Biology Commons^™

Draft Assembly And Annotation Of The Cuban Crocodile (Crocodylus Rhombifer) Genome, Robert W. Meredith, Yoamel Milián-García, John Gatesy, Michael A. Russello, George Amato

Department of Biology Faculty Scholarship and Creative Works

Objectives: The new data provide an important genomic resource for the Critically Endangered Cuban crocodile (Crocodylus rhombifer). Cuban crocodiles are restricted to the Zapata Swamp in southern Matanzas Province, Cuba, and readily hybridize with the widespread American crocodile (Crocodylus acutus) in areas of sympatry. The reported de novo assembly will contribute to studies of crocodylian evolutionary history and provide a resource for informing Cuban crocodile conservation. Data description: The final 2.2 Gb draft genome for C. rhombifer consists of 41,387 scaffolds (contigs: N50 = 104.67 Kb; scaffold: N50-518.55 Kb). Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 92.3% of the 3,354 genes …

Ecological Epidemiology Of The Fungal Pathogen Ophidiomyces Ophiodiicola In Southeastern U.S. Snake Populations: Distribution, Drivers, And Anthropogenic Risk Factors, Shivam Shukla

USF Tampa Graduate Theses and Dissertations

Studying wildlife diseases is an important conservation measure, as many pathogens are a critical threat to biodiversity worldwide. Ophidiomycosis is an emerging infectious disease caused by the invasive fungal pathogen Ophidiomyces ophiodiicola that affects a wide variety of snake species, often causing mortality. There has been limited surveillance for ophidiomycosis in the southeastern United States’ (US) snake populations and research into the effects of anthropogenic disturbance on disease spread is also lacking. Thus, this project aimed to quantify the distribution and drivers (taxonomic, anthropogenic, and morphological) of ophidiomycosis in Florida, Louisiana, and Mississippi’s free ranging snakes as well as study …

Chasing A Little-Known Fairy Bee (Perdita Meconis) In A Dynamic Desert Landscape, Sarit Chanprame, Colleen Meidt, Terry Griswold, Joseph S. Wilson, Kelsey K. Graham

Biology Student Research

The Mojave poppy bee, Perdita meconis Griswold, is a small fairy bee endemic to the eastern Mojave Desert, known to be associated with the Las Vegas Bearpoppy, Arctomecon californica. Because of the reported decline in populations of P. meconis, it has been targeted for protection under the Endangered Species Act. Here, we present the results of a 3-year study investigating the current distribution and floral preferences of P. meconis in Clark County, Nevada. We found that populations of P. meconis fluctuated dramatically from 2020 to 2022. This area experienced extreme drought conditions during these years, which consequentially affected …

What Drives Gut Microbial Diversity And Community Structure Among Closely-Related Host Species?, Rylee Jensen

All NMU Master's Theses

The gut microbiome (GMB) of mammals hosts an important community of microbes that perform countless micro-ecosystem services for the host and are influenced by numerous factors including host physiology, environment, and phylogeny. Phylogeny may have a unique effect on GMB diversity and community structure (i.e., a GMB profile) via phylosymbiosis, a theory in which the evolution of hosts matches the evolution of their associated microbiota. Elucidating phylosymbiosis in mammals is difficult because multiple intrinsic and extrinsic factors collectively drive individual GMB variation. Thus, there is a need to simultaneously analyze the role of physiology, environment, and phylogeny on shaping host …

Integrating Multiple Biodiversity Metrics To Assess Diatom Diversity And Diatom/Macrophyte Host Specificity In Four Florida Benchmark Lakes, Alana Jade Bronk

USF Tampa Graduate Theses and Dissertations

Biodiversity is declining across all natural environments, however, freshwater systems are thought to be among the most threatened. Quantifying and understanding trends in freshwater biodiversity has become more urgent as rapid biodiversity loss continues. To provide a robust ecological assessment, more than one bioindicator should be used, along with multiple biodiversity metrics. Macrophytes and diatoms are important components of aquatic systems, especially in shallow lakes. The relationship between macrophytes and epiphytic diatoms, though, is not clearly understood, and has not been well-studied, particularly in Florida, which has the largest abundance of natural freshwater lakes in the southeastern U.S This study …

Effects Of Roadways On Seasonal Movement Strategies And Mate Location Success In An Imperiled Pit Viper (Crotalus Horridus), Elizabeth J. Noble

Graduate Research Showcase

A detailed understanding of animal movement behavior is fundamental to effective conservation and management. Within populations, a diversity of movement strategies can be displayed in search of critical resources, and these strategies are influenced by multiple interacting factors related to individuals and the environment. Mating partners are one critical resource that often serves as a prominent selective force shaping movement during mating seasons. For many large-bodied snakes, such as pit vipers (Viperidae: Crotalinae), male mate- searching movements are the primary determinant of mate location success. During this time, males incur significant risks associated with elevated movement. In an increasingly human- …

A Triumph Of Conservation: The University Of South Carolina Aiken’S Bluebird Trail, Alyssa Godfrey, Emory Owens, Quinn Schreiber, Michelle L. Vieyra

