Theses
Permanent URI for this collectionhttps://hdl.handle.net/1969.6/1140
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Browsing Theses by Department "Fisheries and Mariculture"
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Item Linking shape to substance: Exploring morphometrics and geochemical records in eastern oyster shells from subtropical estuarine systems(2023-08) Randall, Jessica; Walther, Benjamin; Pollack, Jennifer; Bahr, KeishaThis study aimed to investigate the resilience of eastern oysters (Crassostrea virginica) exposed to environmental stressors such as droughts and floods. The primary objectives were to assess the potential of geochemical records within oyster shells to discern past environmental variability and to evaluate the growth performance of these oysters in dynamic, subtropical estuarine systems subject to these major climactic events. Eastern oysters have been established as reliable bioindicators of water quality and records of their native habitats. Previous studies utilizing stable isotopes (?13C and ?18O) to track freshwater inflow patterns faced challenges due to multiple covarying factors. This study employed Ba/Ca ratios as an alternative proxy and examined their relationship with salinity. Notably, shell ?13C values demonstrated a remarkable match with estimated salinity values, highlighting the usefulness of this chemical proxy alone or in combination with ?18O for similar investigations. Despite their resilience, oyster growth performance can be adversely affected by environmental disturbances. Oysters from low, fluctuating salinity environments exhibited the greatest shell growth, followed by those inhabiting intermediate, then high, stable salinity environments. Which suggests that freshwater inflows following flood events positively influence estuarine functioning and oyster health, likely due to increased water turbidity, food availability, and reduced susceptibility to predation and disease. With projections of drier climates and variable precipitation patterns leading to more extreme temperature and salinity levels, eastern oysters may face greater growth limitations in the future. Therefore, understanding how environmental disturbances, including freshwater inflow dynamics, differentially impact oyster growth is crucial for the management and protection of this increasingly vulnerable keystone species.Item Whole genome sequencing century-old ethanol-preserved Philippine fishes(2023-08) Roberts, Roy Lonnie; Bird, Christopher; Seemann, Frauke; Portnoy, DavidThe genomes of organisms stored in museums hold a wealth of information that is challenging to access. Recent success in sequencing desiccated museum insects involved using Whole Genome Amplification (WGA) and enzymatic repair of deoxyribose nucleic acid (DNA) damage. However, these techniques have not been tested on fishes preserved in ethanol for over a century. Here, I tested for the effects of WGA, repair, and the amount of template DNA on whole genome sequencing of historical (1908-09) and contemporary (2017-19) Philippine reef fishes. I attempted to construct 178 shotgun libraries (Illumina 2 x 150bp, 92 contemporary, 86 historical) using commercial kits and successfully produced 130 libraries (86 contemporary, 44 historical). Contrary to expectation, WGA had a negative effect on success of libraries, and repair had a small number of minor positive effects. A greater proportion of historical libraries treated with WGA failed than those that were not (37% +WGA, 65% -WGA, p=0.007). While the -WGA, historical libraries that succeeded produced less reads per unit effort than contemporary libraries (p=1.60E-07), this can be addressed by increasing the amount of DNA from historical specimens in the sequencing library. Increasing the template DNA mass was one of the best ways to improve library success, except when WGA was employed. However, only a limited amount of DNA can be obtained from historical samples using a standard commercial kit, and it would be useful to explore alternative protocols. Overall, I found the basic library preparation protocol without WGA or repair to be the best alternative for sequencing historical ethanol-preserved fish. This methodology is relatively cost-effective and can unlock the genomes of historical, ethanol-preserved fishes stored on the shelves of museums.