Marine Biology Commons^™

Global Genetic Connectivity And Diversity In A Shark Of High Conservation Concern, The Oceanic Whitetip, Carcharhinus Longimanus, Cassandra L. Ruck

HCNSO Student Theses and Dissertations

The oceanic whitetip shark, Carcharhinus longimanus, is a circumtropical pelagic shark of high conservation concern (IUCN Red List: “Critically Endangered” in the Western North and Western Central Atlantic and “Vulnerable” globally). I present the first, population genetic assessment of the oceanic whitetip shark on a global scale, based on analysis of two mitochondrial genome regions (entire 1066-1067 bp control region and 784 bp partial ND4 gene), and nine nuclear microsatellite loci. No population structure was detected within the Western Atlantic. However, highly significant population structure was detected between Western Atlantic and Indo-Pacific Ocean sharks across all markers. Additionally, a …

A Comparison Of Qualitative And Quantitative Data Collection Techniques To Assess Mapping Accuracy In The Florida Keys, Ian K. Rodericks

HCNSO Student Theses and Dissertations

Benthic habitat maps provide the spatial framework for many research science and management activities in coastal areas such as coral-reefs. Accuracy, the degree to which information on a map matches true or accepted values, of benthic habitat maps is important because often times the map will be used in decision-making processes about how we manage our marine resources. It is critical that some measure, such as the accuracy, of the map be known in order to give a sense of how the overall map portrays the seascape. This study compared the accuracy in the following map classes; major structure, major …

Reef Fish Spatial Distribution And Benthic Habitat Associations On The Southeast Florida Reef Tract, Dana Fisco

HCNSO Student Theses and Dissertations

The Florida Reef Tract (FRT) extends from the tropical Caribbean up the southeast coast of Florida into a temperate environment where tropical reef assemblages diminish with increasing latitude. This study used data from a three-year comprehensive fishery-independent survey to quantify reef fish spatial distribution along the Southeast FRT and define where the assemblage shifts from tropical to temperate. A total of 1,676 reef fish visual census samples were conducted to assess the populations on a stratified-random selection of sites of marine hardbottom habitats between the Miami River and St. Lucie inlet. Multivariate analyses were used to investigate differences in assemblages …

Clumped Isotope Composition Of Cold-Water Corals: A Role For Vital Effects?, Peter T. Spooner, Weifo Guo, Laura F. Robinson, Nivedita Thiagarajan, Katharine R. Hendry, Brad E. Rosenheim, Melanie J. Leng

Marine Science Faculty Publications

The carbonate clumped isotope thermometer is a promising tool for determining past ocean temperatures. It is based on the temperature dependence of rare isotopes ‘clumping’ into the same carbonate ion group in the carbonate mineral lattice. The extent of this clumping effect is independent of the isotope composition of the water from which carbonate precipitates, providing unique advantages over many other paleotemperature proxies. Existing calibrations of this thermometer in cold-water and warm-water corals suggest clumped isotope ‘vital effects’ are negligible in cold-water corals but may be significant in warm-water corals. Here, we test the calibration of the carbonate clumped isotope …

Chromosomal-Level Assembly Of The Asian Seabass Genome Using Long Sequence Reads And Multi-Layered Scaffolding, Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, Laszlo Orban

Biology Faculty Articles

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications …

Genomic Variation Among Populations Of Threatened Coral: Acropora Cervicornis, C. Drury, K. E. Dale, J. M. Panlilio, S. V. Miller, D. Lirman, E. A. Larson, E. Bartels, D. L. Crawford, M. F. Oleksiak

Marine & Environmental Sciences Faculty Articles

Background:  Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species’ ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef …

Population Fluctuation Of The Nodular Coral Psammocora Stellata In The Galápagos Islands, Ecuador: An Indicator Of Community Resilience And Implications For Future Management, Kathryn Brown

