Zoology - Theses
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ItemFish responses to seagrass habitat fragmentation(University of Melbourne, 2009)Marine organisms that inhabit coastal waters increasingly have to deal with habitat fragmentation and concomitant increases in edge habitat. Effective conservation of coastal habitats requires an understanding of how and why organisms respond to these habitat changes. Seagrass is a critical marine habitat that is becoming increasingly fragmented. To understand how fish living in seagrass respond to fragmentation, I actively fragmented artificial seagrass habitats (single, continuous 9 m2 patches fragmented to 4 discrete 1 m2 patches) and evaluated changes in fish abundance. Total fish abundance was unaffected by fragmentation, and this was consistent through time (1 day, 1 week, 1 month). If fish crowded into remnant seagrass fragments, then crowding effects may explain the lack of decline in fish abundance that would otherwise be expected from seagrass habitat loss. Progressive removal of seagrass (16 m2 patches to 4 m2) showed that fish temporarily (?1 day) crowd into remnant patches, but crowding effects could not explain the longer-term persistence of fish in fragmented seagrass. I then tested the hypothesis that fish are more abundant at seagrass edges than interiors (i.e. �positive edge effects�) and that the effects of seagrass habitat loss on fish abundance were offset by an increase (25%) in edge habitat in fragmented patches. I found that fish were 3 times more abundant at edges than interiors in continuous seagrass (single, 9 m2 patches), but in patchy seagrass (4 discrete 1 m2 patches) there was no difference, which is probably because pipefish perceived patchy seagrass as consisted entirely of �edge� habitat. To test whether the observed edge effects in continuous seagrass were caused by increased availability of food at edges, I estimated the abundance of food across continuous seagrass patches. Food abundance peaked at seagrass edges and was 16% higher than samples taken from patch interiors. To separate causality from correlation, I supplemented interiors of continuous seagrass with food and found that edge effects ceased, which indicated that fish were moving from patch edges to interiors in response to food supplementation. This provided evidence that fish were more abundant at seagrass edges due to greater food availability.
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ItemThe importance of edge effects in determining fish distributions in patchy seagrass habitats( 2009)Boundaries between adjacent habitats can create unique biotic and abiotic conditions, varying species compositions and abundances between the edge and interior of habitats. As habitats become fragmented, the relative amount of edge increases. Understanding the role that habitat edges have in determining species compositions and abundances is fundamental for conservation and management of habitats, particularly those under threat from fragmentation. Seagrass habitats are common nearshore habitats that harbour a rich and diverse faunal assemblage that are under threat worldwide from human disturbance. Human induced fragmentation, and the propensity of seagrass to form naturally patchy landscapes, makes it an ideal system to study the effects of edges on fauna. Evidence of fish displaying edge effects in seagrass habitats is equivocal. Assessment of fish edge effects was done by sampling seven positions within seagrass habitats at fine spatial scales. Strong, consistent patterns in fish distributions demonstrated clear edge effects both within and alongside seagrass at these sites. The total number of fish sampled was greater at the seaward seagrass edge than the seagrass middle, but there was little difference between the seagrass middle and the shoreward seagrass edge. Four individual fish species showed preferences for the seagrass edges. Further investigation revealed that patch size could influence the magnitude of edge effects in seagrass beds. Fish were sampled in ten variously sized seagrass patches in three positions within each patch. Two species showed variations in edge effects across patches which could be attributed to the area of the patch. Changes in patch size can influence the magnitude of edge effects that species display, suggesting that patch area effects (fish density varying with patch size) could be caused by edge effects. Food availability and predation are mechanisms commonly used to explain edge effect patterns. Gut analysis was done on Stigmatopora nigra sampled at the edge and middle of patches to determine if prey consumption varied between positions, and explain S. nigra distribution. There was little difference in prey consumed by S. nigra at the edge and middle of patches, suggesting that food was unlikely to be causing S. nigra edge effects, or that the influence of prey distribution was being masked by other factors such as seagrass structure. Predator abundances and foraging efficiency may vary at the edge and middle of patches, and consequently influence the distribution of prey fish within patches. Underwater videos were placed at four positions within seagrass habitats to assess predator distributions. Predatory Australian salmon, Arripis spp., spend more time over adjacent sand than other positions, while small potential prey species (King George whiting, Sillaginodes punctata, recruits) appear to prefer the middle of seagrass patches, possibly to avoid encounters with salmon. To test if the predator-prey distributions reflected actual predation pressure, a tethering experiment was done to determine if predation was causing edge effects in small fishes. King George whiting recruits and pipefish (Stigmatopora spp.) were tethered at each of the four positions