No description available.

The global decline of coral reef biodiversity requires rapid, efficient and practical solutions. No-take marine reserves and reserve systems and other managed marine conservation areas are currently considered one of the most effective management methods to deal with this ongoing decline. Although the effects, design, and establishment of coral reef reserves have been widely debated in the literature, few examples of systematic approaches to the design of reserve systems exist. Systematic conservation planning is a procedure to prioritise sites for their inclusion in reserve systems based on data and a set of conservation principles. For coral reefs the systematic design of reserve systems has been hampered by the lack of spatially explicit data, and the lack of practical recommendations to resource managers of how to apply new scientific findings. This thesis fills critical gaps at the interface between theory, planning, and implementation of coral reef reserve systems, and provides practical guidance to reef managers. In the first chapter, literature on marine reserves is discussed and the implications for coral reef reserves are considered. Chapter 2 discusses the lessons learned in the design and implementation of a community-based marine reserve in the Philippines. Reviewing relevant literature, a framework of ‘lessons learnt’ during the establishment of local protected areas is presented, highlighting the importance of a number of factors that are vital to the success of these reserves: (a) an island location; (b) small community population size; (c) minimal effect of land-based development; (d) application of a bottom-up approach; (e) an external facilitating institution; (f) acquisition of title; (g) use of a scientific information database; (h) stakeholder involvement; (i) the establishment of legislation; (j) community empowerment; (k) alternative livelihood schemes; (l) surveillance; (m) tangible management results; (n) continued involvement of external groups after reserve establishment, and (o) small-scale project expansion. To manage coral reef species it is important to understand the processes that influence their distribution. Chapter 3 identifies the environmental factors most influential in determining coral reef fish species distributions on a regional scale. Logistic regression models for 227 fish species related presence-absence data to four remotely determined environmental predictor variables: depth 500 m away from a reef, presence of a land-sea interface, exposure, and the distance to the nearest estuary. A novel method of evaluating model significance identified suitable models for 134 species. All four predictor variables were important for the distributions of the chosen suite of fishes. Depth was the most frequently significant variable in single variable models, and the proximity of a reef to an island was the least frequently important variable. For combinations of two predictor variables, depth and exposure as well as depth and distance from the nearest estuary were the prevalent predictors of fish distributions. Several fish species responded to the combination of the distance from an estuary and the presence of the terrestrial-marine interface, indicating that these species depend on intact coastal reef habitat, which is in decline near the main sediment-laden rivers. Significant models were predominantly developed for habitat specific species. These habitat specific species are of greater conservation concern than widespread species because of their restricted range, or because threats affect them more severely if they are selectively affecting their habitat. For this reason, species distribution modelling may be an efficient method to inform reserve design. The relevance of cross-taxon congruence to the suitability of taxa as conservation representation surrogates of coral reef biodiversity across the Indo-Pacific is tested in Chapter 4, using species lists of fishes, corals, and molluscs. Congruence is identified with a linear regression analysis of dissimilarity values. The utility of a surrogate was determined by the degree to which each taxon can represent the others in a marine reserve network using a greedy reserve selection algorithm. None of the taxonomic groups examined was capable of acting as a general conservation representation surrogate. Even a data-rich taxon like fishes could be severely under-represented in reserve systems designed based on a surrogate taxon such as corals, implying that data-deficient taxa are unlikely to be represented adequately where surrogate taxa are used for planning. Despite the high cross-taxon congruence between fishes and corals, and between corals and molluscs for some regions, cross-taxon congruence was not always a reliable indicator of conservation representation surrogacy. Consequently, in Indo-Pacific coral reef ecosystems one can only be sure that a target taxon is represented fully in a marine reserve network when data on this taxon are used to select reserve sites. The fifth chapter provides a theoretical and practical framework for incorporating ecological processes that span terrestrial, marine, and freshwater environmental realms into systematic conservation planning. Firstly the types of processes are classified as interactions that exist: a) on narrow interfaces such as inter-tidal zones; b) on broad interfaces such as mangrove swamps; c) along constrained connections such as corridors used by amphibian movements between natal ponds and adult habitat; and d) through diffuse connections like bird migrations. A framework of conservation planning approaches to promote the persistence of these types of processes and examples of how they might be implemented is developed. The framework focuses both on problem formulations consistent with existing decision support tools, such as the conservation planning software MARXAN, and on new methods. The review is aimed at a broad audience of scientists, planners, and managers and takes a practical and illustrative approach, providing examples of existing work and pointing readers to tools that are available to enhance conservation planning across realms. In the concluding chapter ideas from all chapters are synthesised. This chapter discusses how the approaches and frameworks presented here could be extended, and profitable areas for future research are suggested. Overall this thesis provides new insights, concepts, and tools that can assist reef managers and scientists struggling to minimise the loss of coral reefs.