HCNSO Student Theses and Dissertations

Corals are experiencing a worldwide decline in abundance and diversity. Reasons for this include anthropogenic impacts and associated changes to environmental conditions, including global climate change. Increasing atmospheric CO₂ levels lead to a coordinated increase in sea surface temperatures and decrease in oceanic pH. Warming events associated with El Niño-Southern Oscillation (ENSO) amplify the impacts of steadily increasing temperatures. For example, coral communities in the Galápagos Islands experienced mortality rates of up to 95-99% during severe ENSO warming in 1982-1983. Persisting through such extreme conditions imposes additional challenges to survival in already marginal environments for coral growth and development …

A Picture Is Worth A Thousand Words: Using Anecdotal Data And Photographic Evidence To Obtain Baseline Data For Southeast Florida Reefs, Catherine Brady

HCNSO Student Capstones

By using first-hand accounts, interviews, and photographs from fishermen throughout the region (Martin, Palm Beach and Broward counties), this paper will provide evidence of changes in recreational fish catches. It will also identify a shift in commonly caught fish species, factors that affect the head boat business, environmental changes and suggestions for management. Head boat fishing is a favorable activity for tourists and regular anglers in the state as well as the region. Upon returning from their day trip, companies often provide photo opportunities to display the day’s catch, as part of the fishing experience. Companies that have been around …

Science-Based Policy Plan For Australia's Coral Reefs, David Booth, Lauren Nadler, Steve Doo, Elizabeth Madin, Sue-Ann Watson

Marine & Environmental Sciences Faculty Reports

Australia’s coral reefs are currently under threat from a range of short-­‐ and long-­‐term stressors. The ability of corals to recover from acute disturbance events, such as bleaching, cyclones and crown-­of-thorns seastars outbreaks, is greatly influenced by the multitude of stressors reefs are currently experiencing (1). Since healthy coral habitat is essential for the persistence of associated fish and invertebrate communities, as well as the industries that rely on them (2), all possible action must be taken to reduce stress factors to corals and associated organisms. Practical changes to current reef policies will reverse the decline in the health of …

Coral-Associated Bacterial Diversity Is Conserved Across Two Deep-Sea Anthothela Species, Stephanie N. Lawler, Christina A Kellogg, Scott C. France, Rachel W. Clostio, Sandra D. Brooke, Steve W. Ross

Marine Science Faculty Publications

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA …

The Response Of Runoff And Sediment Loading In The Apalachicola River, Florida To Climate And Land Use Land Cover Change, Paige A. Hovenga, Dingbao Wang, Stephen C. Medeiros, Scott C. Hagen, Karim Alizad

Faculty Publications

The response of runoff and sediment loading in the Apalachicola River under projected climate change scenarios and land use land cover (LULC) change is evaluated. A hydrologic model using the Soil and Water Assessment Tool was developed for the Apalachicola region to simulate daily runoff and sediment load under present (circa 2000) and future conditions (2100) to understand how parameters respond over a seasonal time frame to changes in climate, LULC, and coupled climate/LULC. The Long Ashton Research Station-Weather Generator was used to downscale temperature and precipitation from three general circulation models, each under Intergovernmental Panel on Climate Change (IPCC) …

Tidal Hydrodynamics Under Future Sea Level Rise And Coastal Morphology In The Northern Gulf Of Mexico, Davina L. Passeri, Scott C. Hagen, Nathaniel G. Plant, Matthew V. Bilskie, Stephen C. Medeiros, Karim Alizad

Faculty Publications

This study examines the integrated influence of sea level rise (SLR) and future morphology on tidal hydrodynamics along the Northern Gulf of Mexico (NGOM) coast including seven embayments and three ecologically and economically significant estuaries. A large-domain hydrodynamic model was used to simulate astronomic tides for present and future conditions (circa 2050 and 2100). Future conditions were simulated by imposing four SLR scenarios to alter hydrodynamic boundary conditions and updating shoreline position and dune heights using a probabilistic model that is coupled to SLR. Under the highest SLR scenario, tidal amplitudes within the bays increased as much as 67% (10.0 …

Telonicher Marine Laboratory, Hsu Telonicher Marine Laboratory

Newsletters

No abstract provided.

