Although DNA repair capacity has been correlated with lifespan in terrestrial vertebrate species, it remains unknown how evolutionarily conserved the process is across all vertebrate taxa. In particular, chondrichthyan fishes have lifespans that range from 3-350 years and they are evolutionarily separated from modern humans Homo sapiens by approximately 400 million years. We hypothesized that chondrichthyan fishes would show significant homology in nuclear excision repair (NER) genes with humans, and that the expression of NER genes will correlate with the lifespan of the respective assessed species. For this study, DNA repair gene homology and expression was performed on the nurse shark Ginglymostoma cirratum (n=3) and yellow stingray Urobatis jamaicensis (n=3). The five main NER pathways were analyzed and compared to see the differences in both elasmobranch species, then compared with human foreskin fibroblast samples (n=3). RNA sequencing was used to determine the extent of gene expression in each species, comparing the read counts in each gene and comparing between the two species. The elephant shark Callorhinchus milii reference genome was used to align the nurse shark and yellow stingray samples. Homology of each gene of the NER pathways was assessed by the NCBI BLAST software. Results show that the MMR pathway has all the significant genes in higher frequencies in the nurse shark than in human. Within elasmobranchs in the five DNA repair pathways, the longer-lived species (nurse shark) has a significant higher gene expression than shorter-lived species (yellow stingray). Genes involved in the NER and BER pathways showed significantly lower expression in elasmobranch than in humans. However, there were significantly higher expression of more genes for the HR and MMR pathways in elasmobranchs than in humans.

Title from PDF of title page. / Document formatted into pages; contains 89 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The ability of an organism to modulate its feeding behavior is an important focus of feeding ecology studies. Modulation is the ability to distinctly and consistently alter a behavior to accommodate different stimuli. The goal of this study was to examine the ability of the nurse shark Ginglymostoma cirratum to modulate its food capture behavior with different sizes and types of food items. This was carried out through kinematic and electromyographic analysis. Eight sub-adult specimens of G. cirratum were filmed feeding on two different food types (squid and fish) and sizes (gape size and larger than gape size). Filming consisted of high-speed videography utilizing a low-light digital video system. Kinematic variables related to lower jaw movement, mouth width, and head angle were measured from video footage. Up to twelve muscles in each of six specimens were implanted with bipolar electrodes to measure the onset and duration of motor activity. / ABSTRACT: There were no significant differences between food sizes and any of the kinematic variables. Only two muscles showed significant differences in onset time based on food size. In regards to food types, squid bites were significantly faster than fish bites, but when examined proportionately to bite duration only the time to jaw closure remained significantly different. The motor pattern of G. cirratum demonstrates an anterior to posterior sequence, which corresponds to the anterior to posterior kinematic sequence. Little cranial elevation is present during feeding sequences and is not thought to contribute significantly to feeding. Ginglymostoma cirratum is a stereotyped, inertial suction feeder. There is little evidence that there is modulation in feeding behavior based on food size or food type. If modulation does exist in the feeding behavior, it is more likely to occur after prey capture while the prey is being processed and manipulated prior to transport. / ABSTRACT: Initial observations suggested that a novel behavior termed 'spit-suck manipulation' is utilized for larger prey items. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

The instantaneous mortality rate (M) is an important parameter in elasmobranch management and conservation, but is difficult to estimate directly. Thus, indirect estimates based on relatively easily obtained life history parameters are commonly used. Many indirect methods incorporate one or more parameters from the von Bertalanffy growth model (VBGM), which is often criticized for its inability to describe changes in growth associated with maturity. The Lester growth model (LGM) is a biphasic alternative to the VBGM that incorporates trade-offs between reproduction, growth, and survival, and may therefore more accurately estimate M. I used published data from 29 elasmobranch species to compare the performance of the LGM to four conventional growth models and nine conventional methods for indirectly estimating M. For three species (Heterodontus portusjacksoni, Rhizoprionodon taylori, and Carcharhinus limbatus), I obtained direct estimates of M to evaluate the accuracy of indirect M methods. According to AICc, the LGM was the best fitting model for 80.8% of datasets. Using one-sample t-tests, I found that five indirect M methods (two of which are dependent on the LGM) consistently generated estimates of M that were in close agreement with direct estimates. The most common methods in elasmobranch literature appear to be overestimating M by factors of 1.34 – 1.91. However, further research is needed to verify these results across a wider range of species. Overall, I recommend using the LGM to describe the lifetime growth of sharks, and estimating M by averaging across five indirect methods.

