Zoology - Theses
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ItemDefining the master regulator of urethral closure in mouse( 2017)Hypospadias is the ectopic placement of the urethral opening on the underside of the penis and is one of the most common developmental abnormalities in humans, occurring in approximately 1 in every 125 live male births. In addition, we have observed a doubling in the incidence of hypospadias over the past several decades suggesting an environmental component likely in the form of estrogen mimicking chemicals generally referred to as environmental endocrine disruptors (EEDs). Current models fail to explain these observations. The goal of this thesis is to produce a theory that describes the development and genetic regulation of urethral closure, and use it to explain the aetiology, spectrum, and rise in incidence of hypospadias observed in humans. The work presented in this thesis was performed using a novel mouse model (OVE442) with isolated hypospadias. This model was used to define the role of the urorectal septum (URS) during urethral closure. The process of urethral closure is generally thought to occur by tissue fusion. However, we provide immunohistological evidence that suggests the urethra is internalized by growth of the URS, which contributes tissue to the ventral aspect of the penis during embryonic development. The OVE442 model was next used to define a key regulator of the URS during urethral closure. Initial characterization of a genomic mutation in OVE442 model led us to discover a long non-coding RNA, designated Leat1, which was deleted near EfnB2. Loss of signalling through the EPHRINB2 protein was previously shown to cause severe hypospadias in mouse, however little is known about EfnB2 gene regulation during urethral closure. Leat1 was characterized, functionally examined, and shown to regulate EfnB2 expression through direct interaction with the EPHRINB2 protein. We further showed that Leat1 expression is differentially regulated in males and females, and that it is supressed by estrogen. These results showed that EfnB2 drives growth of the URS during urethral closure and provided the first experimental evidence revealing the genetic mechanism that causes male and female urethral anatomy to diverge. These observations were used together with our anatomical descriptions to produce a developmental theory that explains urethral formation in mouse. We extended our understanding further by using comparative time series RNA-Seq to describe global transcription and ChIP-Seq to identify genes actively regulated by estrogen and androgen during urethral. From these data, we identify potential urethral closure genes downstream of Leat1 and EfnB2 including genes that are likely responsive to sex hormones. This work has provided fundamental insights on the anatomy and genetic regulation of urethral closure. I have shown that male urethral closure is driven by growth of the URS and that this growth is regulated by the long non-coding RNA Leat1 in mouse. Furthermore, I have produced a list of potential EED targets that may lead to better understanding the causes of hypospadias. Through this work I have produced a theory that explains the spectrum of urethral malformations observed in human, defects associated with hypospadias such as chordee, and the genetic mechanism that is likely disrupted by EEDs. These findings fundamentally change the way we consider urethral development and may help to find ways to reduce the incidence or prevent hypospadias in humans.
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ItemLife-history strategies of five species of intertidal limpet( 1977)The life-long strategies of five species of intertidal limpet, Cellana tramoserica, Notoacmea petterdi, Patella peroni, Patelloida alticostata, and Siphonaria diemenensis, which occur on the same shore but in different tidal zones, are considered in relation to their different environments. Attention is focused upon reproductive effort, which is defined as the percentage of assimilated energy devoted to reproduction, and which is measured for each species by using annual energy budgets. Environmental and demographic factors, which previous workers have suggested may have important influences on the level of reproductive effort, are investigated. In particular, interspecific differences in reproductive effort are compared with differences in the availability of food resources, differences in the magnitude of density-independent causes of mortality, differences in adult mortality rates and differences in extrinsic adult mortality rates (i.e. the adult mortality rates that would occur in the absence of expenditure of energy in reproduction.) The results of the present study indicate that reproductive effort is correlated with the availability of food resources, but that the primary determinant of the optimum level of reproductive effort is the rate of extrinsic adult mortality.