White Shark Research Report Q And A - Based On Fisheries Research Report 273: Evaluation Of Passive Acoustic Telemetry Approaches For Monitoring And Mitigating Shark Hazards Off The Coast Of Western Australia, Department Of Fisheries, Western Australia

Fisheries Research Reports

This document is a Question and Answer summary based on Fisheries Research Report 273: Evaluation of passive acoustic telemetry approaches for monitoring and mitigating shark hazards off the coast of Western Australia.

Shark attacks are rare but traumatic events that involve complex and dynamic interactions between sharks’ ecology and human demographics and behaviours. To better understand the biological and ecological factors contributing to the series of incidents of white shark (Carcharodon carcharias) attacks off Western Australia, sharks were fitted with acoustic transmitters (‘tags’) that emit unique identification codes every 50 to 150 seconds. Tagged sharks were monitored by up to …

Experimental Demonstration Of An Allee Effect In Microbial Populations, Rajreni B. Kaul, Andrew M. Kramer, Fred C. Dobbs, John M. Drake

OES Faculty Publications

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: ‘Everything is everywhere, but the environment selects’. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predationby the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive densitydependence is around 5, 20 or …

Bridge Over Troubled Waters: A Synthesis Session To Connect Scientific And Decision Making Sectors, Kaitlin Goldsmith, Elise F. Granek, Amy Lubitow, Michael Papenfus

Environmental Science and Management Faculty Publications and Presentations

Lack of access to relevant scientific data has limited decision makers from incorporating scientific information into their management and policy schemes. Yet, there is increasing interest among decision makers and scientists to integrate coastal and marine science into the policy and management process. Strategies designed to build communication between decision makers and scientists can be an effective means to disseminate and/or generate policy relevant scientific information. Here researchers develop, test, and present a workshop model designed to bridge the gap between coastal and marine decision makers and scientists. Researchers identify successful components of such a workshop as well as areas …

The Function Of Second-Order Male Alliances In St. Johns River Dolphins (Tursiops Truncatus), Arien D. Widrick

UNF Undergraduate Capstone Projects and Honors Theses

Bottlenose dolphins (Tursiops truncatus) have a sexually segregated fission-fusion society, in which males and females form different types of social groups for different purposes. Social interactions among dolphins are frequent, and group composition changes just as often. Male-male association patterns reveal the formation of alliances, which range in complexity. Recently, second-order alliance formation was confirmed in the St. Johns River, but the function of these alliances is unknown. To investigate their function, this research analyzes the seasonality of first and second-order alliance formation, and whether female presence plays a role. It was hypothesized that higher level male alliances form in …

Seagrass Community Change At Three High Risk Ports In The Great Barrier Reef World Heritage Area From 2005 To 2014, Celeste Venolia

Independent Study Project (ISP) Collection

Seagrass meadows are extremely valuable and dynamic ecosystems currently facing pressure from anthropogenic disturbances. Seagrass ecosystems are declining globally because of direct and indirect threats that shift environmental conditions controlling seagrass distribution. Seagrass species responses to disturbances vary based on a number of factors including life history strategy. The goal of this study was to map and analyze patterns of dominant seagrass species change at Cairns and Gladstone from 2005-2014 and Townsville from 2007-2014. This compilation data set was symbolized according to the life history strategy of the species. The major disturbances during this time period were physical damage from …

Bacterial Diversity And Community Composition From Seasurface To Subseafloor, Emily A. Walsh, John B. Kirkpatrick, Scott Rutherford, David C. Smith, Mitchell Sogin, Steven D'Hondt

Arts & Sciences Faculty Publications

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (≥1.5 meters below seafloor). Abundance-weighted community compositions …

Symbiont Type And Photophysiology Of Acropora Loripes And Platygyra Daedalea Under Future Scenarios Of Rising Ocean Temperatures And Pco2, Lauren Howe-Kerr