at different depths. Survival time of whiting recruits was greater in the middle of shallow seagrass patches than other positions. Few pipefish were preyed upon, and survival time was lower over sand adjacent to seagrass than at the seagrass edge or middle. Video footage revealed that salmon was the dominant predator of both whiting recruits and pipefish. The distribution of predators and associated predation can explain edge effects for some species (whiting) but other mechanisms, or a combination of mechanisms, are determining edge effects for other species (pipefish). Edge effects were common amongst fish species in seagrass habitats, and included permanent, temporary and predatory species. Patch size was found to influence the extent of the edge effect. There was little evidence to support prey consumption as an underlying mechanism causing higher fish abundances at the interior or edge of patches, however there was evidence that predation could be causing edge effects. Changes in fish distributions within seagrass patches due to patch size and predation when seagrass undergoes fragmentation need to be considered by not only ecologists, but also by managers in the development of plans for seagrass conservation. Future studies should investigate the relative contribution of different edge characteristics in determining the degree of seagrass edge effects.
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ItemUnderstanding the hormonal regulation of mouse lactogenesis by transcriptomics and literature analysis( 2009)The mammary explant culture model has been a major experimental tool for studying hormonal requirements for milk protein gene expression as markers of secretory differentiation. Experiments with mammary explants from pregnant animals from many species have established that insulin, prolactin, and glucocorticoid are the minimal set of hormones required for the induction of maximal milk protein gene expression. However, the extent to which mammary explants mimic the response of the mammary gland in vivo is not clear. Recent studies have used microarray technology to study the transcriptome of mouse lactation cycle. It was demonstrated that the each phase of mouse lactation has a distinct transcriptional profile but making sense of microarray results requires analysis of large amounts of biological information which is increasingly difficult to access as the amount of literature increases. The first objective is to examine the possibility of combining literature and genomic analysis to elucidate potentially novel hypotheses for further research into lactation biology. The second objective is to evaluate the strengths and limitations of the murine mammary explant culture for the study and understanding of murine lactogenesis. The underlying question to this objective is whether the mouse mammary explant culture is a good model or representation to study mouse lactogenesis. The exponential increase in publication rate of new articles is limiting access of researchers to relevant literature. This has prompted the use of text mining tools to extract key biological information. Previous studies have reported extensive modification of existing generic text processors to process biological text. However, this requirement for modification had not been examined. We have constructed Muscorian, using MontyLingua, a generic text processor. It uses a two-layered generalizationspecialization paradigm previously proposed where text was generically processed to a suitable intermediate format before domain-specific data extraction techniques are applied at the specialization layer. Evaluation using a corpus and experts indicated 86-90% precision and approximately 30% recall in extracting protein-protein interactions, which was comparable to previous studies using either specialized biological text processing tools or modified existing tools. This study also demonstrated the flexibility of the two-layered generalization-specialization paradigm by using the same generalization layer for two specialized information extraction tasks. The performance of Muscorian was unexpected since potential errors from a series of text analysis processes is likely to adversely affect the outcome of the entire process. Most biomedical entity relationship extraction tools have used biomedical-specific parts-of-speech (POS) tagger as errors in POS tagging and are likely to affect subsequent semantic analysis of the text, such as shallow parsing. A comparative study between MontyTagger, a generic POS tagger, and MedPost, a tagger trained in biomedical text, was carried out. Our results demonstrated that MontyTagger, Muscorian's POS tagger, has a POS tagging accuracy of 83.1% when tested on biomedical text. Replacing MontyTagger with MedPost did not result in a significant improvement in entity relationship extraction from text; precision of 55.6% from MontyTagger versus 56.8% from MedPost on directional relationships and 86.1% from MontyTagger compared to 81.8% from MedPost on un-directional relationships. This is unexpected as the potential for poor POS tagging by MontyTagger is likely to affect the outcome of the information extraction. An analysis of POS tagging errors demonstrated that 78.5% of tagging errors are being compensated by shallow parsing. Thus, despite 83.1% tagging accuracy, MontyTagger has a functional tagging accuracy of 94.6%. This suggests that POS tagging error does not adversely affect the information extraction task if the errors were resolved in shallow parsing through alternative POS tag use. Microarrays had been used to examine the transcriptome of mouse lactation and a simple method for microarray analysis is correlation studies where functionally related genes exhibit similar expression profiles. However, there has been no study