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ItemThe effect of disturbance on the breeding biology of hooded plovers( 2000)Disturbance of birds by humans is a growing problem. This thesis examines the mechanisms through which disturbance may reduce reproductive success in the Hooded Plover Thinornis rubricollis, a solitary-nesting shorebird for which disturbance is thought to constitute a conservation threat. As a precursor to examining disturbance in this species, breeding biology, life history and parental care were investigated in a colour-banded population of Hooded Plovers in coastal Victoria, Australia. Pairs bred in widely dispersed territories, and intact pairs bred in the same territories year after year. The breeding season was asynchronous and protracted, lasting up to eight months. Breeding success was low, but pairs re-nested frequently and rapidly after nest and brood failure, and sometimes after successfully fledging young. Survival of juveniles was similar to that reported for other plovers, and adult survival was high compared with other plovers. However, it was estimated that only 34% of adults were expected to live 11 years, the average period needed for a pair to replace itself (produce two young). One unusual feature of the life cycle of Hooded Plovers was the complete temporal overlap of adult wing moult with breeding. Complete biparental care occurred throughout the breeding cycle. There is some evidence that males undertook more of the nocturnal incubation while females undertook more of the diurnal incubation but overall, pair members shared incubation equally. Levels of incubation were high and constant over the incubation period. Once chicks hatched, the average number of parents nearby and the frequency of distraction displays increased. Additionally, adults fed less after their chicks hatched, and adult body mass decreased. Brooding decreased as chicks grew. A number of mechanisms through which disturbance could reduce reproductive success were examined. Disturbance resulted in egg temperatures moving above and below benchmark values, potentially leading to thermal stress in eggs. At least some recorded egg temperatures were potentially lethal. The proportion of abandoned eggs was highest in foredune nests, followed by beach then dune nests. This pattern mirrored the pattern of disruption of incubation by humans between habitats, suggesting thermal stress due to disturbance caused egg mortality. Thermal stress could also kill chicks, and disturbance disrupted brooding. Failure of adults to defend eggs or chicks due to disturbance did not lead to nest or brood failure. Adults defended nests and broods, but predation events were only observed during undisturbed conditions. For broods, foraging time decreased and the level of the habitat used for foraging changed with increasing levels of disturbance. Energetic stress is therefore another potential mechanism that could decrease chick survival. This study uncovered potential mechanisms through which disturbance could decrease hatching and fledging success in Hooded Plovers. Identification of the mechanisms through which disturbance acts, suggests that a management approach that emphasises managing the effect of disturbance rather than the response to it, will be a necessary component of the recovery of this species.
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ItemEcological and physiological studies of Sminthopsis crassicaudata (Marsupialia : Dasyuridae)( 1976)This study aimed to identify the major adaptations enabling a small insectivorous marsupial, Sminthopsis crassicaudata, to inhabit a variety of open grassland and desert environments. A series of integrated investigations of behaviour, reproduction and physiological ecology was carried out. S. crassicaudata displays a "drifting home range" pattern of social organization, there is little evidence of territorial behaviour, and individuals are solitary during breeding but gregarious in autumn and winter. In both arid and comparatively mesic habitats, breeding occurs from late winter until early autumn; there is no evidence that opportunistic breeding takes place in late autumn or early winter. During the breeding season each female attempts to raise two litters; few individuals of either sex breed in more than one season. All these characteristics are interpreted as adaptations to both long-term (seasonal) and short-term variability in food supply. S. crassicaudata can survive without drinking water when fed on a diet of insects. This independence is made possible by the high water content of the food, and not by physiological restriction of water loss as is seen in granivorous desert-dwelling rodents. Similarly, the energy metabolism of S. crassicaudata shows no evidence of specific adaptations to aridity. The apparent physiological specializations - brief diurnal torpor and fat storage - seem to be related to the problem of fluctuation in food supply, and not to aridity as such. Thus the biology of S. crassicaudata is interpreted as reflecting specific adaptation to variability in food supply; this variability seems to be the major problem facing a nocturnal insectivore inhabiting open environments.
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ItemAspects of the reproductive endocrinology of the echidna, Tachyglossus aculeatus( 2000)This thesis investigated some aspects of the reproductive endocrinology the shortbeaked-echidna, Tachyglossus aculeatus. Measurements of seasonal changes in plasma steroid testosterone and corticosteroids were made in captive and free-ranging male echidnas. Non-invasive faecal sampling techniques were developed as an alternative to blood sampling for measuring endocrinological changes in both sexes. This thesis focussed on male reproduction for two reasons. First, it has long been suggested that female echidnas do not breed every year and will enter periods of torpor or inactivity during the breeding season if they are non-breeding (Broom, 1895; Griffiths, 1968; Rismiller, 1992; Rismiller and McKelvey, 1996). Males, however, are generally more active during the breeding season and have been observed to actively seek out females moving from train to train (Rismiller, 1992), thus making them easier subjects for study. Secondly, none of the females used for the blood sampling study were observed to mate or produce young during the course of the study, so making it difficult to adequately describe female reproduction in terms of the changes that occur in plasma concentrations of steroids. (From Abstract)