Independent Study Project (ISP) Collection

Coral cover is declining at an alarming rate, and it is estimated that 60% of reefs worldwide may be lost by 2030. Elevated seawater temperatures and ocean acidification are contributing to an increase in the frequency and severity of bleaching events. These events disrupt the symbiosis between corals and their photosynthetic dinoflagellates (Symbiodinium spp). Relatively little is known about the ability of corals to acclimatize to changing environmental conditions or whether the rate of climate change is too fast for corals to keep up, limiting the accuracy of future predictions for reef resilience. However, the ability of some coral species …

Bacterial Indicators Of Fecal Pollution: Exploring Relationships Between Fecal Coliform And Enterococcus Groups In Central And South Florida Surface Waters, Shelby G. Craig

HCNSO Student Theses and Dissertations

Ambient and recreational surface waters worldwide experience fecal pollution due to a variety of anthropogenic sources. Fecal waste has been proven, for over a century, to harbor pathogenic microorganisms which subsequently cause a variety of disease and illness in human hosts. The benefits of utilizing fecal indicator bacteria (FIB) as a simple, inexpensive means to detect fitful human pathogens within a variety of water matrices are vast. However, no universal agreement exists in regard to which indicator is best suited for detection of fecal contamination and pathogens in environmental waters, and no single standard for bacterial indicators has been federally …

The Role Of Traditional Knowledge About And Management Of Seaworms (Polychaeta) In Making Austronesian Worlds, Cynthia Twyford Fowler

Faculty Scholarship

This paper discusses how Kodi make their worlds cognitively as well as experientially, and how these worlds relate to sustainability and wellbeing. Kodi construct their cognitive worlds as well as their biophysical landscapes whilst interacting with many other species. This presentation focuses on human-polychaete interactions in order to illustrate world making processes. Seaworm traditions have deep historical roots in Austronesian societies and continue to be crucial for the wellbeing of contemporary communities. World-making processes are evident in what Kodi people say about seaworms and how they move through space relative to seaworms. While Kodi construct time they simultaneously construct space …

Identification Of A Mycobacterium Sp. As The Causative Agent Of Orange Nodular Lesions In The Atlantic Sea Scallop Placopecten Magellanicus, Catherine Grimm, Carl Huntsberger, Kathryn Markey, Susan Inglis, Roxanna Smolowitz

Arts & Sciences Faculty Publications

The Atlantic sea scallop Placopecten magellanicus is an economically important species in the offshore fisheries on the east coast of the USA. Recently, animals collected from waters ranging from Massachusetts to Maryland have shown variably sized (up to 1 cm in diameter) orange nodular foci, predominantly in the adductor muscle tissue, but also in other organs. Histological evaluation of the nodular lesions showed rod-shaped bacteria that stain acid-fast positive and Gram-positive. PCR methodology was employed to identify the causative organism of the nodules as a Mycobacterium sp. using analysis of the partial 16S gene and the 16S-23S internal transcribed spacer …

Coral Genotype Influence On Growth And Stress Resistance In Acropora Cervicornis: Investigating Potential Energy Tradeoffs, Peter T. Grasso

HCNSO Student Theses and Dissertations

Over the last few decades coral reefs have faced unprecedented declines in health due to natural and anthropogenic sources. Until recently few studies have examined genotypic variation of growth and thermal stress resistance in Acropora cervicornis. This study aims to assess the potential for energy trade-offs between growth and thermal stress resistance by following 120 coral fragments from 12 genotypes of Acropora cervicornis over the course of 15 months to determine average growth rates for each genotype. Following the completion of the growth observation a bleaching event occurred in the lower Florida Keys providing the opportunity for examining thermal …

An Endemic Commensal Leucothoid Discovered In The Tunicate Cnemidocarpa Bicornuta, From New Zealand (Crustacea, Amphipoda), Kaitlyn M. Brucker

