Thesis (M.S.)--University of North Carolina at Wilmington, 2003.

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Aim: This series of studies assessed the influence that digenean parasites exert on a host population beyond the initial cost of infection. It aimed to address the discrepancy between the exclusion of parasites from most ecological studies, and their functional importance within the wider free-living community. It also assessed methodologies that utilise the diversity of the parasite community as well as the phenotypic effects of parasitism, as potential tools for ecology and palaeoecology. Results: From 2004-2007, in excess of 53,000 snails were dissected during the course of these studies. Making it one of the most detailed parasitological studies undertaken on a single host parasite interaction in this field. Community studies - Parasite diversity was found to be influenced by local scale abiotic, as well as large scale environmental patterns. Parasite diversity correlates with the distribution of definitive avian hosts, which in turn correlates with intertidal benthic communities. These correlations provide an effective methodology for monitoring ecosystem health. Behavioural studies - A critical assessment of parasite mediated behavioural change revealed the indirect cost of gigantism in the host population to be a side effect, and that differences in behaviours were often a result of size rather than infection. Growth/Morphometric studies - Gigantism was revealed as both infection and environment driven. Finally, morphometric analysis revealed conchiometric markers that provide tools for reconstructing past environments and infection prevalence. Main conclusions: The functional importance of digenean parasitism within the intermediate host snail Hydrobia ulvae, extends far beyond the individual. Digeneans directly and indirectly manipulate the host population, in turn affecting wider community structure. Environmental, abiotic and biotic factors can leave observable imprints on the infected and uninfected host population. Such markers can provide tools and methodologies for furthering our understanding of both extinct and extant host-parasite populations.

No description available.

Increased abstraction of water in the catchment results in a reduced or altered pattern of river flow and this holds serious consequences for the downstream estuarine ecosystem. In South Africa this is a serious concern because freshwater is in limited supply and the demand for freshwater can be expected to increase in the future. A large multi-disciplinary consortium of South African scientists are working on projects to determine the freshwater requirements of estuarine ecosystems. As part of this, this thesis reports on research undertaken to develop mathematical models to determine the freshwater requirements of estuarine macrophytes. Three key macrophytes are selected. The macrophytes are Zostera capensis Setchell, Ruppia cirrhosa Grande, and Phragmites australis. They are common macrophytes in South African estuaries. Zostera and Ruppia are submerged macrophytes and Phragmites is an emergent macrophyte. They have different freshwater environments and therefore respond differently to alterations in freshwater flow. A first order differential equation model is used to determine the effect of different combinations of open and closed mouth conditions of the estuary on Zostera and Ruppia. The scenarios are selected to determine whether achieving a switch in states from a Zostera-dominated estuary to a Ruppia-dominated estuary is possible. To predict encroachment rates and colonisation patterns, a cellular automaton of the vegetative spread of existing Zostera beds is developed. After analysing various scenarios accounting for both an increase and a decrease in freshwater supply, the cellular automaton is extended to include interactions between Ruppia and Phragmites. The multi-species model is applied to the Kromme estuary, South Africa and the Great Brak estuary, South Africa. Various freshwater scenarios are examined from the natural runoff condition to the situation of no freshwater inflow. A sensitivity analysis of the spatial model with Zostera, Ruppia and Phragmites is conducted. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1998.

Increased abstraction of water in the catchment results in a reduced or altered pattern of river flow and this holds serious consequences for the downstream estuarine ecosystem. In South Africa this is a serious concern because freshwater is in limited supply and the demand for freshwater can be expected to increase in the future. A large multi-disciplinary consortium of South African scientists are working on projects to determine the freshwater requirements of estuarine ecosystems. As part of this, this thesis reports on research undertaken to develop mathematical models to determine the freshwater requirements of estuarine macrophytes. Three key macrophytes are selected. The macrophytes are Zostera capensis Setchell, Ruppia cirrhosa Grande, and Phragmites australis. They are common macrophytes in South African estuaries. Zostera and Ruppia are submerged macrophytes and Phragmites is an emergent macrophyte. They have different freshwater environments and therefore respond differently to alterations in freshwater flow. A first order differential equation model is used to determine the effect of different combinations of open and closed mouth conditions of the estuary on Zostera and Ruppia. The scenarios are selected to determine whether achieving a switch in states from a Zostera-dominated estuary to a Ruppia-dominated estuary is possible. To predict encroachment rates and colonisation patterns, a cellular automaton of the vegetative spread of existing Zostera beds is developed. After analysing various scenarios accounting for both an increase and a decrease in freshwater supply, the cellular automaton is extended to include interactions between Ruppia and Phragmites. The multi-species model is applied to the Kromme estuary, South Africa and the Great Brak estuary, South Africa. Various freshwater scenarios are examined from the natural runoff condition to the situation of no freshwater inflow. A sensitivity analysis of the spatial model with Zostera, Ruppia and Phragmites is conducted. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1998.

No description available.

