Marine Biology Commons^™

Population Genomics, Ecology And Conservation Of Asterias Sea Stars In The North Atlantic, Melenia I. Giakoumis

Dissertations, Theses, and Capstone Projects

Uncovering how species respond to environmental change is a central question in biology (Ehrlén & Morris 2015; Habibullah et al. 2022). It is the key to elucidating the past, understanding the present and predicting the future of species’ population dynamics. This dissertation investigates the influence of environmental change on intertidal species’ distributions and genomics at several timescales, with implications for conservation.

Environmental changes have occurred throughout history, on a geological scale, and have shaped the global patterns of species’ distributions and population sizes. Biologists have long studied how geological history has shaped species distributions (Sanmartín 2012) in both terrestrial (Liu …

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

Characterizing Endogenous Dicer Products To Unravel Novel Rnai Biogenesis Pathways, Jacob Oche Peter

Dissertations

ABSTRACT

RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms …

Phylogenetic And Geographic Relationships Of Cheilostome Bryozoans In The Eastern Pacific, Hannah E. Lee

Cal Poly Humboldt theses and projects

The phylum Bryozoa is an incredibly diverse group of marine invertebrates with a widespread global distribution that is well suited for evolutionary studies but whose phylogenetic relationships are still poorly understood. Although recent studies on bryozoan taxonomies and phylogenies have increased, there is still a lack of assessment of species found at shallow water (<1 m) to intertidal depths. In this study, I aimed to expand the taxonomic sampling and assessment of the phylogenetic diversity of cheilostome bryozoans along the California coastline by utilizing mitochondrial DNA as well as inferring potential correlations between species presence and dispersal range both within and between rocky outer coast and sheltered harbor habitats. Illumina high-throughput sequencing was used to produce mitogenomes for cheilostome bryozoan samples collected off rocks from two rocky intertidal sites and off settlement panels from two harbor sites. Phylogenetic analyses generated evolutionary hypotheses of species relationships alongside geographic mapping of their distribution. This study identified 15 distinct species that represent 10 different families to form the first comprehensive phylogeny for multiple bryozoan families in California across a total range of approximately 973 km of coastline. Three genetically distinct species were found at multiple sites that are separated by a combination of rocky shores and sandy beaches, which indicates that the dispersal range of these species are not limited by geographic barriers along the coast of California. These results provide a future opportunity for further integration of this data with the phylogenies generated in this study to examine more robust evolutionary hypotheses for the phylogenetic and geographic relationships of Californian bryozoan species.

An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy

UNF Graduate Theses and Dissertations

Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and F_ST data indicated the boundary of the area of …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Comparative Genomics Methods And Applications, Emily N. Alden

Biomedical Sciences ETDs

Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the …

From Phocine Distemper To Avian Influenza: A Study Of Immunogenetic Diversity In Two Sympatric Pinniped Species, Alayna K. Gigliotti

Electronic Theses and Dissertations

Gray (Halichoerus grypus) and harbor (Phoca vitulina) seals are sympatric species that inhabit the North Atlantic and have been subject to mortality events from disease outbreaks, particularly phocine distemper and avian influenza virus. Across mortality events, gray seals tend to exhibit a higher survival rate, which could be explained by various ecological factors impacting rates or direction of selection in parts of the genome related to the immune system. These factors could include haul-out site density, habitat, and degree of inter/intraspecies interaction. This research aims to compare genetic diversity within the Major Histocompatibility Complex (MHC) class …

Linking Crude Oil And Dispersant Effects To Gene Expression Of Marine Sponge Cinachyrella, Yvain Desplat

All HCAS Student Capstones, Theses, and Dissertations

Because of their filter-feeding lifestyle, sponges (Phylum Porifera) have shown to be bio-accumulators of heavy metals, and bio-monitors for polychlorobiphenyl (PCB) contaminants. Furthermore, marine sponges have been shown to be regulators of reef ecosystems by fulfilling many ecological functions. However, very little is known about their behavior in the face of environmental changes. Consequently, our lab has developed the reef sponge Cinachyrella spp. as novel experimental model. We have designed an experiment to study the effects of WAF (Water Accommodated Fraction), Corexit 9500 dispersant, and CE-WAF (Chemically Enhanced Water Accommodated Fraction)mixtures, in an effort to mimic the conditions of the …

Natural Variation And Evolutionary Responses To Climate Change Stressors In Marine Invertebrates, Joanna Sarah Griffiths

LSU Doctoral Dissertations

Our rapidly changing climate is putting many species at risk of extinction and there is an urgent need to understand how species will respond to these changes. In this dissertation, I evaluate how three species of marine invertebrates (corals, oysters, and copepods) respond to stressful conditions in their current environments and how plasticity and evolutionary adaptation could alter their response to future climate change stressors. I first employed a space for time study to elucidate population differences in the response of cold-water corals, Balanophyllia elegans, to future ocean acidification. I found evidence that upwelling history (natural low pH exposure) influences …