The global decline of coral reef biodiversity requires rapid, efficient and practical solutions. No-take marine reserves and reserve systems and other managed marine conservation areas are currently considered one of the most effective management methods to deal with this ongoing decline. Although the effects, design, and establishment of coral reef reserves have been widely debated in the literature, few examples of systematic approaches to the design of reserve systems exist. Systematic conservation planning is a procedure to prioritise sites for their inclusion in reserve systems based on data and a set of conservation principles. For coral reefs the systematic design of reserve systems has been hampered by the lack of spatially explicit data, and the lack of practical recommendations to resource managers of how to apply new scientific findings. This thesis fills critical gaps at the interface between theory, planning, and implementation of coral reef reserve systems, and provides practical guidance to reef managers. In the first chapter, literature on marine reserves is discussed and the implications for coral reef reserves are considered. Chapter 2 discusses the lessons learned in the design and implementation of a community-based marine reserve in the Philippines. Reviewing relevant literature, a framework of ‘lessons learnt’ during the establishment of local protected areas is presented, highlighting the importance of a number of factors that are vital to the success of these reserves: (a) an island location; (b) small community population size; (c) minimal effect of land-based development; (d) application of a bottom-up approach; (e) an external facilitating institution; (f) acquisition of title; (g) use of a scientific information database; (h) stakeholder involvement; (i) the establishment of legislation; (j) community empowerment; (k) alternative livelihood schemes; (l) surveillance; (m) tangible management results; (n) continued involvement of external groups after reserve establishment, and (o) small-scale project expansion. To manage coral reef species it is important to understand the processes that influence their distribution. Chapter 3 identifies the environmental factors most influential in determining coral reef fish species distributions on a regional scale. Logistic regression models for 227 fish species related presence-absence data to four remotely determined environmental predictor variables: depth 500 m away from a reef, presence of a land-sea interface, exposure, and the distance to the nearest estuary. A novel method of evaluating model significance identified suitable models for 134 species. All four predictor variables were important for the distributions of the chosen suite of fishes. Depth was the most frequently significant variable in single variable models, and the proximity of a reef to an island was the least frequently important variable. For combinations of two predictor variables, depth and exposure as well as depth and distance from the nearest estuary were the prevalent predictors of fish distributions. Several fish species responded to the combination of the distance from an estuary and the presence of the terrestrial-marine interface, indicating that these species depend on intact coastal reef habitat, which is in decline near the main sediment-laden rivers. Significant models were predominantly developed for habitat specific species. These habitat specific species are of greater conservation concern than widespread species because of their restricted range, or because threats affect them more severely if they are selectively affecting their habitat. For this reason, species distribution modelling may be an efficient method to inform reserve design. The relevance of cross-taxon congruence to the suitability of taxa as conservation representation surrogates of coral reef biodiversity across the Indo-Pacific is tested in Chapter 4, using species lists of fishes, corals, and molluscs. Congruence is identified with a linear regression analysis of dissimilarity values. The utility of a surrogate was determined by the degree to which each taxon can represent the others in a marine reserve network using a greedy reserve selection algorithm. None of the taxonomic groups examined was capable of acting as a general conservation representation surrogate. Even a data-rich taxon like fishes could be severely under-represented in reserve systems designed based on a surrogate taxon such as corals, implying that data-deficient taxa are unlikely to be represented adequately where surrogate taxa are used for planning. Despite the high cross-taxon congruence between fishes and corals, and between corals and molluscs for some regions, cross-taxon congruence was not always a reliable indicator of conservation representation surrogacy. Consequently, in Indo-Pacific coral reef ecosystems one can only be sure that a target taxon is represented fully in a marine reserve network when data on this taxon are used to select reserve sites. The fifth chapter provides a theoretical and practical framework for incorporating ecological processes that span terrestrial, marine, and freshwater environmental realms into systematic conservation planning. Firstly the types of processes are classified as interactions that exist: a) on narrow interfaces such as inter-tidal zones; b) on broad interfaces such as mangrove swamps; c) along constrained connections such as corridors used by amphibian movements between natal ponds and adult habitat; and d) through diffuse connections like bird migrations. A framework of conservation planning approaches to promote the persistence of these types of processes and examples of how they might be implemented is developed. The framework focuses both on problem formulations consistent with existing decision support tools, such as the conservation planning software MARXAN, and on new methods. The review is aimed at a broad audience of scientists, planners, and managers and takes a practical and illustrative approach, providing examples of existing work and pointing readers to tools that are available to enhance conservation planning across realms. In the concluding chapter ideas from all chapters are synthesised. This chapter discusses how the approaches and frameworks presented here could be extended, and profitable areas for future research are suggested. Overall this thesis provides new insights, concepts, and tools that can assist reef managers and scientists struggling to minimise the loss of coral reefs.