to date using text mining to sieve microarray analysis to generate new hypotheses for further research in the field of lactational biology. Our results demonstrated that a previously reported protein name co-occurrence method (5-mention PubGene) which was not based on a hypothesis testing framework, is generally more stringent than the 99th percentile of Poisson distribution-based method of calculating co-occurrence. It agrees with previous methods using natural language processing to extract protein-protein interaction from text as more than 96% of the interactions found by natural language processing methods coincide with the results from 5-mention PubGene method. However, less than 2% of the gene co-expressions analyzed by microarray were found from direct co-occurrence or interaction information extraction from the literature. At the same time, combining microarray and literature analyses, we derive a novel set of 7 potential functional protein-protein interactions that had not been previously described in the literature. We conclude that the 5-mention PubGene method is more stringent than the 99th percentile of Poisson distribution method for extracting protein-protein interactions by co-occurrence of entity names and literature analysis may be a potential filter for microarray analysis to isolate potentially novel hypotheses for further research. The availability of transcriptomics data from time-course experiments on mouse mammary glands examined during the lactation cycle and hormone-induced lactogenesis in mammary explants has permitted an assessment of similarity of gene expression at the transcriptional level. Global transcriptome analysis using exact Wilconox signed-rank test with continuity correction and hierarchical clustering of Spearman coefficient demonstrated that hormone-induced mammary explants behave differently to mammary glands at secretory differentiation. Our results demonstrated that the mammary explant culture model mimics in vivo glands in immediate responses, such as hormone-responsive gene transcription, but generally did not mimic responses to prolonged hormonal stimulus, such as the extensive development of secretory pathways and immune responses normally associated with lactating mammary tissue. Hence, although the explant model is useful to study the immediate effects of stimulating secretory differentiation in mammary glands, it is unlikely to be suitable for the study of secretory activation.
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ItemDemography of Australian fur seals (Arctocephalus pusillus doriferus)( 2009)The Australian fur seal (Arctocephalus pusillus doriferus) population has displayed a relatively slow rate of recovery since being hunted by commercial sealers during the early 19th century. Despite this, population abundance doubled in the past 2 – 3 decades, indicating that the population growth rate has recently increased. Yet, the factors influencing the population’s dynamics are poorly understood, primarily because basic demographic rates are unknown. Female age, survival, fecundity, breeding and physiology were studied at Kanowna Island, Bass Strait, Australia, between 2003 – 2006 by conducting censuses and captures (n = 294). Mark-recapture estimates of pup production were used to validate direct pup counts, allowing a 9-year dataset to be used for calculation of the population growth rate (2.2% p.a.) and investigation of environmental influences on reproductive success. Annual pup production (x = 3108) was synchronous, with 90% of births occurring within 28 days of the median birth date of 23 November. Births occurred earlier in years when pup production and female body condition were high and these factors were correlated with local oceanographic indicators, suggesting that reproductive success is constrained by environmentally-mediated nutritional stress. Pregnancy was assessed by blood plasma progesterone radioimmunoassay and the pupping status of the same females was observed during breeding season. Despite high mid-gestation pregnancy rates (x = 84%), the birth rate was lower than in other fur seals (x = 53%), suggesting that late-term abortion is common. Lactating females were less likely to pup, indicating that nutrition may be insufficient to support concurrent lactation and gestation. Age and morphometric data were used to construct body growth, age structure and survivorship models. Adult female survival rates were similar to those of other fur seals (x = 88.5%). A life table was constructed and its age-specific survival and fecundity rates used in a Leslie-matrix model to project the population growth rate (2.2% p.a.) and determine the relative influence of each parameter. The abundance of female non-pups was 6 times greater than that of female pups, which is approximately 50% higher than previous conversion factors used to extrapolate population abundance from pup censuses in Australian fur seals. However, if the non-pup sex ratios of other otariids are considered, the pup:population conversion factor is 4.5. Compared to a study performed before the recent population increase, the modern population displays similar body growth and fecundity rates but higher survival rates. This suggests that recent population growth resulted from a relaxation of hunting and/or predation mortality rather than from increased food availability. The low population growth rate is attributed to a low birth rate associated with nutritional stress, yet despite this, body growth occurs rapidly. Such characteristics are typical of sea lions rather than fur seals, perhaps because Australian fur seals employ the typical sea lion strategy of using benthic foraging to exploit a continental shelf habitat. The effect of ecological niche on population dynamics in the Otariidae is discussed.
