

This thesis uses molecular genetics as a tool to uncover information about the population structure and genetic variation in Hector’s dolphin (Cephalorhynchus hectori), to track population declines and to assess the evolutionary origins and taxonomic status of this species. A high-resolution genetic analysis of population structure was considered important for the determination of population boundaries and delimitation of conservation management units due to potentially unsustainable fisheries-related mortality. Population structure and dispersal rates were assessed using 281 samples collected from individual Hector’s dolphins of ten population groups representing the known geographic range of this species. Variation among mitochondrial DNA sequences (ΦST = 0.545) and microsatellite allele frequencies at six loci (RST = 0.252) indicated the presence of four genetically isolated regional populations, North Island (n = 29), East Coast South Island (n = 110), West Coast South Island (n = 122) and South Coast South Island (n = 19). Significant levels of genetic differentiation were not detected within local sub-populations of the East Coast and West Coast regional populations. However, the estimated geneflow between these sub-populations fitted a one-dimensional stepping-stone model (r2 = 0.6225) suggesting a vulnerability of local populations to fragmentation. A measure of expected mtDNA diversity (Tajima’s D statistic) suggested decline in eight of the ten populations. Microsatellite heterozygosity was also lower than expected in the East Coast and North Island regions, suggesting either further regional sub-structuring (Wahlund effect), loss of diversity due to population decline or the presence of null alleles. Examination of all Hector’s dolphin museum specimens of known origin (n = 55) enabled comparison of historic (1870 - 1987) genetic diversity to contemporary (1988 – 1999) diversity in two regional populations to assess the possibility that these populations have undergone recent declines. Over the last 20 years the North Island population has been reduced from at least three lineages (h = 0.41) to a single lineage (h = 0, p < 0.05). The diversity of the East Coast, South Island population has declined significantly from h = 0.65 to h = 0.35 (p < 0.05). These results suggest that the low abundance currently observed is due to recent population declines and that the North Island population is threatened with extinction in the near future. Based on a trend analysis of the mtDNA, it can be predicted that the East Coast South Island population may lose all mtDNA diversity within the next 20 years. Alternatively, detection of a one dimensional dispersal pattern may indicate that some populations are at risk of extirpation while others may not be in decline. If this is the case then the East Coast regional population is at risk of fragmentation. On a wider evolutionary scale, Hector’s dolphin is one of four species of the genus Cephalorhynchus, all of which suffer fisheries–related mortality. To describe the origin and radiation of these species, 485 bp of the mitochondrial DNA control region was sequenced from 320 individuals (including previously sequenced 200 Hector’s dolphins) representing nine of the ten species in the sub-family Lissodelphininae. The hypotheses that either Cephalorhynchus is a monophyletic genus or that the four species have arisen separately from pelagic Lissodelphine species and have converged morphologically were tested. The mtDNA phylogeny supported the monophyly of the genus and suggested that the genus Cephalorhynchus originated in the waters of South Africa and, following the West Wind Drift, colonised New Zealand and then South America. Secondary radiations resulting in two genetically isolated populations were found for the Kerguelen Island Commerson’s dolphin and the North Island Hector’s dolphin. A comparison of the genetic differentiation between the Commerson’s dolphins of the Kerguelen Islands (n = 11) and the coast of South America (n = 35), and between the North Island (n = 14) and South Island (n = 185) Hector’s dolphins, was conducted in order to assess the conservation and taxonomic status of these populations. A single fixed substitution in the mtDNA control region was diagnostic for the Kerguelen Island compared to South America (FST = 0.306, ΦST = 0.602) and the North Island compared to the South Island (FST = 0.442, ΦST = 0.495). Population differentiation of four microsatellite alleles (including unique alleles in each of the four populations) between the Kerguelen Island and South American Commerson’s dolphin (FST = 0.036, RST = 0.0493) and between the North and South Island Hector’s dolphins (FST = 0.391, RST = 0.3197) indicated restricted nuclear as well as maternal geneflow. These data, combined with additional evidence of morphological and geographic isolation, indicated that the Kerguelen Island Commerson’s dolphin and the North Island Hector’s dolphin are likely to be reproductively isolated from their alternate con-specific populations. Examination of various species concepts and definitions of conservation units leads to the conclusion that these four populations should each be considered unique at the subspecies level for the purposes of management, protection and evolutionary potential. These results lead to the conclusion that the Hector’s dolphin consists of highly subdivided populations. As a result of this and a low reproductive potential, Hector’s dolphin populations are vulnerable to extirpation through even low levels of human induced mortality. To manage such populations, it is appropriate to consider each of the two islands as separate sub-species. Within the South Island, the populations may be further subdivided into three demographically independent Management Units – the East, West and South Coasts. The South Coast management unit is vulnerable due to its low abundance and isolation and requires further investigation. Population modelling will need to reflect the fact that the local populations within the East and West coast regions share only limited dispersal with immediately adjacent populations and are thus susceptible to fragmentation. These results also show that the population declines of the East Coast South Island and the North Island populations are of recent origin thus implicating fisheries-related mortality as the principal threat to Hector’s dolphin. To prevent further decline or fragmentation of South Island populations more stringent control of inshore gillnet fisheries is required. By contrast, current decline of the North Island population may be a result of inbreeding depression. Given the low abundance and rapid decline of the North Island population, it is imperative to evaluate the potential for inbreeding depression while continuing to mitigate all human-related threats.