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ItemPopulation biology and dynamics of the gummy shark (Mustelus antarcticus) harvested off southern Australia( 2010)The aim of the present study was to determine the key parameters describing the population biology and the fishing gear selectivity of gummy shark (Mustelus antarcticus) and to develop three fishery population models that make use of these parameter estimates and available fishery monitoring data. Observational biological data and experimental fishing data were collected during 1973–76, 1986– 87, and 1990–01, and monitoring data on annual catch are available since 1932 and on fishing effort and sex- and length-frequency composition of the catch since 1970. Movement rates among various broad regions of the fishery, estimated using the Integrated Tag Model, are sufficiently low to treat M. antarcticus as several separate stocks across southern Australia for assessment purposes. The sex- and age-structured Stock Assessment Model (main model) consists of a series of equations forming ‘sub-models’, where parameters representing shark growth and reproduction and gillnet and hook selectivity were estimated independently of the model (exogenously) and parameters representing catchability and natural mortality were estimated by the model (endogenously). The model avoids the common assumption of constant annual recruitment and avoids estimating stock-recruitment parameters to incorporate density-dependent population-regulation. Instead, the model calculates the number of births each year determined from the proportion of surviving female sharks in the population breeding annually (expressed as a function of shark length by a logistic equation) and from the number of births per female at each pregnancy (expressed as a function of maternal length by an exponential equation). A ‘u-shaped’ function to vary natural mortality with age over the entire life span of the sharks replaces the usual assumption of constant natural mortality for animals recruited to the exploited phase of the life cycle. This allows natural mortality to decrease rapidly with age during the early ages of life, as the sharks grow and become better able to catch prey and to escape predators, and allows natural mortality to increase during later ages with senescence. In addition, natural mortality varies with stock biomass to allow for density-dependent regulation of the population. Density-dependent natural mortality is the principal mechanism for population regulation in M. antarcticus, evidenced from undetectable decompensation in growth rate and in reproductive rate when measured before and after major changes in population size in response to large changes in fishing mortality. The model provides forward projections of the effects of alternative harvest strategies on stock biomass, recruitment, and catch for each of the two specific regions of Bass Strait and South Australia in southern Australia. Separate estimates of growth parameters for the population of M. antarcticus in Bass Strait during 1973–76, when comparatively lightly fished, and during 1986–87, when heavily fished, indicate a reduction rather than an increase in growth rate, as expected had there been a density-dependent response in growth rate to population depletion. Similarly, estimates of reproductive rates in waters east of longitude 138°E (eastern end of Kangaroo Island) for 1973–76 and 1986–87 indicate a reduction rather than an increase in reproductive rate, as expected had there been a density-dependent response in reproductive rate to population depletion. Consistent with this response, the reproductive rate increased from 1986–87, when heavily fished, to 1998–01, when moderately fished. Hence, if density-dependent changes in growth and reproductive rates occurred in response to changes in population size caused by changes in fishing mortality, then some other stronger offsetting effect, such as the effect of length-selective fishing mortality, must have masked any measurable density-dependent response. Selectivity (expressed as a function of mesh size for gillnets or hook size and of length of shark according to the gamma probability distribution function) markedly affected parameter estimates for growth and reproduction. The von Bertalanffy and Fabens growth equations were reformulated and reparameterised with Francis parameters to provide stochastic frameworks to correct the sampling bias caused by the selectivity of gillnets used to capture the sharks and to represent variation in length-at-age to simulate the effects of length-selective fishing mortality. Comparison of mean length of shark at each age among regions and periods, detection of ‘Rosa Lee’s phenomenon’ from comparing radii of vertebral growth-increment bands among several ages, and application of the Length-Selective Simulation Model provide evidence for the ‘phenomenon of apparent change in growth rate’ caused by high length-selective fishing mortality. The ovarian and parturition cycles are mostly annual to the west, but biennial to the east of Kangaroo Island, although in both these regions, the gestation period is about 1 year and parturition occurs mostly during November– December. The difference in the reproductive cycle between west and east of Kangaroo Island is attributable to environmental differences. Differences in male and female maturity ogives and in maternity ogives among the three data collection periods east of Kangaroo Island, however, are attributed to the ‘phenomenon of apparent change in size-at-maturity’ and the ‘phenomenon of apparent change in size-at-maternity’ caused by length-selective fishing mortality. Mustelus antarcticus predominantly inhabits sandy substrates in depths mostly less than 80 m, with neonates, other juveniles and large females tending to be inshore, but the species does not have well defined nursery areas. The species has a tendency to form aggregations with animals of similar sex and size. Experimental fishing indicated that both gillnets and longlines are much more effective at catching chondrichthyan species than teleost species, and the number of animals caught for species of cephalopoda, bivalvia, gastropoda, mammalia, aves and reptilia are negligible or zero. The effect of gillnet mesh-size on catch rates is strong, whereas the effects of gillnet hanging-ratio, hook size, hook shank-length, and hook spacing are all weak. Because the effects of gillnet mesh-size on catch rates and size of shark caught are strong, it was necessary to develop an appropriate sub-model to express relative selectivity of gillnets as a function of mesh size and of length of shark for inclusion in the Stock Assessment Model. Conversely, because the effects of gillnet hanging-ratio, hook size, hook shank-length, and hook spacing are all weak, these effects do not need to be accounted for in the Stock Assessment Model. Tailoring the models, and where necessary developing new methods to account specifically for the peculiarities of shark biology and for the complexities of highly length-selective fishing gear deployed in the fishery markedly reduced risk associated with uncertainty from the lack of knowledge and has resulted in improved predictive power. There is now high confidence in the stock assessments of M. antarcticus and the fishery is now one of Australia’s most securely managed fisheries. Furthermore, the present study demonstrates that the effects of sampling and, more importantly, of intense fishing using length-selective gear produce various biases in the data and parameter estimation that are likely to occur in many other fisheries. The study also demonstrates that a shark species of medium biological productivity can be harvested sustainably, whereas earlier there were doubts about whether any shark species could be sustainably harvestable.