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ItemThe distribution and ecology of ants in vineyards( 2009)Ants are highly abundant and ubiquitous in many terrestrial ecosystems. They perform many important ecological functions and have been widely employed as bioindicators for various terrestrial monitoring programmes. In agroecosystems, their role is controversial because ants can act as predators against herbivorous pest but also associate with and protect honeydew-producing hemipteran pests. The ecology, function and interactions of ants with other arthropods in vineyards are poorly known and this thesis therefore examines their distribution and ecology in south-eastern Australian vineyards. An extensive survey of 50 vineyards distributed in five regions in South Australia and Victoria recorded 147 native ant species and one invasive species, Linepithema humile (Mayr). Species richness, compositional similarities and assemblage structure varied within and across regions. High species turnover and variation in assemblage structure were found across regions and implications of these patterns are discussed. The invasive L. humile was only detected in some vineyards in one region. The potential impact of management practices and off-farm vegetation on augmenting ant diversity and conserving biodiversity are considered. The impact of non-target agrochemical applications on ants was investigated in 19 vineyards that received varying levels of agrochemical input. Ant assemblage structure and assemblages were not found to be impacted by pesticides. In contrast, ant assemblage structure was influenced by the presence of shelterbelts near the sampling area. Reasons for the resilience of ants to pesticides are given and assessment at the colony level instead of worker abundance is suggested. An ant-exclusion experiment was designed to test the impact of native ants on both canopy and ground arthropods concurrently. The potential influence of ants on predation and parasitism on eggs of light brown apple moth (LBAM), a grape pest, was also examined. Adult grapevine scale insects and earwigs under bark were also counted after a season of ant-exclusion. While ant exclusion was successful, there was no detectable difference in the abundance of most arthropod orders and feeding groups between ant-excluded and control vines, although ground spiders were more abundant under ant-excluded vines, despite increased ground ant foraging pressure. LBAM egg parasitism and predation were low and probably affected by weather and other arthropods. Ant exclusion did not reduce survival of scale insects, although the distribution and abundance of scale insects were negatively associated with earwigs. Reasons for the lack of negative effects of ants are discussed. The spatial patterns of ants were investigated with intensive pitfall trappings in two vineyards to examine if non-random patterns occur and whether these might be the result of competitive species interactions as well as non-crop vegetation adjacent to the vineyards. Null model analyses suggested competitive species interactions within ant assemblages that might have been driven by dominant species even though both positive and negative associations between dominants were also found. Consistent spatial aggregations indicated significant spatial overlap in distributions of some species. Such overlap suggests that potential co-existence might be attributed to temporal partitioning or differences in foraging strategies. The presence of vegetation had a marked influence on ant assemblage structure and competitive interactions, and might also facilitate co-existence by increasing resource heterogeneity. The implications of these findings for sampling strategies and ecological processes within vineyards are discussed. This thesis has provided new information about ants in vineyards. The high ant diversity could be important in maintaining ecosystem services. Among the 33 ant genera recorded, Iridomyrmex, Paratrechina and Rhytidoponera have the greatest potential in contributing to canopy pest suppression although their associations with honeydew-producing hemipterans need to be considered. Stable isotope analysis or/and molecular gut content analysis should reveal their trophic position in vineyards. Evaluation of crop yield that is directly attributed to soil conditioning by ants in agroecosystems should be explored. The importance of landscape composition, complexity and connectivity is highlighted and role of agroecosystems in conserving biodiversity is emphasised. Future research should be directed towards understanding how landscape composition and complexity may enhance ant diversity and alter dynamics and interactions that may be functionally important (biological control, soil conditioning, etc) in a landscape context.