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.

The use of enterococci as a microbiological indicator of water quality requires an understanding of the sources, persistence, and ecology of this group of bacteria in the environment. This research describes a series of investigations undertaken to describe the abundance, occurrence, and diversity of enterococci from aquatic and terrestrial environments. A screening protocol for environmentally sourced enterococci was developed to describe species and sub-species variability. This protocol combined classical microbiological methods of selective culture and biochemical characterisation, with molecular techniques including gene probe screening for identity and RAPD-PCR for genotypic diversity. Preliminary studies on the occurrence of enterococci in terrestrial and aquatic environments suggested that these organisms are ubiquitous. However, abundance varied between individual samples taken from terrestrial (e.g. leaf litter, sand, seaweed, animal faeces) or aquatic (marine or freshwater) environments, complicating the ability to predict the enterococci load from these sources. Enumeration of enterococci from bathing beach environments indicated occasionally high levels from seaweed and sand, where levels of up to 660 CFU/100 g (wet weight) were recorded from aged and degrading seaweed but not from fresh seaweed samples. Restriction enzyme analysis (REA) of isolates from degraded seaweed indicated a dominance of clonal populations and supported the notion of replication or survival of strains. Laboratory studies conducted to investigate enterococci persistence and growth on seaweed were not conclusive, although there was some evidence to suggest enterococci replication was occurring. This was indicated by molecular fingerprinting (REA analysis), which showed that the inoculated strain persisted for the full duration of experiments (up to 28 days). The isolation of non-inoculum strains from seaweed treatments, combined with increased abundance of these strains with incubation, suggested the persistence or replication of enterococci that were naturally occurring on seaweed. To investigate the occurrence of enterococci in bathing environments a statistical analysis of Auckland Regional Council (ARC) bathing water quality data was undertaken. This analysis indicated a strong positive correlation between enterococci and turbidity, and hence turbidity may serve as a useful physical measure to indicate deteriorating water quality. Surveys of three marine bathing beaches on Auckland's North Shore (Long Bay, Mairangi Bay, and Rothesay Bay) indicated the abundance of enterococci in all bathing beach environments surveyed. These included marine and fresh water, sand, seaweed, and stream sediment, and a significant association between enterococci levels found in the sand and in the seaweed. Enterococci screening protocols were evaluated for use in describing enterococci species and sub-species diversity in bathing beach environments. This investigation showed a diversity of enterococci from all beach environmental sources, with highest levels of species diversity from marine and stream water. Enterococci diversity did not provide clues as to the sources in marine water samples. RAPD-PCR analysis and phenotypic screening of enterococci isolates did not indicate a pattern of niche-specific associations of enterococci strains, and there was no strong evidence from this study that enterococci sub-species associate with specific environments. However, the presence of identical genotypes indicated that enterococci can persist and possibly replicate in environments such as sand and seaweed. Calculation of similarity coefficients from Ent. faecalis and Ent. casseliflavus sub-species groupings indicated a greater level of sub-specific similarity between selected environments, for example, seaweed:sand, marine water:stream water, seaweed:marine water, although this was not a guarantee that environments were biologically or ecologically associated. Where an elevated level of enterococci is measured in the absence in identifiable pollution source the separation of pigmented from non-pigmented enterococci was proposed as an indicator of the environmental or faecal nature of the enterococci within the sample. Although not tested under controlled conditions, this concept was found to have good utility for discriminating sources from elevated marine bathing water samples. Enterococci from one of 13 elevated ARC marine water samples examined was shown to be environmentally derived, with 5 of the 13 samples attributed to putative human or animal faecal sources. With further validation, this concept may be a useful means of determining source.