Characterization Of Bacterial Communities In Biscayne Bay Through Genomic Analysis, Eric Fortman

HCNSO Student Theses and Dissertations

Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. This study examined the bacterial community at 14 stations throughout Biscayne Bay —6 stations were located at the mouths of canals; 1 upstream-canal station; 6 stations in the center of the bay; and one ocean influenced station, located near the entrance to the bay. One liter, surface water samples were …

Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani

HCNSO Student Theses and Dissertations

Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …

Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto

Electronic Theses and Dissertations

Anthropogenic carbon released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world’s oceans, most prominently in northern latitudes. The geographic range of the iconic American lobster (Homarus americanus) spans a steep thermal gradient and one of the most rapidly warming oceanic environments. Understanding the interactive effects of ocean warming and acidification on this species’ most vulnerable early life stages is important to predict its response to climate change on a stage-specific and population level. This study compares the responses of lobster larvae from two sub-populations spanning New England’s north-south temperature gradient (southern …

Characterization Of The Bioluminescent Symbionts From Ceratioids Collected In The Gulf Of Mexico, Lindsay L. Freed

HCNSO Student Theses and Dissertations

Anglerfishes are easily one of the most popular deep-sea creatures due to their menacing appearance, extreme sexual dimorphism, parasitic mating approach, and eye catching bioluminescent lure. Unlike most bioluminescent fishes, which intrinsically generate light, female anglerfishes belonging to nine of the 11 families within the suborder Ceratioidei (deep-sea anglerfishes) have developed a symbiotic relationship with bioluminescent bacteria that are housed within the light organs. Previous molecular work had identified symbionts from two anglerfish species as novel and possibly unculturable taxa (Haygood et al., 1992), but nothing more has been revealed about the bioluminecent symbionts of ceratioids. As part of …

Convergent Evolution Of Biochemical Innovations In Polychaetes: Characterizing The Molecular Basis Of Bioluminescence And Venom Production, Aida E. Verdes Gorín

Dissertations, Theses, and Capstone Projects

The convergent evolution of phenotypic traits is a widespread phenomenon across the tree of life and is explained as the outcome of different taxa facing similar selective forces or environmental conditions. A longstanding question in evolutionary biology is whether the evolution of convergent phenotypes in unrelated lineages is driven by similar or different molecular processes. The research presented here investigates this question by characterizing the molecular basis of two biochemical innovations, bioluminescence and venom production, that have evolved independently in different lineages of polychaetes worms (Annelida). We use an integrative approach, combining next-generation sequencing, phylogenetics and computational tools to evaluate …

Nuclear Genome Size Diversity Of Marine Invertebrate Taxa Using Flow Cytometric Analysis, Kyle Roebuck

HCNSO Student Theses and Dissertations

Genomic analysis provides a substantial amount of information on evolutionary history, novel genes, transcriptomic expression and regulation in response to environmental stimuli, how efficiently organisms utilize their genome, and directional genome evolution. Genome size analysis serves as the first step in the sequencing process, because sequencing and annotation costs are directly correlated with genome size. Invertebrates represent the vast majority of faunal diversity on the planet, and, to a greater extent, the marine environment, although they are vastly understudied when compared to vertebrate genomes. Flow cytometry is a widely used, reliable, and accurate means of estimating genome sizes and has …

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer

Doctoral Dissertations

The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including …

Multi-Stress Proteomics: The Global Protein Response To Multiple Environmental Stressors In The Porcelain Crab Petrolisthes Cinctipes, Michael A. Garland

Master's Theses

Global climate change is increasing the number of hot days along the California coast as well as increasing the incidence of off-shore upwelling events that lower the pH of intertidal seawater; thus, intertidal organisms are experiencing an increase in more than one stress simultaneously. This study seeks to characterize the global protein response of the eurythermal porcelain crab Petrolisthes cinctipes to changes in thermal, pH, and tidal regime treatments, either combined or individually. The first experiment examined temperature stress alone and sought to determine the effect of chronic temperature acclimation on the acute heat shock response. We compared the proteomic …

Bridging Functional Genomics And Toxicogenomics Through Dna Microarrays In A Fish Model, Shuzhao Li

Dissertations

In a case study of finding gene expression signatures for environmental stressors in Cyprinodon variegatus, this dissertation examines several important issues of applying DNA microarray technology to fish toxicogenomics. The most relevant disciplines, fish toxicogenomics and computational systems biology are reviewed in Chapter 1. Chapter 2 reviews major aspects of DNA microarray technology.

On DNA microarrays, even for probes that target the same transcript, large variations are seen in the probe signals. These variations are partly dependent and partly independent on probe sequences. Chapter 3 estimates the sequence independent variation by combining experimental and computational approaches. Chapter 4 and …