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Mobile Bay is a dynamic estuary home to a diverse faunal assemblage, which includes several species of batoid fishes (Chondrichthyes: Batoidea). To better understand the dynamics of this batoid assemblage, batoids were opportunistically sampled from 440 trawls performed in and around Mobile Bay from 2016 to 2017. The species Hypanus sabinus and Gymnura lessae were the most common batoids collected (86% of catch). PERMANOVA analysis found the variables day length, location, year, and water temperature best described catch variability. Furthermore, stomach contents from Gymnura lessae were sampled to investigate its diet. Most prey were heavily degraded, thus DNA metabarcoding was used to enhance prey identification. Most prey (88.3%) were from the families Sciaenidae and Engraulidae, and the variables season and sex best explained the dietary variability. These data will be necessary for modeling potential habitat and dietary shifts of Mobile Bay’s batoids as climate change and anthropogenic disturbances alter estuaries.

The purpose of this study was to apply oxygen and carbon stable isotope microsampling techniques to the seasonal banding of the otoliths of the Atlantic cod, Gadus morhu~ in order to determine their potential use in reconstructing the environmental conditions experienced by cod. A reconstruction of the changes in environmental temperature is seen as particularly applicable to the determination of cod migration routes based on the known temperature profile of the North Atlantic. Transverse thin sections of six otoliths from cod taken off the coast of Atlantic Canada were prepared using standard methods. Material was sampled from each semiannual band of the otoliths and run on a Finnigan MAT 251 ratio mass spectrometer to determine 0180 and 013C. The results for 0180 indicated that the otoliths had an approximate initial value of either 1.4%o or l.O%o for sample material taken from the nucleus. The 0180 signal was characterized by oscillating values in which sample material from hyaline bands corresponded predominantly with the troughs and sample material from the opaque bands corresponded with the peaks. The average range of 0180 was found to be 0.87%o corresponding to a temperature range of 3.6°C which was within the expected 3 to 4 °C seasonal average temperature shift experienced by cod. Seasonal cycling was apparent in three of the otoliths, with semi-annual values alternating between high opaque bands and low hyaline bands. It was concluded that seasonal temperature changes due to migration from offshore to inshore waters are recorded in the 0180 signal and that future sampling should attempt to resolve several samples within each seasonal band in order to resolve the migratory changes in temperature on an sub-annual basis. It is also suggested that experiments be carried out to determine the species specific 0180 versus temperature relationship for cod to make accurate interpretation of the data possible. The o13C signal was found to be characterized by an increasing logarithmic trend in o13C. The 013C signal was observed to increase over the first three years of growth and to level off at age 4 and fluctuate at a value close to O%o. The otoliths of cod were found to contain a high proportion of inorganic carbon with a minimum 013C value of -4.53%o and a maximum of 0.23%o. It was suggested that the initial increase in 013C was a product of a combination of factors affecting metabolic rate and therefore, indirectly, the amount of metabolically derived carbon circulating in the blood. It was concluded that further research into the growth and development of cod was necessary in order to reach a comprehensive understanding of the biological processes responsible for the observed trends in 013C. 0180 was plotted against 013C for samples from growth bands of age four or greater and found to have a positive correlation with a slope of 0.269 (S.E. 0.049) and an r-squared of 0.537, P < 0.0001 when the results for otolith 176 were excluded due an anomalous trend in that data set. Two hypotheses were suggested to account for the observed positive correlation, a metabolic/temperature effect, and a depth/temperature effect. It was concluded that, with further research into the controlling factors behind the fluctuations in 013C, the 013C signal may provide a second source of information with regards to changes in habitat and environmental characteristics over the life time of the cod. It is suggested that a study be carried out to determine the amount of metabolic carbon incorporated into the otolith in order to clarify the observed trends. / Thesis / Candidate in Philosophy