The global decline of coral reef biodiversity requires rapid, efficient and practical solutions. No-take marine reserves and reserve systems and other managed marine conservation areas are currently considered one of the most effective management methods to deal with this ongoing decline. Although the effects, design, and establishment of coral reef reserves have been widely debated in the literature, few examples of systematic approaches to the design of reserve systems exist. Systematic conservation planning is a procedure to prioritise sites for their inclusion in reserve systems based on data and a set of conservation principles. For coral reefs the systematic design of reserve systems has been hampered by the lack of spatially explicit data, and the lack of practical recommendations to resource managers of how to apply new scientific findings. This thesis fills critical gaps at the interface between theory, planning, and implementation of coral reef reserve systems, and provides practical guidance to reef managers. In the first chapter, literature on marine reserves is discussed and the implications for coral reef reserves are considered. Chapter 2 discusses the lessons learned in the design and implementation of a community-based marine reserve in the Philippines. Reviewing relevant literature, a framework of ‘lessons learnt’ during the establishment of local protected areas is presented, highlighting the importance of a number of factors that are vital to the success of these reserves: (a) an island location; (b) small community population size; (c) minimal effect of land-based development; (d) application of a bottom-up approach; (e) an external facilitating institution; (f) acquisition of title; (g) use of a scientific information database; (h) stakeholder involvement; (i) the establishment of legislation; (j) community empowerment; (k) alternative livelihood schemes; (l) surveillance; (m) tangible management results; (n) continued involvement of external groups after reserve establishment, and (o) small-scale project expansion. To manage coral reef species it is important to understand the processes that influence their distribution. Chapter 3 identifies the environmental factors most influential in determining coral reef fish species distributions on a regional scale. Logistic regression models for 227 fish species related presence-absence data to four remotely determined environmental predictor variables: depth 500 m away from a reef, presence of a land-sea interface, exposure, and the distance to the nearest estuary. A novel method of evaluating model significance identified suitable models for 134 species. All four predictor variables were important for the distributions of the chosen suite of fishes. Depth was the most frequently significant variable in single variable models, and the proximity of a reef to an island was the least frequently important variable. For combinations of two predictor variables, depth and exposure as well as depth and distance from the nearest estuary were the prevalent predictors of fish distributions. Several fish species responded to the combination of the distance from an estuary and the presence of the terrestrial-marine interface, indicating that these species depend on intact coastal reef habitat, which is in decline near the main sediment-laden rivers. Significant models were predominantly developed for habitat specific species. These habitat specific species are of greater conservation concern than widespread species because of their restricted range, or because threats affect them more severely if they are selectively affecting their habitat. For this reason, species distribution modelling may be an efficient method to inform reserve design. The relevance of cross-taxon congruence to the suitability of taxa as conservation representation surrogates of coral reef biodiversity across the Indo-Pacific is tested in Chapter 4, using species lists of fishes, corals, and molluscs. Congruence is identified with a linear regression analysis of dissimilarity values. The utility of a surrogate was determined by the degree to which each taxon can represent the others in a marine reserve network using a greedy reserve selection algorithm. None of the taxonomic groups examined was capable of acting as a general conservation representation surrogate. Even a data-rich taxon like fishes could be severely under-represented in reserve systems designed based on a surrogate taxon such as corals, implying that data-deficient taxa are unlikely to be represented adequately where surrogate taxa are used for planning. Despite the high cross-taxon congruence between fishes and corals, and between corals and molluscs for some regions, cross-taxon congruence was not always a reliable indicator of