Pacific oyster (Crassostrea gigas) farming in New Zealand has reached a point where the pressures on resources appear likely to constrain current, and future, development. To maintain industry growth, security of juvenile oyster (spat) supply and productivity gains within the existing farm leases, are becoming industry imperatives. The use of hatchery technology could achieve both of these requirements, but it is expensive to establish and maintain. The additional expense of a hatchery could be offset by the establishment of, for example, a selective breeding program to enhance oyster productivity and/or marketability. Consequently a pilot-scale oyster hatchery facility was constructed to investigate the potential for establishing hatchery production of Pacific oysters in New Zealand. This study showed that in the pilot-scale hatchery, oysters could be successfully spawned from in-season broodstock, the eggs fertilised and the resultant larvae reared through to settlement for on-growing to adult size. This process was successful for both oysters selected for morphological characteristics and those which were not. On-growing of the resultant stock indicated growth rate could be normal relative to wild caught oysters spat, although data was limited by the small scale of the experiment. However, an investigation of broodstock conditioning, to achieve out-of-season spawning, was less successful. Disease occurred and condition was lost in some broodstock, suggesting they were enduring stress within the conditioning system. The microalgal food supply was examined but the clearance rate of the microalgal species suggested they were an acceptable feed supply which agreed with previous reports of successful conditioning techniques. Comparing the pilot-scale facility in this study with descriptions of facilities which reported successful broodstock conditioning suggested that the use of a microfiltered recirculating water supply, as opposed to the more common flow-through, natural seawater systems containing a range of small size particles, limited necessary nutrient and/or maturation factors and may have had a significant impact on conditioning. The nanoplanktonic (< 10 μm), food resource, which includes key microalgal species such as Chaetoceros spp. and Isochrysis spp., is generally considered the primary food resource for suspension feeding bivalves, including C. gigas. However, the picoplanktonic fraction (< 3 μm) can provide the largest proportion of this food resource in the water column in terms of abundance and biomass. Consequently, an investigation of the in situ retention of picoplankton populations (picoeukaryotes, Synechococcus-type cyanobacteria and heterotrophic bacteria) by oysters was undertaken. Flow cytometry was used to quantify the picoplankton populations in water samples taken from the inhalant and exhalant feeding currents of individual oysters, allowing retention efficiency of the particles to be calculated. Five picoplankton populations were identifiable by flow cytometry (picoeukaryotes, heterotrophic bacteria and 3 populations tentatively identified as cyanobacteria) and accounted for a large proportion (up to 97 %) of the estimated available carbon (picoplankton + microalgae) in Kerikeri Inlet water. Generally the heterotrophic bacteria accounted for the largest proportion of the biomass with up to 564 ± 51 ng C ml-1. Retention of each picoplankton population was found to be variable and not directly related to particle concentration. Cyanobacteria (Cy2 population) were retained with the greatest efficiency (up to 42 ± 4.4 %), followed by heterotrophic bacteria (up to 38 ± 4.5 %) and picoeukaryotes (up to 12 ± 3.8 %). Overall more picoplankton biomass was retained during the summer months, of which the heterotrophic bacteria made the largest contribution in either cell number or estimated carbon retained. Tracking of the condition and constituent fractions (glycogen, lipid and protein) of the subject oysters showed that in the summer months, post-spawn, these levels were lowest, indicting a period of nutritional stress. This appeared to suggest that C. gigas was able to alter its retention efficiency to expand the range of particles captured, and consequently the available nutrient pool. The retention of greater quantities of heterotrophic bacteria may allow for the acquisition of essential nutrients required for growth and later gametogenesis (such as B vitamins). However, it is also possible that the heterotrophic bacteria mediate access to otherwise inaccessible, or inefficiently accessed, nutrient resources through their degradation of, for example, crystalline cellulose. Consequently, the microbial flora associated with the oyster gut was investigated. An initial investigation, cultivating bacteria from gut contents, showed considerable variability in the numbers of colonies present within and between samples, but was inconclusive for identifying differences in species diversity. Using culture independent histological and 16S rDNA PCR/RFLP techniques to investigate the oyster gut microflora a spirochaete flora, commonly associated with bivalve crystalline styles, was clearly present. Molecular analyses provided evidence of other bacterial in the gut. A signature RFLP band pattern was found in oysters at low tide and this generally reoccurred in oysters that had been immersed for varying lengths of time up to high tide. However, the signature RFLP pattern became more dilute as immersion time/potential feeding time extended. The isolation of culturable bacteria from the oyster gut allowed characterisation and identification of a subset of the oyster gut microflora. 16S rDNA sequence analysis from selected isolates showed a predominance of Vibrio spp. These bacteria had previously been associated with marine molluscs, including as symbionts. Characterisation of these and other isolates from oyster gut showed a diversity of attributes including the ability to degrade cellulose. This suggests the bacterial production of enzymes, such as cellulases, which have been reported by other researchers as being present in ineffectual or low native levels in oysters. Consequently the bacterial presence in the oyster gut may be essential to efficient nutrient acquisition. The results of these investigations have highlighted the potential importance of the heterotrophic bacteria to C. gigas. To date, bacteria have received relatively little attention in terms of their potential nutritive contribution to oysters, primarily due to observations that they are retained with low efficiency. However, even at low retention efficiencies the potential nutritive contribution is large due to the available abundances of heterotrophic bacteria. While the mechanisms and controls of bivalve suspension feeding have yet to be fully elucidated, the published literature indicates that selective mechanisms are available to bivalves including C. gigas and this current research suggests that even pico-sized particles, retained with apparently low efficiency, can be subject to selection. The importance of the heterotrophic bacteria to C. gigas requires further investigation as it will have implications for not only hatchery production, but also farm management, public health and environmental impact monitoring.