The otolith organs are housed in the inner ear and are responsible for sensing accelerations and gravity. These inertial sensing systems are modeled in this thesis as a three material system consisting of a rigid otoconial plate attached to the skull by a gel layer, surrounded by a viscous endolymph fluid. The gel layer is considered to be a viscoelastic solid, and modeled as a simple Kelvin element. The governing differential equations are derived and nondimensionalized, yielding three nondimensional parameters: nondimensional density, R, nondimensional viscosity, M, and nondimensional elasticity, 6. The equations are solved using uÌ nite difference techniques on a digital computer. By comparing the modelâ s response with previous biological research, values for the nondimensional parameters are found. The value of R is 0.75 and the value of 6 is between 0.3 and 0.075. While the value of M is placed between 5. and 10., results indicate that to properly model the long time response of the otolith, a single and constant value for viscosity is not feasible. / Master of Science

published_or_final_version / abstract / Physiology / Doctoral / Doctor of Philosophy

published_or_final_version / Physiology / Doctoral / Doctor of Philosophy

Otoliths are stone-like structures in the inner ear of fish that play a crucial role in fish hearing. The original object of this research was to determine if any rocking motion was present in an otolith suspended in tissue phantom when subjected to a plane acoustic wave. Measuring the motion of an actual otolith proved to be beyond the limits of project's resources, so an aluminum hemisphere suspended in water was studied instead. The hemisphere was chosen because it was the easiest shape to measure accurately, had the asymmetry necessary to investigate the relevant physics, and had been the subject of some theoretical modeling. A plane standing wave was generated in a short open ended thick-walled cylindrical-waveguide with the waveguide's axis perpendicular to the symmetry axis of the hemisphere. Measurements were taken along the hemisphere from top to bottom to determine if any rocking actually occurred. The expected vertical vibrational motion and symmetry-forbidden horizontal vibrational motion were also measured. The horizontal displacement of the hemisphere at each point was determined by using an ultrasonic vibrometer. The vertical motion was measured using alternative other sensors and methods, such as an accelerometer and Laser Doppler Vibrometer (LDV). The results from this experiment showed a small amount of rocking, but less than predicted. The vertical motion was around ten times greater in magnitude than the rocking motion at the edge, where it is largest. Additional follow-up experiments were then conducted to determine if any experimental artifacts, such as position in the tank and method of mounting, contributed to the overall result. Additional testing was then done on a series of semicircular cylinders to determine if their motion matched theoretical predictions. In this case, rocking was also present and was found to be on the order of the motion of the hemispheres. This motion was found to be smaller than published theoretical results. These results can ultimately be used to predict and understand the motion of more complex geometries, like otoliths.

published_or_final_version / Physiology / Master / Master of Philosophy

I use microchemistry in fish otoliths to test the hypothesis that diverting Colorado River flow from reaching the Gulf of California has impacted two endemic fish: the threatened gulf Corvina, (Cynoscion othonopterus) and the endangered totoaba (Totoaba macdonaldi). The oxygen and carbon stable isotope ratios in otoliths help to reconstruct conditions of the environment during key life history stages before and after the damming and diverting the Colorado River. The δ¹⁸O in otoliths illustrate that both C. othonopterus and T. macdonaldi seek out brackish habitat provided by the Colorado River during their early life history. The δ¹⁸O of C. othonopterus otolith have a strong negative correlation with Colorado River flow. I found that previously published relationships between otolith δ¹⁸O and ambient temperature along with δ¹⁸O of the water are sufficient to predict ranges of expected δ¹⁸O values for T. macdonaldi in the field. The δ¹⁸O in pre-dam T. macdonaldi otoliths show significant divergence from modern T. macdonaldi otoliths’ values, indicating that these fish used the brackish waters of the Colorado River estuary. The δ¹³C in T. macdonaldi otoliths has a significant proportion of its δ¹³C derived from diet. Pre-dam T. macdonaldi juveniles have a significantly different diet, which reflects that the Colorado River estuary had higher productivity before diversion of the river. Lastly, T. macdonaldi grew faster before the dams and in association with Colorado River flow measured by the δ¹⁸O.

Capelin is an important forage fish species in the Northwest Atlantic and the primary prey species of many top predators. Capelin undergo extensive inshore migrations (> 350 km) to coastal spawning grounds in the spring where the timing of inshore arrival is highly variable. I investigated the influence of intrinsic factors and proxies for extrinsic factors on the timing of arrival of capelin at spawning sites on the northeast coast of Newfoundland (2012 and 2013). Despite high inter-annual variation in almost all factors examined, intrinsic factors, specifically length and age, consistently varied with timing of arrival at spawning sites for both males and females, unlike proxies for extrinsic factors. These results are important for the management of this critical fish species, as selective harvesting by the capelin fishery of early-arriving fish may impact the age/size structure of the population, recruitment, and result in increased variability in the timing of spawning.