The deep-sea is the largest habitat on earth, containing over 90 percent of the world’s oceans and home to over 20,000 species. Deep-sea ecosystems are increasingly impacted by human activities including fishing and oil extraction. To understand potential impacts on deep-sea food webs, it is crucial to gather baseline data in these systems. I quantified the trophic interactions of three groups of deep-water animals across a range of trophic levels living in the northern and eastern Gulf of Mexico using stable isotope analysis. First, I propose methods for correcting δ15N values for the presence of nitrogenous metabolic waste products (e.g., urea) in muscle tissue using chemical extractions and/or species-specific mathematical normalizations. Significant differences in δ15N, %N, and C:N values as a result of extractions were observed in eight of ten shark and all three hagfish species. The δ15N values increased, but shifts in %N and C:N values were not unidirectional. Mathematical normalizations for δ15N values were successfully created for four shark and two hagfish species. I then describe the trophic interactions of three consumer assemblages. Carbon isotopic values indicate a heavy reliance on allochthonous nutrient inputs from surface waters. Nitrogen isotopic values reveal somewhat atypical taxa as top predators in the deep sea. Shark, teleost, and invertebrate species across a wide range of body sizes are feeding at a similar trophic level. This apparent lack of size structuring could be the result of a high degree of opportunistic scavenging or perhaps feeding at many trophic levels simultaneously in an oligotrophic system. There was a high degree of isotopic niche overlap among species within each consumer assemblage, perhaps the result of limited nutrient resources in the deep-sea. In general, individuals from the northern sampling stations displayed higher δ13C and δ15N values than those from the eastern sites. With the exception of a few species, there were no strong relationships between body size and isotopic values. The present study is among the first characterizations of the trophic structure of deep-sea organisms in the Gulf of Mexico and establishes system baselines for future studies describing deep-water systems and investigating anthropogenic impacts.

Conservation of elasmobranch populations is often inhibited by a lack of data, particularly in understudied regions like the Red Sea. Survey efforts in this region have been infrequent and often highly localized. Establishing a broad baseline for elasmobranch diversity and abundance along the Saudi Arabian Red Sea coast could inform both conservation efforts and a nascent ecotourism industry. In this thesis, I describe a pilot study comparing biodiversity data from baited remote underwater video stations (BRUVS), unoccupied aerial vehicle surveys (UAVs), and eDNA sequencing at five islands in the Farasan Banks region of the Saudi Arabian Red Sea. Estimates of relative abundance were also compared between the BRUVS and UAVs. Each method identified species missed by the other two, but all three techniques exhibited clear habitat- and taxa-specific biases. I was able to identify key concerns for each approach that need to be addressed before large-scale implementation. If carefully planned and executed well, a full assessment of the Saudi Arabian coastline could establish a true baseline for shallow water elasmobranchs in the eastern Red Sea. Informing best conservation practices and identifying potential ecological attractions in accordance the environmental and economic goals of Saudi Arabia’s Vision 2030.

Vitellogenin (Vtg) is a precursor to yolk-proteins produced in the liver of many invertebrates and non-mammalian vertebrates; its synthesis is stimulated by the hormone estradiol (E2). This study is the first to characterize vitellogenin synthesis in a placental viviparous elasmobranch, the yolk-sac placental bonnethead shark, Sphyrna tiburo. This study focused on determining where and when Vtg is produced, as well as what hormonal factors regulate Vtg production. The liver was confirmed as the site of Vtg production via immunohistochemistry. Immunoreactivity was also observed within granulosa cells of ovarian follicles; further experimentation is needed to determine if this is indicative of Vtg production by these cells. Using immunoblotting, the highest proportions of Vtg positive females were found in March, with Vtg production continuing into April and May. Putative Vtg production was found to begin in August for some individuals, with production continuing throughout the fall and winter months. In regards to hormonal regulation, immunohistochemical analysis identified receptors for E2 and progesterone (P4) within the liver. Comparison of the monthly E2 and Vtg cycles provides evidence that E2 stimulates Vtg production in S. tiburo, as high or increasing concentrations of E2 correlated with Vtg presence in the plasma. Preliminary results also suggest in vitro production of Vtg by liver tissue when exposed to E2. Comparison of the monthly P4 and Vtg cycles suggests P4 may inhibit Vtg synthesis, with higher levels of P4 found in the months when Vtg production declines. Additionally, the methods developed for this study were able to identify Vtg in the plasma of other elasmobranch species. Vtg detection in plasma may thus be an ideal new, nonlethal method for characterizing elasmobranch reproductive periodicity, which will aid in assessing population growth and allow for managers to possess more accurate information to make appropriate decisions for the populations.