Confronting Barriers to Ecological Information Transfer in New Zealand's Fisheries Management system: Towards Developing a Trajectory for Trans-disciplinary Inquiry This thesis confronts barriers to ecological information transfer in New Zealand's fisheries management system. The investigation reveals a wider problematic within the governmental institutions of the fisheries milieu. The thesis deploys Callon's (1991) concept of translation to ask new questions regarding the conduct of fisheries science and management, which since the introduction of the Quota Management System in 1986, has been defined through the practices of commercial stakeholder groups. These stakeholders enrol ecological information through a narrowly defined and non-reflexive discourse of sustainable utilisation to serve specific purposes that suit their own needs. The thesis uses imaginaries to illustrate how sustainable utilisation has marginalised those stakeholders with different views on how ecological information could be used in fisheries management decision making. Moreover, the thesis contends that the milieu's hegemonic ontological environment prevents translation by mitigating the potential for dialogue between stakeholder groups. The thesis engages with a wide range of literature and cuts through established modes of thinking, developing a trans-disciplinary discourse that re-conceptualises the fisheries management problematic in process terms. The thesis demonstrates how trans-disciplinary dialogue that might transcend the current impasses in the New Zealand fisheries milieu will only develop through a network of previously unconnected groups. The thesis proposes a series of policy and behavioural interventions aimed at shifting the existing hierarchies of power and realigning established networks to ensure such dialogue is possible. Keywords: trans-disciplinary research, translation, network alignment, New Zealand, ecological information transfer, fisheries management.

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.

The biochemical pathways involved in nitrogen (N) utilisation by marine phytoplankton have received considerable attention over the last forty years, but our understanding of these processes, and how they are affected by environmental change is still far from complete. This study investigates N metabolism in marine phytoplankton in both a controlled laboratory environment (using the coastal marine diatom Phaeodactylum tricomutum), and in the open ocean (e.g. Jellicoe Channel and the Subtropical Convergence Zone, New Zealand). Although the characteristics of ammonium uptake have been extensively studied in marine phytoplankton, comparatively little information exists on rates of assimilation. In this study, a robust method for measuring the rate of ammonium assimilation after a transient addition of ammonium is described. The method relies on the measured ability of the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) to release unassimilated ammonium from the cell and prevent further assimilation. There was little or no correspondence between the rate of ammonium assimilation and rates of ammonium uptake or maximum glutamine synthetase (GS) activity in Phaeodactylum tricomutum. Moreover, in N-limited cells maximum GS activity was a poor measure of N incorporation under steady-state conditions. However, GS activity did provide reliable information on N status (e.g. increased GS activity with increased N-limitation). Comparisons of the effects of varying N-source suggest that nitrate-grown cells are not disadvantaged under conditions of N-limitation due to the extra costs associated with nitrate reductase (NR) and nitrite reductase (NiR) activity. The metabolic costs of growth on nitrate may be significantly increased under iron (Fe)-limitation, as both NR and NiR require Fe. Fe-limited chemostat cultures excreted nitrite and ammonium when grown on nitrate. This release is probably a response to insufficient photoreductant under Fe-limited conditions. However, under Fe-limitation cellular N and C was similar to that of Fe-replete cells, suggesting that the N-source used for growth (nitrate or ammonium) did not influence N-assimilation (i.e. that nitrate-grown cells were able to secure the extra reductant required to support growth) under Fe-limited, light saturating conditions. The Gln:Glu ratio (an index of the cellular N-status) was significantly reduced under N-limitation, but not under Fe-limitation. Measurement of several biochemical indicators of the physiological state of phytoplankton cells (e.g. Gln:Glu ratio, GS activity, and Fv/Fm ratio) permitted the nutrient status of phytoplankton populations to be investigated during the NIWA Ocean Fronts programme over the Subtropical Convergence Zone, New Zealand. Low Gln:Glu ratios suggested that phytoplankton in both Subtropical and Subantarctic waters were N-limited, with a marked increase in this ratio when Fe was added to Subantarctic phytoplankton. The temporal utilisation of N by neritic phytoplankton was also investigated in Jellicoe Channel, northeastern New Zealand. Again, several biochemical indicators (e.g. Gln:Glu ratio, GS activity, and Fv/Fm ratio) were used to identify the N-status of this neritic phytoplankton assemblage both during bloom and non-bloom periods.