HCNSO Student Theses and Dissertations

Precise descriptions and comprehensive taxonomies of species and their ecology are essential in monitoring changes in marine biodiversity at multiple spatial scales. A currently undescribed species of commensal amphipod in the genus Leucothoe is reported from New Zealand, collected from the endemic tunicate Cnemidocarpa bicornuta. This species differs from others in the genus in having a one-articulate first maxilla palp and an apically produced tuberculate lobe on the inner margin of the outer plate of the maxilliped. Previous taxonomic surveys in New Zealand waters did not document this species, indicating that it may be a recent arrival. This research …

Benthic Foraminifera Abundance, Stable Isotopes, Desoto Canyon Sediments, 2010-2012, Patrick Schwing

C-IMAGE data

Spatial and temporal compilation of benthic foraminiferal abundance based on individually counted foraminifera from washed sediment samples, del13C measurements from Cibicidoides sp. measured by the SIRMS instrument at USF, CMS, all presented in the context of depth in each sediment core as well as by short-lived radioisotope age models. Spreadsheet: Benthic Foram Taxonomy, Foram Abundance Manuscript title: Quantifying the ecological impact of the Deepwater Horizon event on benthic foraminifera and subsequent rates of recovery Spreadsheet: Benthic Foram Stable Carbon Isotopes Manuscript title: Persistent δ13C depletion in benthic foraminiferal carbonate following the Deepwater Horizon event

West Florida Shelf Beach Sediment Pah And Dioctyl Sodium Sulfosuccinate Concentrations, Microtox Luminescence And Microscreen Mutagenicity Data, 2010 To 2013, Lauren D. Mcdaniel

C-IMAGE data

Six cohesive sand patty sediments were collected on a West Florida Shelf beach in St. Petersburg Florida, January, 2013. These were analyzed for presence of PAH compounds and the composition compared to measurements from known Deepwater Horizon contaminated beach sediments. Known contaminated samples were collected from Santa Rosa Florida in July 2010 and January 2011, and from Gulf Shores Alabama in December 2012. The same samples were also analyzed for biological activity and the presence of Corexit dispersant (DOSS). This dataset includes concentration data for PAHs and DOSS in these samples. The biological activity in the water accommodated fraction of …

Chemical Analysis Of Sediment And Fish Species Near The Hercules 265 Blowout, Gulf Of Mexico, 2013, Isabel Romero

C-IMAGE data

On July 23, 2013 a marine gas rig (Hercules 265) ignited in the northern Gulf of Mexico. The rig burned out of control for several days before being extinguished. We conducted a rapid-response sampling campaign near Hercules 265 after the fire to ascertain if sediments and fishes were polluted above earlier baseline levels. Sediment cores were collected to the SE of the rig at a distance of ~0.2 km, 8 km and 18 km using a multicorer, and demersal fishes were collected from ~0.2 to 8 km SE of the rig using a longline (508 hooks). Recently deposited sediments document …

Spatial Distributions Of Fish And Invertebrates In The Gulf Of Mexico For 2010-01-01 Estimated Using A Statistical Model, Michael Drexler

C-IMAGE data

A generalized additive modelling (GAM) approach is used to describe the abundance of 40 species groups (i.e. functional groups) across the Gulf of Mexico (GoM) using a large fisheries independent data set (SEAMAP) and climate scale oceanographic conditions. Predictor variables included in the model are chlorophyll a, sediment type, dissolved oxygen, temperature, and depth. The GAM approach was shown to be robust despite zero-inflated data. article: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0064458

Dataset For: Simulating Cell Death In The Termination Of Karenia Brevis Blooms: Implications For Predicting Aerosol Toxicity Vectors To Humans, Jason M. Lenes

C-IMAGE data

A non-linear lysis term for simulation of K. brevis HAB termination on the West Florida Shelf is introduced, with the assumption that particle encounters of planktonic microalgae and bacteria can be described as the square of the phytoplankton biomass. This formulation also accounts for nutrient-limitation of K. brevis as a precondition for susceptibility to bacterial and viral attack, and potentially programmed cell death. Two model simulations were run of linear and non-linear lysis cases. Model output was compared against observed weekly maximum K. brevis concentrations, with statistical metrics calculated over three HAB phases during 2001. Introduction of the non-linear lysis …