Diets of large marine predators have been extensively studied to assess interactions with fisheries, monitor links between diet and reproductive success, and understand trophic interactions in marine ecosystems. Since marine species can rarely be observed foraging directly, most studies rely on the identification of prey remains in stomach contents or faeces to determine the prey items being consumed. While this approach has provided a wealth of information, it has several limitations resulting primarily from difficulties identifying digested prey and from biased recovery of remains due to differential digestion. My thesis explores the use of molecular genetic methods in dietary studies of large marine predators. DNA-based identification techniques have been used in several diet studies, but the methods and applications are still in the early stages of development. Through a number of studies, I investigated the ability to recover genetic data from various dietary samples using a range of genetic techniques. A) Genetic screening for prey in the gut contents from a giant squid - I assessed the use of polymerase chain reaction (PCR)-based methods for isolation of prey DNA from an Architeuthis gut content sample. A taxonomically informative molecular marker was selected and a screening method developed using denaturing gradient gel electrophoresis. The methodology was used to identify prey from otherwise unidentifiable hard-part remains and the amorphous slurry component of the squid gut sample. The techniques developed here provided a framework for later chapters. B) Analysis of prey DNA in faeces of captive sea lions Part I: DNA detection, distribution and signal persistence - A feeding trial with captive Steller sea lions (Eumetopias jubatus) was carried out to investigate the use of genetic faecal analysis as a tool to study diet. I used group-specific PCR detection to determine: (i) the reliability of prey DNA recovery, (ii) the distribution of prey DNA within faeces and (iii) the persistence of the genetic signal after a prey item was removed from the diet. The proportions of prey DNA in several samples were also determined using a clone library approach to determine if DNA quantification could provide semi-quantitative diet composition data. Results show that the prey DNA could be reliably detected in sea lion faeces and the genetic signal could persist in samples up to 48 hours after ingestion. Proportions of prey DNA isolated from faeces were roughly proportional to the mass of the prey items consumed. Part II: DNA quantification - Quantitative real-time PCR was used to further investigate if quantitative diet composition data could be obtained through quantification of the DNA present in faeces. I quantified the relative amounts of DNA in three fish species being fed to captive sea lions, then determined the amount of DNA recovered from these prey items in the sea lions - faeces. The results indicate that diet composition estimates based on the relative amounts of DNA in faeces can be biased due to the differential survival of DNA from different fish species; however, these biases may be less than those commonly observed in the conventional analysis of prey hard remains. C) Quantification of damage in DNA recovered from faecal samples - I developed a general method to quantify the frequency of DNA damage present in specific gene regions. The technique was applied to assess the amount of DNA damage in predator and prey DNA recovered from sea lion faeces. The estimated frequency of DNA damage was always higher for the prey DNA than for the predator DNA within a faecal sample. The findings have implications for marker development and comparison of results obtained in future DNA-based diet studies. D) Studying seabird diet through genetic analysis of faeces - I investigated the diet of macaroni penguins (Eudyptes chrysolophus) through conventional analysis of stomach contents and through the analysis of prey DNA extracted from faeces. Genetic data was obtained from faecal samples using PCR tests to determine the presence or absence of DNA from potential diet items and also using a clone library approach. Approximately half of the faecal samples tested positive for one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in early stages of chick rearing and DNA from a myctophid fish was prevalent in faeces collected later; this trend mirrored the data obtained from the stomach contents. Analysis of prey sequences in 'universal'clone libraries revealed a highly biased recovery of sequences from fish prey; this bias is most likely caused by the use of degenerate primers with a higher binding affinity for fish DNA template compared to DNA from other prey groups. Results obtained from the genetic and traditional approaches are compared, and potential future applications of the genetic techniques to studying seabird diet are discussed. This series of studies has contributed significantly to our understanding of the strengths and the limitations of DNA-based diet analysis. The work identifies situations where genetic methods can be successfully applied to study the diet of marine predators and provides guidance for future studies in this emerging field.

The currently most accepted population theory for reef fish was developed on tropical reefs and suggests that populations of most reef fish species are limited primarily by recruitment, with little post-recruitment resource limitation. I tested the validity of this theory for temperate reef fishes by examining growth rates in six common species from a number of isolated populations for evidence of resource limitation. If resources are limiting, spatial and temporal variation in recruitment and mortality should lead to isolated populations experiencing differing levels of resource availability, particularly food availability, which will be reflected in growth rates. I worked with six of the most common reef fishes found in Tasmanian waters so that any findings would form the basis of a broadly applicable model. These were Notolabrus tetricus, Notolabrus fucicola, Pictilabrus laticlavius, Pseudolabrus psittaculus, Penicipelta vittiger, and Meuschenia australis. Before examining growth rates it was first necessary to define the scale at which populations could be considered to be isolated. The short and long-term movement patterns of each species were studied using visual observations to interpret short-term patterns, and recaptures of tagged fish to interpret the long-term patterns. Methods of ageing each species were developed and validated, with growth rates of tagged fish being used to validate the use of otoliths for ageing. General growth curves are presented. For most of the species, there was some uncertainty in current texts about the sexual system used and the relationship between sex and dichromatism and dimorphism. To clarify this situation the reproductive biology of each species was examined. The relationship between sex and growth rate was also examined. For two species (N. tetricus and N. fucicola) annual growth data from tagged fish were obtained over a 3-4 year period, allowing inter-annual growth variability to be examined. As well as providing an insight into the variability of growth with time, these results also aid in the interpretation of growth curves determined from otolith ageing. In all species investigated, no significant differences in growth rates were detected between populations occupying similar habitats and subject to similar environmental conditions. These results suggest that post-recruitment resource limitation in the form of food limitation may not be an important factor influencing the post recruitment growth and survival of many temperate reef fishes with pelagic larval stages. This agrees with the assumptions made, but rarely tested, in current theories concerning the regulation of populations of reef fish, particularly those on temperate reefs.