This study focuses on an assessment of the health status of the yellowbelly flounder (Rhombosolea leporina) from two estuarine locations (site 1 – the mouth of the Henderson Creek; site 2 – the mouth of the Whau Creek) in the Waitemata Harbour. This harbour borders the highly urbanised and industrialised Auckland City metropolitan area. Whangaparaoa Peninsula, located approximately 30 km north of the other two collecting sites (away from the main urban area), was chosen as a reference site for comparative purposes. Physico-chemical analyses revealed differences in water quality at the sampling sites. A lower pH, oxygen deficiency and higher temperature were recorded in both the Waitemata Harbour locations in comparison with the reference site. Histopathological analyses revealed significantly higher prevalences and severity of pathological changes in the gills, blood, liver, kidney and gonads of the yellowbelly flounder from both harbour locations in comparison with fish from the reference site. ln addition, some types of lesions (eg. neoplasms) were observed in fish from the two harbour locations only. Abnormalities in the gill structure of fish from both harbour sites included: epithelial swelling (hyperplasia and hypertrophy), necrosis, and lifting with oedema; the fusion of secondary lamellae; aneurysms; filamental deformities; mucous cell proliferation, and infestation by Trichodina. The abnormalities found in the blood of these fish were manifested as: polycythaemia; erythrocytosis; erythroblastosis; leucocytosis (increased neutrophils); poikilocytosis; anisocytosis and an increased prevalence of erythrocytes undergoing necrosis. Vacuolar degeneration of the hepatocellular parenchyma due to lipid or glycogen accumulation was the most prominent liver change observed in fish from all sampling sites. The other liver abnormalities observed in flounder from the two harbour sites included: foci of cellular alterations (clear, basophilic and necrotic), congestion of the sinusoids, infestation by nematodes, and anaplastic growths (cholangiocellular carcinoma and teratoma). Pathological changes found in the kidneys of flounder collected at both harbour sites were classified as glomerular abnormalities (atrophy and dilatation of the glomerular tuft; enlargement of Bowman's space) and tubular vacuolar degeneration and necrosis. The presence of myxosporean parasites was also a common finding in the kidneys of harbour fish. Follicular atresia was the most prevalent change observed in the ovaries of flounder from the two harbour sites. Biochemical analysis of plasma proteins and electrolytes of flounder from the three sampling sites revealed hyperbilirubinaemia, hypoalbuminaemia and uraemia in those inhabiting both harbour sites. In addition, the concentration of total liver microsomal proteins was significantly depressed in flounder from harbour sites 1 and 2 when compared to that of fish from the reference site. Concentrations of heavy metals in the livers of flounder from different sampling localities were found to decrease in the order: site 2 > reference site > site 1, and did not correlate with the prevalences of liver abnormalities. Significantly more prominent pathological changes were thus observed in fish from both estuarine harbour sites in comparison with those from the reference open water site. The pathological changes noted are believed to occur in response to environmental changes. Contamination by different xenobiotics in the Whau and Henderson Creeks, which have been recorded in previous studies, suggest the possibility of direct toxic effects of the water contaminants on flounder from the estuarine parts of these creeks. In addition, the relatively high temperature, low pH and low oxygen levels recorded at the two sites in the Waitemata Harbour are believed to have induced oxygen deficiency-related tissue hypoxia which could then have led to the expression of a variety of diseases of which some have been detected in this study. However, the possibility that some unknown and unmeasured causal factors may have produced the observed pattern of flounder diseases cannot be eliminated.