conservation representation surrogacy. Consequently, in Indo-Pacific coral reef ecosystems one can only be sure that a target taxon is represented fully in a marine reserve network when data on this taxon are used to select reserve sites. The fifth chapter provides a theoretical and practical framework for incorporating ecological processes that span terrestrial, marine, and freshwater environmental realms into systematic conservation planning. Firstly the types of processes are classified as interactions that exist: a) on narrow interfaces such as inter-tidal zones; b) on broad interfaces such as mangrove swamps; c) along constrained connections such as corridors used by amphibian movements between natal ponds and adult habitat; and d) through diffuse connections like bird migrations. A framework of conservation planning approaches to promote the persistence of these types of processes and examples of how they might be implemented is developed. The framework focuses both on problem formulations consistent with existing decision support tools, such as the conservation planning software MARXAN, and on new methods. The review is aimed at a broad audience of scientists, planners, and managers and takes a practical and illustrative approach, providing examples of existing work and pointing readers to tools that are available to enhance conservation planning across realms. In the concluding chapter ideas from all chapters are synthesised. This chapter discusses how the approaches and frameworks presented here could be extended, and profitable areas for future research are suggested. Overall this thesis provides new insights, concepts, and tools that can assist reef managers and scientists struggling to minimise the loss of coral reefs.

No description available.

The Pitt Water Estuary is a shallow, barrier estuary, with typically normal marine salinity, which has been subject to considerable anthropogenic modification. Modern seafloor environments were described using the distribution of sedimentary facies and foraminiferal and ostracod assemblages, examined from surficial sediment samples. Ten sedimentary facies were identified by grouping sediment samples using particle-size distribution data and lithic sand content. Faunal assemblages were identified by cluster analysis, with twelve sample, and eight species associations defined by foraminifera, and eight sample, and six species associations defined by Ostracoda. The distribution of sedimentary facies varies, firstly, with the upstream change in relative current energy (tidal versus fluvial) as reflected by the relative proportion of quartzose to lithic sand in sediment; and, secondly, with the water depth variation in current strength, as reflected by the sand grain size and mud content. The distribution and composition of foraminiferal and ostracod assemblages is determined mainly by average salinity and pH. The position of species along the axis of the estuary correlates with the altered salinity profile inferred to occur during floods, with tolerance to lowered salinity being greater further upstream. Low pH conditions are widely distributed (due to the anoxia of stagnant, nutrient-enriched waters), causing calcareous test dissolution which, in some areas, totally excludes calcareous foraminifera and ostracods. Illumination is also important in controlling ostracod distribution, being lowest in widespread turbid waters. Additional factors controlling foraminiferal and ostracod distribution include: substrate mobility, nutrients, seagrass distribution, tidal exposure, and tolerance to varying temperature. Recent seafloor environments were described using the distribution of sediments, foraminifera and ostracods in short cores and previous spatial surveys. They have changed considerably since the late 19th century, mainly as a result of human activities which continue to affect the estuary. During periods of increased agricultural activity (1920’s-1940s; 1960’s-present), greater land clearance, cultivation and fertiliser usage within the catchment area lead to increased sediment and nutrient loading of fluvial waters entering the estuary. This lead to increased sedimentation, mud accumulation, turbidity, and lowered dissolved oxygen and pH within the estuary, causing the demise of dense clam and oyster beds, reduced distribution of ostracods and calcareous foraminifera, increased distribution of agglutinated foraminifera, and increased faunal abundance within nutrient-enriched sediments. Dam construction and irrigation activities during the 20th century, reduced rainfall over the last thirty years, and causeway construction during the 1870’s, have all contributed to increased water stagnation, reduced flushing, and more upstream penetration of the estuary by marine waters.

