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

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

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

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

‘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.

‘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.

‘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.

No description available.

No description available.

‘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.