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In 1986 the New Zealand system of fisheries management was reformed. The Quota Management System (QMS) augmented the existing input control regulatory instruments with a system of output controls: individual transferable quota (ITQ). This thesis examines a number of aspects of the QMS in the context of a case study of the SNA1 snapper fishery. The QMS model is contrasted with a dynamic optimization model of rights based fishing which shows the effectiveness of ITQ systems in resolving the open access problem and that proportional share ITQ prices potentially contain information about the biological and economic state of a fishery. Departures of the QMS from the theoretical model are noted, particularly the allocation mechanism, the continued application of open access input control apparatus, and the basis of total allowable catch definition. Input control is considered in a bioeconomic model of the Hauraki Gulf sub-stock of the SNA1 fishery that features a sea surface temperature recruitment sub-model. Changes to the minimum legal size regulation (MLS) and the effect of differing inter-temporal recruitment structures on rent generation are evaluated. The biological and economic inefficiency of size regulation and the unequal distribution of risk between sectors in this fishery under the current management regime are demonstrated. The potential role for discount rates as performance indicators is shown. An intra-cohort stock externality due to growth overfishing is evident. The productive capacity of the SNA1 fishery system is presently not fully utilized. Output control is examined through time series analyses of prices in SNA1 ITQ markets. To date government has relied on the results of stock assessment research when setting the allowable harvest and monitoring the performance of fisheries policy. Excessive reliance on biological data, in particular modelling outputs, has attracted criticism. An alternative, a minimum information system uses information contained in quota prices as indicators of the biological and economic health of a fishery. SNA1 quota ownership and lease markets are found to exhibit the characteristics of weak form efficiency. Prices reflect expected rents in the fishery. However, at this stage of their development prices also reflect firms' uncertainty over expectations of fishery management agency behavior. Concern has been expressed that ITQ systems may be compromised by market failure through the exercise of market power. Evidence of market power is found in the SNA1 market for ITQ lease title. Explicit non-commercial quota, a review of the effectiveness of remnant pre-QMS regulatory instruments, and a substantial role for economic information in the total allowable catch setting process and as performance indicators form the basis of recommendations for policy.

Two subtidal reef communities characterised by sponges were examined to assess two distinct aspects of marine benthic community ecology which have not previously received much attention. The first study focused on the role of settlement events in the origin and maintenance of community structure and involved investigation of factors affecting dispersion, settlement and recruitment of sponge propagules. The second examined how natural gradients in ambient physical conditions, in the absence of disturbance, affected size structure and species interactions within the community. Settlement events were examined on a reef flat which was covered by a shallow sediment overlayer. The distribution and abundance of established sponges was found to be highly correlated with sediment regimes. The sponge community was shown to be stable over time and able to resist disturbance by storms because of the presence of turfing algae. Sponge settlement was inhibited by the sediment overlayer. Established sponges were found clumped into oblong groups orientated east-west and there were many instances where sponges were found closely associated. Adjacent areas were characterised by deeper unstable sediments and fewer sponges. Storms contoured sediments into ripples and scoured oblong east-west orientated patches of basal rock. Sediments were also sorted during storms such that particles of large grain size were left around the edges of ripples and over the scoured rock patches. The basal reef of both the stable and unstable areas was covered in a mosaic of encrusting algal and sponge species which tolerated the sediment overlayer. This assemblage was also exposed during storms. Sponges reproduced in a number of ways, but asexual propagules were the most successful. Sponges from several orders produced buds which developed in a complex manner. Buds adhered to rock and shell fragments of large size which acted as anchors, or attached to other buds irrespective of genotype. The change in weight and shape increased the likelihood that buds would gravitate into the scoured patches of basal rock. Bud loss off the reef was minimal. Buds were able to settle onto the basal rock patches and did so almost exclusively onto bare rock. A high degree of 'selectivity' of settlement site by buds was imparted by altering developmental rate during the settlement process in response to the substrate type. Polymastia granulosa buds exhibited an additional developmental sequence not previously reported for any colonial organism. Buds either settled directly in suitable conditions, or developed further along a different pathway. Buds which did not come into contact with basal rock elongated and appeared to be capable of digging into sediments. The elongated bud then broke up along its length into smaller particles, termed 'beads', which were capable of movement and invariably settled onto gravel fragments. Sponges were shown to settle onto scoured rock patches during storms and were eventually covered by sediments. Subsequent survivorship and recruitment depended species specifically on sediment depth and quality. Settlement patterns matched the observed dispersion patterns of established sponges and suggested a mechanism whereby the community had originated and how structure was maintained. These hypotheses were tested experimentally in situ and in the laboratory. The importance of asexual modes of reproduction, and settlement mediated by physical disturbance appears to be a common formula for recruitment by colonial marine organisms. Recruitment events were found to explain the distributional patterns of the established population. The structure of populations of thin encrusting species on vertical reef walls was examined in a novel manner whereby the mean size and density of individuals was quantified and related to gradients in the ambient physical environment. This was achieved by examining the benthic communities on a range of subtidal reef walls of uniform slope and aspect, but which were subject to natural gradients in physical conditions. The species composition of each of the six reefs studied was similar but the size structure of communties changed within each reef system in response to gradients in light intensity and water movement. Fish and urchin disturbance was shown to be unimportant and there was no indication that storms disrupted communities. The implications of changes in size structure of populations on interactions between component species in different ambient conditions were examined. The eastern wall of two cave, archway and open reef systems was surveyed according to a stratified sampling design where each reef was divided by depth and distance along the wall. Different taxonomic/morphological groups were found at particular positions on reef walls. Thin encrusting algal species were found to be one of the most abundant groups. It was assumed that the individual size of encrusting species at each wall position reflected long term ambient environmental conditions as well as the ability of each species to maintain itself against overgrowth by neighbours. By relating the population size structure of different taxa with indices for light intensity and water movement recorded at each wall position within each reef, it was shown that community structure varied markedly on the same reef wall as a function of ambient physical conditions. Changes in proportional species composition, notably from thin encrusting algal dominated assemblages to sponge characterised assemblages, with decreasing light intensity were accompanied by changes in the individual size structure of populations. At each wall position all species exhibited similar individual size. Individual size decreased and density of individuals of all species increased with decreasing light intensity. In conditions where light levels were not sufficient to support algae, individual size of encrusting fauna increased with increasing water movement. The implications of these observations on competitive interactions between encrusting species was examined. The outcome of competitive interactions between the same species was found to vary depending on wall position.

