Thesis (M.Sc. (Ichthyology & Fisheries Science)) - Rhodes University, 2009.

Thesis (M.Sc. Biological Sciences)--University of Waikato, 2009. / Title from PDF cover (viewed October 2, 2009) Includes bibliographical references (p. 59-74)

Thesis (Ph. D.)--University of California, Los Angeles, 2003. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--Université de Nantes, L'U.E.R. des Sciences de la Nature, 1979. / Accompanying map: "Carte des points de prélèvements éffectués dans l'estuaire de la Loire." Includes bibliographical references (p. 213-227).

Thesis (Ph.D.) - University of Queensland, 2006. / Includes bibliography.

Thesis (M.S.)--University of Akron, 2006. / Title from PDF title page (viewed on Jan. 25, 2007). Includes bibliographical references (p. 62-68).

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.