A pesca de fauna acompanhante, o âbycatchâ, pode ser considerada uma das maiores ameaÃas à vida nos oceanos. A influÃncia das capturas de fauna acompanhante nos ecossistemas marinhos faz com que esta seja uma das questÃes de conservaÃÃo da natureza mais importantes atualmente. Por vÃrias dÃcadas existiu na costa de Fortaleza uma intensa atividade da pesca de arrasto de camarÃo, que acidentalmente capturava raias, com o uso de embarcaÃÃes motorizadas. Tal atividade foi proibida a partir de 2003, pela Portaria no 35 do MinistÃrio do Meio Ambiente (Instituto do Meio Ambiente e dos Recursos Naturais RenovÃveis). O objetivo do presente estudo foi avaliar se a proibiÃÃo da pesca de arrasto de camarÃo utilizando-se embarcaÃÃes motorizadas em Ãreas costeiras (1) afeta a abundÃncia de raias demersais; (2) que parcela das populaÃÃes dessas raias està sujeita ao efeito da proibiÃÃo da referida atividade pesqueira; (3) se espÃcies consideradas pela LegislaÃÃo Brasileira atual como sob algum grau de ameaÃa tambÃm sÃo afetadas por esta proibiÃÃo. No presente estudo, foram realizadas 14 amostragens cientÃficas na enseada do Mucuripe, Fortaleza/CE, entre setembro de 2004 e novembro de 2010, cada uma com 10 arrastos de fundo a cerca de 14 m de profundidade, utilizando rede de arrasto-de-portas. Foram ainda, compilados dados nÃo publicados de abundÃncia de raias capturadas como fauna acompanhante da pesca de arrasto de camarÃo, utilizando-se embarcaÃÃo motorizada, na enseada do Mucuripe, entre 1997 e 1998. A proibiÃÃo da pesca de arrasto de camarÃo utilizando-se embarcaÃÃes motorizadas, em Ãreas costeiras, afeta positivamente a abundÃncia de raias demersais previamente impactadas por essa atividade. AlÃm disso, Ãrea costeira investigada abriga todas as classes de tamanho das raias Dasyatis guttata e Gymnura micrura e portanto pode ser considerada uma Ãrea importante para a reproduÃÃo destas espÃcies. Por fim, essa mesma Ãrea abriga, ainda, diversas espÃcies consideradas pela LegislaÃÃo Brasileira atual como ameaÃadas (n=4) ou sobreexplotadas ou ameaÃadas de sobreexplotaÃÃo (n=7). / Bycatch fisheries may be considered one of the greatest threats to marine life. The influence of these captures in marine ecosystems makes it one of the most pressing issues on nature conservation today. For decades, there was in Fortaleza, CE, a shrimp otter trawl fisheries activity conducted by motorized boats that accidently captured batoids. This activity has been prohibited by the Brazilian Ministry of Environment since 2003. The goal of the present study was to evaluate if the prohibition of shrimp otter trawl fisheries activity conducted by motorized boats on coastal areas (1) affects the abundance of demersal batoids; (2) which portion of these batoidsâ populations is under the effect of the prohibition of this fishery activity; and (3) if species considered by the current Brazilian legislation as under any level of threat also are effected by this prohibition. In the present study, fourteen scientific sampling were carried out on Mucuripe Bay, Fortaleza, CE, between September 2004 and November 2010. During each survey, 10 stations were sampled with otter trawl net, circa 14 m depth. In addition, unpublished data on the abundance of batoids captured as bycatch by shrimp fisheries in this same bay, between 1997 and 1998, were compiled. The prohibition of the shrimp fisheries using motorized boats, in coastal areas, affects positively the abundance of demersal batoids previously impacted by this activity. Furthermore, the coastal area studied is used by all size classes of the batoids Dasyatis guttata and Gymnura micrura and, therefore, it may be considered important for reproduction of these species. Lastly, this same Bay is also home for several species that currently are considered by the Brazilian legislation as endangered (n=4) or overexploited or threatened of overexploitation (n=7).

This study examined mercury and methylmercury concentrations in shark species in order to determine differences between shark species and between locations. Stable isotope ratios were determined to see if interaction existed between approximate trophic level and mercury concentrations. Sharks were sampled from Florida Bay where muscle tissue biopsies and blood samples were extracted upon capture. Stable isotope ratios for carbon-13 (δ13C) and nitrogen-15 (δ15N) from freezedried blood samples were compared with levels of organic and inorganic mercury species from tissue samples in seven different shark species, focusing on blacknose, blacktip, bull, and lemon sharks. Pre-caudal length (PCL) was strongly correlated to mercury concentration and δ13C but not with δ15N. Ratios of δ15N between shark species were in agreement with observed trophic-level behavior of blacktip sharks feeding on blacknose sharks, indicated by greater values for δ15N ratios in blacktip sharks. Calculated length-normalized stable isotope ratio values correlated strongly to values for mercury concentrations in blacktip sharks, indicating a potential method for forecasting inorganic or organic mercury concentrations without the use of more expensive mercury tests. This calculation also provided validity for a new metric involving the use of stable carbon isotope ratio divided by length (PCL) to be compared with other metrics. Correlations between δ15N values and mercury values indicate some level of interaction between trophic level and quantity of mercury contaminants in shark muscle tissue.