Appendix 4.4 removed due to copyright restrictions: Suepaul, R.B., Alley, M.R., Jansen van Rensburg, M., 2010, Salt gland adenitis associated with bacteria in blue penguins (Eudyptula minor) from Hauraki Gulf (Auckland, New Zealand). Journal of Wildlife Diseases, 46(1) : 46-54. / According to the New Zealand Threat Classification, little blue penguin (LBP) (Eudyptula minor) populations are under ‘gradual decline’. Although long-term data are available for some mainland populations, the status of LBP on offshore islands remains largely unknown. Most studies have focussed on breeding success and foraging ecology. However, there is a paucity of data pertaining to diseases and parasites, and the potential effects of these factors on LBP health, reproductive success and survival. To date, the LBP population on Tiritiri Matangi Island, Hauraki Gulf, Auckland, New Zealand, has only been monitored periodically, despite the island being an important habitat for LBP throughout their annual cycle. The overall aim of this study was to examine the relative importance of parasites and disease in relation to key aspects of LBP life-history, including: the annual cycle; reproductive success; energetic demands, immunity; and mortality. During 2006 and 2007, the reproductive success of LBP on Tiritiri Matangi Island was investigated with respect to lay date, nest site attributes, parental quality and ectoparasite loads. A nest treatment experiment was conducted to explore flea (Parapsyllus longicornis) and tick (Ixodes eudyptidis) effects on breeding success. Overall reproductive output was low, estimated at 33.3%, with an average of 0.67 chicks fledged per pair. Lay date and body condition (BC) appeared to be the main drivers of reproductive success, with early breeders fledging significantly more chicks than late breeders. Increased BC improved reproductive success. Although late breeders exhibited higher BC scores, increased chick mortality indicated that late nests face a reproductive trade-off. Treatment did not prove effective in reducing ectoparasite loads and there was no correlation between ectoparasite abundance in the nest and reproductive success. Throughout their geographic distribution, penguins are host to a range of ectoparasites. Using Ixodes eudyptidis ticks as indicators, ectoparasite-host dynamics were investigated over the course of one year, in relation to LBP life stages, body condition (BC) and haematological parameters. To investigate the presence of vector-borne diseases, blood parasite prevalence was determined using molecular techniques and microscopy. Tick load exhibited significant seasonal variation, being highest during periods of increased host availability i.e. moult and breeding. However, these increases in abundance were not associated with body condition or decreased reproductive success of adults. Nonetheless, LBP exhibited seasonal fluctuations in haematological parameters, with decreases in white blood cell concentrations during periods of increased energy demands and high tick loads. Blood parasite prevalence was low (<1%), determined to be Plasmodium sp. infection. No other blood parasites were found. These results indicate that the lifecycle of I. eudyptidis is tightly linked with that of its LBP hosts, and that infested individuals exhibit physiological responses to tick load. LBP exhibit annual fluctuations in mortality and experience periodic mass mortalities. To examine factors associated with mortality, post-mortems were conducted on 32 LBP from the Hauraki Gulf. Additionally, 128 LBP necropsy records were obtained from the National Wildlife Database (HUIA) for the period spanning April 1993-January 2009, and the causes of mortality were reviewed. Starvation and disease accounted for the highest mortality levels, with 65% of deaths attributed to either one or both of these factors. Furthermore, there was a strong association between starvation and parasites. Parasitic disease and diseases of uncertain aetiology were the most common disease types. In all age groups, the likelihood of infectious, non-infectious and disease of unknown aetiology was significantly higher in LBP that harboured one or more parasite species. Results from this study suggest that starvation and disease, including parasites, are significant factors associated with mortality of LBP in New Zealand, as has been found in Australian LBP populations. Parasites and disease are increasingly recognised as a challenge to the conservation of wildlife, and information regarding endemism of pathogens and parasites within populations is vital for determining ecosystem health, and identifying aberrant diseases.