Research into small-scale fisheries is often insufficient, resulting in limited data, because this type of fishery is inevitably constrained by financial considerations. This creates a challenge to provide adequate information to support sustainable management, particularly given the shift from single species management to more integrated spatial and multi-species management and, ultimately, to ecosystem based fisheries management (EBFM). Striped trumpeter (Latris lineata) is widely distributed around the temperate latitudes of the southern hemisphere. The species is iconic to Tasmania where it supports a small commercial fishery, and it is increasingly targeted by recreational fishers. This fish is common on most rocky reefs between 50 – 250 m around Tasmania. However, the historical data for striped trumpeter from Tasmania is patchy in time and space, reflecting opportunistic sampling over many years. Using striped trumpeter as an example of a small-scale data-limited fishery, this study applies a variety of techniques to describe key biological and ecological processes required for sustainable fisheries management. The study was divided into three themes. First, standard and novel analytical techniques were applied to evaluate data to provide key biological parameters required for single-species assessment. Second, stock structure was investigated on both local and global scales using molecular techniques and otolith morphometrics. Finally, recruitment processes were investigated based on otolith microchemistry and modelling of larval dispersal. Seasonal growth variability was observed over the first five years, with growth rates peaking approximately one month after the observed peak in sea surface temperature. The oldest fish in this study was 43 years. Lifetime growth was modelled using a modified twophase von Bertalanffy growth function, with the transition between growth phases linked to changes in physiological and life history traits, including offshore movement as fish approach maturity. Total mortality was estimated using catch curve analysis based on the standard and two-phase von Bertalanffy growth functions, and estimates of natural mortality were calculated using two empirical models, one based on longevity and the other based on the parameters L1 and k from both growth functions. The spawning season around Tasmania occurs in the austral spring, with peak spawning activity in September and October. Size at 50% maturity was estimated at 543 mm fork length (FL) for females (estimated age = 6.8 years) and 529 mm FL for males (estimated age = 6.2 years). Striped trumpeter is a multiple spawner with batch fecundity estimates ranging from 205,054 for a 2 kg fish (540 mm FL) to 2,351,029 for a 9.5 kg fish (800 mm FL). At the current minimum legal size limit of 450 mm total length (equivalent to approximately 425 mm FL), yield-per-recruit was estimated to be close to maximum, and spawning biomass-per-recruit (SPR) ranged from 35 – 52% of virgin stock, depending on the mortality estimates used. Otolith morphometrics, in particular elliptical Fourier analysis of otolith shape, indicated little to no connectivity between the striped trumpeter population of Tasmania and the St. Paul/ Amsterdam Island populations. A molecular assessment of mtDNA confirmed this finding. In addition, the DNA sequence analysis indicated that the New Zealand striped trumpeter population was genetically distinct from the Tasmanian and St. Paul/ Amsterdam Island populations. DNA sequence analysis also indicated that the population around Tasmania is a single population. The affinity of juvenile striped trumpeter to inshore reefs has been suggested from anecdotal fishing observations. Using otolith microchemistry the comparative contribution of juvenile striped trumpeter from shallow inshore habitats to the adult population was estimated. Juvenile striped trumpeter from a strong recruitment pulse (1993 cohort) were collected at age two from inshore reefs and as adults at age six from deeper offshore reefs around the coast of Tasmania. Natural variations were identified in the concentrations of lithium and strontium within the incremental structure of the observed otoliths. Discriminant analysis suggested that 70% of adults sampled originated from an inshore juvenile habitat, 13% were from deeper reefs and 17% could not be statistically allocated with confidence. An integrated bio-physical larval dispersal model was developed in an attempt to explain the high degree of inter-annual recruitment variability displayed by this species. The model utilised information developed through the course of this study on reproductive biology, ontogenic habitat preferences and stock structuring as well as additional information on striped trumpeter larval biology from aquaculture trials to generate realistic scenarios. While the model was unable to accurately predict observed interannual recruitment variability, it did provide insights to important source and settlement regions as well as the importance of the addition of biological components, such as: timing of spawning, growth and mortality. Through efficient data-mining, novel methods and technological advancements this study has provided robust scientific advice to support the management of the striped trumpeter fishery. Information has been collated to support traditional single-species management and also for developing spatial fisheries measures, leading to a more ecosystem based approach to fisheries management. Otoliths proved to be valuable in several areas, and small-scale fisheries would be advised to initiate otolith collections even though analysis may not be planned for some time. This study demonstrates how targeted research could be used in other small-scale data limited fisheries in a cost effective manner to provide information for sustainable management.