Infrastructure Engineering - Theses
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ItemLinking freshwater flows, salt wedge dynamics and black bream dispersal in the Mitchell River sub-estuary( 2014)For fish species with a planktonic larval stage, transport from the spawning ground to juvenile habitat is a critical aspect of their life history. While certain physicochemical features of the upper estuary, such as the estuarine turbidity maximum, are beneficial to larval survival, dispersal of larvae to suitable recruitment habitat is also important. This dispersal process is influenced by hydrodynamics, egg buoyancy, and larval behaviour. In estuaries, especially where strong stratification is present, variation in currents may occur over scales of centimetres to metres. Vertical variation in salinity can cause large current variations over short vertical distances. For small organisms in aquatic environments, hydrodynamics provides a large physical influence on their transport. Larvae, however, are not passive particles and may behave in ways which alter their location in the water column. The dominant research paradigm frames behaviour as an important feature in determining larval dispersal patterns, despite the magnitude of hydrodynamic influences. This study examines the balance between hydrodynamics and larval behaviour in determining the dispersal patterns of larvae of black bream (Acanthopagrus butcheri), an estuarine dependent species endemic to southern Australia. The study utilises a biophysical modelling approach, informed by empirical studies in both the field and the laboratory, to explore the dispersal of black bream larvae in the Mitchell River sub-estuary, part of the Gippsland Lakes in South-eastern Australia. The thesis begins with a review of literature in the field of biophysical modelling of fish early life history, noting that data assimilation and the integration of empirical data collection and modelling are growing needs. The importance of collecting species-relevant data on the ontogeny of behaviour is also highlighted. The literature review is followed by an empirical field study, which identified the Mitchell River sub-estuary as a micro-tidal system with an extensive salt-wedge that varied with river flow, and extended from the river mouth up to 18 km upstream. Average flows during the spawning season range from around 15 to 55 m3/s, and a flow of approximately 50 m3/s was required to flush the salt wedge from the river. The water column exhibited large vertical salinity stratification, even at flows up to 40 m3/s. Pronounced velocity variation was observed between parcels of water above and below the halocline. The field data also provided observations against which to calibrate and validate the hydrodynamic component of the biophysical model. Next, the thesis documents the development of a vertically layered finite difference hydrodynamic model with baroclinic salinity for the Mitchell River sub-estuary. This model was validated using physicochemical observations. For computational efficiency, a one-cell wide straightened river bathymetry was adopted. The model captured spatio-temporal variation in water level, salinity and velocity in the longitudinal and vertical dimensions. A laboratory study of individual-level behaviours in larval black bream is reported next. In the laboratory black bream larvae were observed to increase in critical swimming speed with size up to a maximum of approximately 0.2 m/s for larvae around 1 cm in length. This is at the higher end of observed critical swimming speeds for larvae of marine demersal fishes, and is above velocities observed beneath the halocline in the Mitchell River sub-estuary. A baroclinic response was observed in late-stage larvae which were bottom associated until depths increased beyond 6 m. Young larvae were surface attracted, but were found significantly deeper in the presence of a halocline than in a homogeneous salinity water column. These observations provided individual-level data to inform a biophysical model of black bream eggs and larvae in the Mitchell. The thesis then details the development of numerical Lagrangian particle modelling software, incorporating modules for the inclusion of behaviours in response to salinity, depth, the presence of a halocline, and positive rheotaxis. A sensitivity analysis of each of the behavioural modules found that retention of particles within the model was more sensitive to the choice of behaviours influencing vertical position of particles than those influencing horizontal position. Results of the sensitivity analysis varied depending on whether the model was forced with high or low flow rates. Finally, using the biophysical model as a virtual laboratory, a series of virtual experiments are described. Longitudinal spawning location was found to be critical to retention of larvae within the sub-estuary. A pattern-oriented modelling approach determined that a biophysical model structure including egg buoyancy but no larval behaviour best explained empirical patterns of black bream egg and larval dispersal in the Mitchell River sub-estuary. This is in contrast to the findings from the laboratory study that black bream exhibit dispersal-relevant behaviour. In conclusion, this study, focussed on the development of a biophysical model, found that estuarine circulation in the Mitchell River sub-estuary provides a greater influence on the dispersal outcomes of black bream eggs and larvae than active behaviours exhibited by the larvae. Biophysical modelling techniques have been successfully applied in a morphologically and hydrodynamically complex system, however there remains scope for improvement, particularly through the use of a hydrodynamic model with a more flexible spatial discretisation to better resolve the estuarine bathymetry. Additionally, the extension of this modelling framework to other estuaries in southern Australia could reveal whether the findings of this study can be generalised to other estuaries which black bream inhabit.