Loss of indigenous biodiversity continues in New Zealand. Despite admirable goals in the NZBS 2000 to the contrary, efforts at improved biodiversity conservation have been insufficient to halt loss of significant amounts of indigenous forest and wildlife habitat. Increasing numbers of native species are moving towards critically endangered and extinction. Whatever we are doing in New Zealand, it is not effective enough. The aim of this study is to firstly identify factors contributing to the failure, “to halt the decline of indigenous biodiversity” in New Zealand and to then consider opportunities to overcome these barriers. In considering opportunities, this study then reviews the emerging discipline of landscape ecology as an answer to, at least, some of those factors and the recurring calls from New Zealand ecologists for a more integrated and holistic approach to biodiversity conservation. Recent advances in the planning framework and particularly provisions for biodiversity conservation in England are explored as a model of practical application of landscape ecological principles to land-use planning. From this review, the study proposes a new ‘LEEP’ model for strategic biodiversity conservation that produces a regional-scale spatial conservation map and accompanying policy and implementation guide. Together they provide an integrated and holistic approach to restoring or creating functional landscapes that also recognises and provides for human activities and development. Application of the LEEP model is demonstrated through a case study of the Wellington region. Benefits and potential uses of the map and policy outputs are canvassed. Interviews with leading New Zealand and international ecologists provide an assessment of the current status of landscape ecology and interviewees also act as an expert ‘test panel’ against which the Wellington maps and guides produced from the ‘LEEP’ model are assessed. Finally, suggestions are provided for development of the new model and future research needs towards fuller and more effective implementation of this approach to biodiversity conservation in the New Zealand context.

Species are one of the fundamental components of biology and the accurate delimitation of species is important in evolutionary, systematic and ecological studies, yet there is still confusion over how species can be recognised. Examining different characters allows multiple lines of evidence for successful and accurate species delimitation and identification. In this thesis, morphological, genetic and behavioural variation is investigated within an endemic species of ground weta, Hemiandrus pallitarsis, in the North Island, New Zealand. Twelve morphological characters were measured, and mitochondrial cytochrome oxidase I DNA sequences were analysed from populations across the distributional range of H. pallitarsis. Both methods provide no evidence of a species complex within H. pallitarsis. Instead, the morphometric results suggest females are significantly larger than males, and ground weta in Palmerston North are significantly smaller than weta further north. Additionally, genetic analyses found substantial population structuring, large genetic distances, and an historical south to north pattern of movement in the North Island. The pattern of vibratory drumming behaviour followed that predicted by morphology and geographic proximity – drumming signals were more similar between geographically close populations and did not match the patterns of genetic isolation. Overall, this thesis was able to show that H. pallitarsis is morphologically, genetically and behaviourally variable across the North Island.

Microbial infection of eggs was originally investigated in terms of human health only. Recently, however, it was found that it can also cause early embryo mortality in birds, mainly through trans-shell infection prior to incubation. Trans-shell infection is highly dependent upon environmental conditions, egg temperature and egg properties such as shell quality and antimicrobial defences. Microbial infection of eggs is more likely to occur in synchronously incubating species as first laid eggs can be exposed for up to several days prior to full incubation. One example of a population that seems at particular risk of egg microbial infection is New Zealand’s little blue penguin (Eudyptula minor) from Tiritiri Matangi Island. This bird lays two eggs on average three days apart, and is believed to begin full incubation only after the second egg has been laid. Both eggs are laid in particularly humid and soiled nests and contain only low levels of lysozyme, an important antimicrobial protein. The aims of this study were therefore to 1) obtain a first examination of the rates of shell and trans-shell microbial infection of chicken eggs in New Zealand and assess the effects of cleaning on those rates, 2) investigate the role of microbes in hatching failure of little blue penguin eggs and 3) investigate other factors affecting little blue penguin egg viability. This study revealed that shell infection in chicken eggs significantly increased with exposure and significantly decreased with cleaning; however, trans-shell infection was only marginally affected by exposure and cleaning. On Tiritiri Matangi Island, Hauraki Gulf, New Zealand, nest type, egg order and shell cleaning did not affect hatching success, suggesting that nest conditions and microbial infection prior to incubation were not a major cause of egg mortality in this population. Temporary abandonment during incubation, however, was very frequent in the second half of the breeding season and fatal to most eggs. These temporary abandonments seemed to be caused by resource limitations, an aspect that should be investigated in future studies.