Journal of the South Carolina Academy of Science

The Eastern Bluebird (Sialia sialis) was once an endangered species, with over 90% of its population declining in the early 1900s (Ritchison, 2000). These birds play a crucial role in regulating insect populations and maintaining the safety of food sources, making them important both economically and environmentally. Eastern Bluebirds are proof that conservation efforts work, as they are now a species of least conservation concern in the United States. Since 2020, undergraduate students at the University of South Carolina Aiken have collaborated with the South Carolina Bluebird Society to establish and monitor 31 nesting boxes across the main campus …

Sex Differences In The Diets Of Forest-Dwelling Baboons (Papio Anubis), Kara Hartunian

Theses and Dissertations

The ability to eat and switch between many food sources is an adaptative feeding strategy utilized for meeting nutritional needs across different environments, seasons, and physiological conditions. Baboons (genus Papio) excel at both dietary flexibility and foraging selectively, and consequently have one of the most widespread geographic distributions in the Order. To further expand to our understanding of baboon feeding ecology, I analyzed foraging activity and the nutritional characteristics of the diets of the relatively understudied rainforest baboons (Papio anubis) living in Kibale National Park, Uganda. I also investigated if there are differences in food type choice …

From Inbreeding To Admixture: How The Diverse Consequences Of Gene Flow Shape Evolutionary Dynamics And Population Viability, Amy L. Springer

All Graduate Theses and Dissertations, Fall 2023 to Present

When Homo sapiens traveled out of Africa and interbred with the Neanderthals of Europe, human genes spread into the Neanderthal population. Likewise, genes from Neanderthals spread into the human genome—genes humans still carry to this day. The process whereby genetic material from one population is spread to another is known as gene flow. Gene flow—or the absence thereof—can have critical consequences for a population’s health and survival. On one hand, if no gene flow occurs, mating among close relatives can lead to high levels of inbreeding. Inbreeding can have devastating consequences for the health of populations, in some cases even …

Assessment Of Georgia’S Royal Catchfly (Silene Regia) Along A Forest-Edge Gradient In A Remnant Prairie Community, Megan Brooks

Master's Theses

Royal catchfly (Silene regia) is a perennial prairie forb known to grow in rocky, alkaline soils within tallgrass prairies of the eastern United States. S. regia is recorded from twelve states, including Georgia, and is now confined to fragmented habitats due to the loss of 95% of its natural environment. The species is now listed as critically imperiled in the state of Georgia. Attempts at reintroduction via outplanting have only shown limited success, necessitating more research on the environmental conditions in which this plant survives in its southern-most distribution. This study investigated the local ecological factors influencing the …

Germination And Seedling Growth Of Native Uae Plant Species: The Combined Effects Of Elevated Co2 And Temperature, Nour Elhouda Debouza

Thesis/ Dissertation Defenses

The dissertation offers an extensive analysis of the physiological adaptations and coping strategies of native plant species in the United Arab Emirates (UAE) to the elevated levels of atmospheric carbon dioxide (CO2) and temperature, within the broader context of human-induced climate change. Given the arid climate of the UAE, understanding how native species respond to environmental stressors is critical for the preservation of biodiversity and the development of sustainable agricultural practices. This study focuses specifically on the germination and early growth stages of three crucial native species—Senna italica, Prosopis cineraria, and Tephrosia nubica—under controlled conditions that simulate future climatic scenarios. …

Genetic Analysis Of Global Sawfish Populations, Kylie Faulkner

Honors Theses

Family Pristidae contains five of the most critically endangered elasmobranch species: Anoxypristis cuspidata, Pristis pristis, Pristis pectinata, Pristis zijsron, and Pristis clavata. The species of this family have suffered drastic population declines and range reductions due to historic patterns of overexploitation, accidental entanglement, and habitat disruption. The conservation of this taxa has been historically complicated by taxonomic uncertainty, as similar morphologies across species make them exceedingly difficult to identify. A morphological and genetic comparison of sawfish specimens collected globally was conducted in 2013, which supported a reduction in the number of described species from seven to …

The Role Of Abu Dhabi's Nearshore Marine Environments In The Ecology Of Elasmobranch Fishes, Stephan Bruns

Dissertations

This dissertation investigated the role of inshore habitats in the ecology of elasmobranch fishes, with a specific focus on the wider Khor Fardiah Region on the eastern site of Abu Dhabi City. Once the vulnerability of these environments to anthropogenic pressure and climate change is recognised, it is clear that nearshore environments are susceptible to adverse outcomes. Hence, this dissertation aims to provide informative data that can help in devising effective conservation strategies. The study used a multi-survey technique approach, including stereo-BRUVS, acoustic telemetry, and satellite tracking, in combination with local ecological knowledge to explore the species diversity and habitat …

Field-Based Measurement Tools To Distinguish Clonal Typha Taxa And Estimate Biomass: A Resource For Conservation And Restoration, Brian M. Ohsowski, Cassidy Redding, Pamela Geddes, Shane Lishawa