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome characterization in a shark (Doane et al., 2017; skin microbiome of the common thresher shark). A comparative characterization of microbiomes sampled from different shark species and anatomical locations will allow an understanding of the differences in microbiomes that may be explained by variance in shark habitat and diet. Florida leads as shark bite capitol of the world, with 778 unprovoked bites recorded since 1837, or 4-5 average bites per year. With only a few bites a year, there is not a lot of opportunities to study these bites. What can be studied, however, is how the microbial environment in shark’s teeth is composed. To understand overall microbiome composition, and if microbiomes are distinct from the environment, or specific by species or anatomical location (henceforth location), we characterized microbiomes from the teeth, gill, skin, and cloacal microbiomes of 8 shark species in south Florida (nurse, lemon, sandbar, Caribbean reef, Atlantic sharpnose, blacktip, bull, and tiger) using high throughput DNA sequencing of the 16S rRNA gene V4 region. There was a significant difference in microbial community richness among species, sample location, but not the interaction between species and location. Microbial diversity by location was significantly different for both the Shannon index and Inverse Simpson index. Samples examined by species had no significant difference in microbial community diversity overall for both Shannon and Inverse Simpson indexes. Microbial community diversity of samples by location and species combined significantly differed when submitted to an analysis of variance with the Shannon index, but not the Inverse Simpson index. Teeth microbial communities showed the most diversity based on both Shannon and Inverse Simpson indices. Teeth microbiomes are distinct but also share taxa with the water they inhabit, including potentially pathogenic genera such as Streptococcus (8.0% ± 9.0%) and Haemophilus (2.9% ± 3.3%) in the Caribbean reef shark. The lemon shark teeth hosted Vibrio (10.8% ± 26.0%) and the Corynebacterium genus (1.6%±5.1%). The Vibrio genus (2.8% ± 6.34%), Salmonella enterica (2.6% ± 6.4%), and the genus Kordia (3.1% ± 6.0%) are found in the nurse shark teeth microbial community. Strikingly, the Vibrio genus was represented in the sandbar shark (54.0% ± 46.0%) and tiger shark (5.8% ±12.3%) teeth microbiomes. One OTU related to traditionally non-pathogenic family Phyllobacteriaceae appear to be driving up to 32% of variance in teeth microbiome diversity. We conclude that south Florida sharks host distinct microbiomes from the surrounding environment and vary among species due to differences in microbial community richness. Future work should focus on bacteria found in shark teeth to determine if those present are pathogenic and could provide insights to bite treatment.

Many elasmobranchs are considered top predators with worldwide distribution, and in general these fish play an important role in the transfer of energy from the lower to the upper trophic levels within the marine ecosystem. Despite this, little research has been done regarding the rates of prey ingestion, digestion, and the processes of energy and nutrient absorption. Specifically understudied is enzymatic digestion within the intestinal brush border, which functions to break down macromolecules into smaller subunits for luminal absorption across the gastrointestinal epithelium. Given their carnivorous diet, the present study sought to expand knowledge on nutrient intake in elasmobranchs by focusing on the uptake of products of protein metabolism. To accomplish this, sequence encoding Peptide Transporter 1 (PepT1), a protein found within the brush border membrane (BBM) of higher vertebrates that is responsible for the translocation and absorption of small peptides released during digestion by luminal and membrane-bound proteases, was molecularly identified in the bonnethead shark (Sphyrna tiburo) using degenerate primers based on conserved portions of known PEPT1 sequences from other vertebrates. Sequence encoding Peptide Transporter 2 (PepT2) was also isolated from the S. tiburo scroll valve intestine using the same methodology. PepT1 was then localized using immunocytochemistry with rabbit polyclonal anti-rat PEPT1 in the esophagus, stomach, duodenum, scroll valve intestine, rectum, and pancreas. Vesicle studies were used to identify the apparent affinity of the transporter, and to quantify the rate of uptake by its H+-dependent cotransporter properties, using 3H-glycylsarcosine as a model dipeptide. The results of this study provide insight into the rate and properties of food passage within S. tiburo, and can lead to future work on topics such as physiological regulation of protein metabolism and absorption and how it may vary in elasmobranchs that exhibit different feeding strategies.