‘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.

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 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.

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.

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.

Cooperative breeding, widely reported in birds, is found in <1–5% of territories in some populations of the Brown skua, Catharacta lonnbergi. In the New Zealand region, up to 30-50% of skua territories may be occupied by trios or larger groups. This study examines its occurrence at the Chatham Islands, east of New Zealand. Here 16% of territories are occupied by trios and 2% by groups. All members of skua trios and groups participate in sexual and other breeding activity, and the associations arc thus communal. Sexual discrimination of breeding birds by morphometric measurements shows that all communal groups known since 1978-79 have been polyandrous. These groups are long-lived associations, some of which are known to have persisted for at least 14 years. Trios are as long-lived and stable as pairs, and birds on communal territories do not move from them even when an appropriate-sex space becomes available on an adjacent pair territory. The members of trios are not close kin. All members of communal associations participate in territorial defence and chick rearing. In trios, the males appear to be equals, although in any one year the actual paternity of offspring may reside with only one of them. Overall reproductive success for Chatham Island skuas is high, for both pairs and communal groups, compared with other populations. However, communal trios and groups have lower reproductive success than pairs even over a l0 year period, particularly when considered on a per adult basis. Furthermore, no improvement in chick ‘quality’ is discernible. Unusually for skuas, the breeding population at the Chatham Islands is non-migratory. Skuas are present on their breeding territories during the winter, and exhibit characteristic territorial and agonistic behaviours, albeit at lower intensity than during the breeding season. It is suggested that communal breeding in this skua population is not adaptive per se, but a secondary consequence of year-round residence. This is a departure from the conventional resolution of communal breeding. Residence is facilitated by benign climatic conditions and year-round prey availability. When territory space becomes available outside the breeding season, in a small number of cases more than a pair of skuas are able to establish themselves. Thereafter, trios and larger groups persist and behave in the same manner as pairs. The flux between trios and pairs when birds are lost is determined, in part, by the sex of that bird. Thus a trio which loses its one female will ‘acquire’ a replacement female and persist as a trio, whereas a trio which loses one of its two males will thereafter continue as a pair. Keywords: Cooperative breeding, communal breeding, polyandry, Stercorariidae, skuas, skua trios, skua behaviour, skua breeding, Chatham Islands
Chapter 1 previously published as: Cooperative breeding in the Skuas (Stercorariidae): History, distribution and incidence. Journal of the Royal Society of New Zealand 24: 245-260 (1994). Publisher version available at http://www.royalsociety.org.nz/Site/publish/Journals/jrsnz/1994/default.aspx
Chapter 2 previously published as: Winter territory occupation and behaviour of Skuas at the Chatham Islands, New Zealand. Emu 90: 108-113 (1990). Publisher version available at http://www.publish.csiro.au/nid/96.htm
Chapter 3 previously published as: Communually breeding Skuas: Breeding success of pairs, trios and groups of Catharacta lonnbergi on the Chatham Islands, New Zealand. Journal of Zoology, London 218: 393-405 (1989). The definitive version is available at www.blackwell-synergy.com

The microbiome plays a key symbiotic role in maintaining host health and aids in acquiring nutrients, supporting development and immune function, and modulating behavior. However, more research is needed to elucidate the potential impact of environmental pollutants on host microbial communities and how microbiomes can modulate the toxicity of contaminants to the host. Through a literature review of 18 studies that assessed the impacts of various anthropogenic chemicals on fish-associated microbiomes, we found that toxicants generally decrease microbial diversity, which could lead to long-term health impacts if chronically stressed, and can increase the host’s susceptibility to disease as well as the chemical resistance of certain microbes. These findings led us to explore the impacts of one of the reviewed contaminants, polycyclic aromatic hydrocarbons (PAHs), typically found in oil. The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and had catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM). This study tested the hypotheses that exposure to weathered oil would cause significant shifts in fish gut-associated microbial communities, with taxa known for hydrocarbon degradation increasing in abundance and that foraging behavior would decrease, potentially due to microbial dysbiosis via the gut-brain axis. We characterized the gut microbiome (with 16S rRNA gene sequencing) of a native GoM estuarine species, the sheepshead minnow (Cyprinodon variegatus). Fish were exposed to High Energy Water Accommodated Fractions (HEWAF; tPAH = 80.99 ± 12.5 μg/L) of oil over a 7-day period and whole gastrointestinal tracts were sampled for microbiome analyses. A foraging behavioral assay was used to determine feeding efficiency before and after oil exposure. The fish gut microbiome did not experience any significant changes in alpha or beta diversity but known hydrocarbon degrading taxa were noticeably present in oil-exposed communities and were absent in controls. We found the order Pseudomonadales, the family Paenibacillaceae, and Pseudomonas pachastrellae to be among these, with Pseudomonadales increasing in abundance. Foraging behavior was not significantly affected by oil exposure. This work highlights the need for further research to elucidate the functional metagenomic responses of the fish gut-microbiome under oil spill conditions.

Knowledge of the interactions among species and communities is vital for their management and protection. Increasingly, the role of marine protected areas in this regard is being recognised, primarily because of the potential for previously-harvested species to increase in density and biomass, and the linkages among species to be restored. Monitoring and research was conducted within and surrounding two marine reserves on the east coast of the North Island of New Zealand – Te Tapuwae o Rongokako, near Gisborne, and Te Angiangi, south of Napier. The aim was to describe the biological characteristics of spiny lobsters (Jasus edwardsii) in the absence of fishing, and to describe the effects of fishing and protection on lobster populations and the communities of which they are a component. Diver and pot surveys showed that lobsters were significantly more abundant within the reserves than in the surrounding fisheries and that the populations were comprised of a larger proportion of legal-sized individuals. Higher female fecundity within Te Tapuwae o Rongokako Marine Reserve compared with the surrounding fishery was proposed to be primarily a result of increased availability of large males within the reserve. The impact of the fishery on lobsters was also evidenced in the lower tail width to carapace length ratio of the fished population compared to the population within Te Tapuwae o Rongokako Marine Reserve, due to the minimum legal size for Jasus edwardsii in New Zealand being based on tail width. The largest tagging study ever to be conducted in a New Zealand marine reserve showed that sublegal male lobsters within Te Tapuwae o Rongokako Marine Reserve were growing on average faster than the same sized individuals outside the reserve, potentially as a result of the effects of handling and / or size-selective fishing. A decrease in growth rate over time was recorded in male lobsters within the reserve, which coincided with an increase in catch per unit effort and may indicate that density-dependent effects are operating. Distinct seasonal movements of tagged lobsters were recorded, with the vast majority of movements taking place within reefs. Where the boundaries of the reserve crossed reef habitat, significant movement of lobsters across the boundaries occurred. Lobsters within Te Tapuwae o Rongokako Marine Reserve not only exhibited cannibalistic behaviour but foraged during the day, including on intertidal reef platforms at high tide, potentially as a behavioural response to increased competition for food – behaviour not previously reported for this species. Outside the reserve, lobster bait apparently provided an alternative protein source but despite this supplementation of diet, these lobsters were in poorer nutritional condition, as evidenced by their lower body weights relative to carapace length and tail width for both sexes. Lobsters outside the reserve were also significantly more affected by a bacterial infection associated with handling, than lobsters within the reserve. These findings have significant implications for fisheries management and for the design and management of marine protected areas (MPAs). This study demonstrates that many of the biological parameters used in evaluating harvest strategies in the New Zealand lobster fishery may be biased unless collected from populations with a natural size structure, such as may occur within marine protected areas.