School of Environmental Sustainability: Faculty Publications and Other Works

Two species of clonal Typha [T. latifolia (native) and T. angustifolia (exotic)] hybridize to form the highly invasive, heterotic (high vigor) T. × glauca in North American wetlands leading to increased primary production, litter accumulation, and biodiversity loss. Conservation of T. latifolia has become critical as invasive Typha has overwhelmed wetlands. In the field, Typha taxa identification is difficult due to subtle differences in morphology, and molecular identification is often unfeasible for managers. Furthermore, improved methods to non-destructively estimate Typha biomass is imperative to enhance ecological impact assessments. To address field-based Typha ID limitations, our study developed a predictive …

Factors Associated With Acoustic Bat Presence During Spring Emergence In The Appalachian Mountains Of Western Virginia, Emily Kirk Pody

Theses, Dissertations and Capstones

Studies of threats that bats face during hibernation have increased in response to white-nose syndrome (WNS), a fungal disease that has ravaged North American bat populations. However, impacts of WNS on bat ecology during spring emergence, when bats are potentially recovering from infection and allocating resources for reproduction, is relatively understudied. As more bat species become listed at the federal and state level, the need to understand the factors associated with spring emergence is critical for improving conservation guidelines and habitat management practices. Acoustic monitoring is an efficient method for monitoring bat presence for prolonged periods of time, giving biologists …

The Impact Of Isolation From Other Members Of The Greater Bamboo Lemur (Prolemur Simus) Species On The Behavior Of A Lone Greater Bamboo Lemur In Ranomafana National Park, Marissa N. Mccandless, Alex Casamassima, Sophie Thomas

Undergraduate Research (Journal)

Across Madagascar, many lemur species are declining in number due to deforestation perpetuated by slash and burn agriculture. Ranomafana National Park hosts 12 unique lemur species, one of which has a local population of just a single individual- the Greater Bamboo lemur (Prolemur simus). Being extremely social beings, we theorize that isolation from members of one’s species will change behavioral patterns. To test this hypothesis, we used focal animal sampling to record the behavior of the Greater Bamboo lemur for about 40 hours over a five day period. We compared our results to behavioral data collected of lemurs in a …

Deepwhalenet: A Climate Change-Aware Fft-Based Neural Network For Underwater Passive Acoustic Monitoring, Nicholas Ryan Rasmussen

Dissertations and Theses

In the face of escalating climate threats, the conservation of whale species has become increasingly critical. Traditional acoustic monitoring methods, burdened by extensive pre-processing and post-processing, need more adaptability and efficiency for effective marine mammal surveillance. This study introduces DeepWhaleNet, a novel deep-learning framework tailored for Underwater Passive Acoustic Monitoring (UPAM). DeepWhaleNet is designed to streamline whale detection by directly analyzing raw log-power spectrograms, thus extracting essential acoustic features to conserve these endangered species. The framework employs an extensive short-time Fourier transform (STFT) for input processing and a customized ResNet-18 architecture for classification, distinguishing whale vocalizations from ambient noise and …

Lessons From An Iconic Grouper: Sex, Science, And Serendipity, Yvonne J. Sadovy De Mitcheson

Gulf and Caribbean Research

From a common little damselfish and spectacular grouper aggregations, to disappearing reef fishes and the dark side of the international seafood trade, my journey has passed through a fascinating and worrying period of change in the way we view and treat our oceans. Although much of my career has been in the Indo—Pacific, I focus here mainly on my professional ‘roots’ in the Caribbean and on the Nassau Grouper Epinephelus striatus, a species that kept me curious, taught me patience, never to assume and always to stay hopeful. This fish is almost an obsession; why can we not better safeguard …

Occupancy Of The Little Grass Frog (Pseudacris Ocularis), An Overlooked Longleaf Endemic, In A Managed Landscape, Anna M. Humphrey

Theses, Dissertations and Capstones

Amphibians are declining globally, with many declines associated with habitat loss. The longleaf pine (Pinus palustris) ecosystem historically covered most of the southeastern United States and supports a host of endemic amphibians. This ecosystem has declined by over 97% in the last two hundred years and many associated species have declined with it. The Little Grass Frog (Pseudacris ocularis) is a longleaf pine endemic anuran that has been understudied and under-surveyed; almost no information is known on the ecology of this species and no population studies have been conducted. My goals were to create an acoustic …

Evaluation Of Conservation Strategies For Blanding’S Turtles (Emydoidea Blandingii), Callie Klatt Golba

Graduate Research Theses & Dissertations

Across the globe, biodiversity is threatened due to anthropogenic changes to the environment and large numbers of freshwater species, especially turtles, are facing population declines. Resources for conservation are limited, making empirically based conservation planning of utmost importance. Effective management strategies incorporate relevant biological information to outline specific and feasible actions that will mitigate the greatest threats to a species. Blanding’s Turtles (Emydoidea blandingii) are a long-lived, semi-aquatic, freshwater species that are classified as endangered in Illinois and internationally. As with other species of concern, Blanding’s Turtles are threatened by habitat loss, fragmentation, and degradation. They are also threatened by …

Characterizing The Ecology Of Plains (Spilogale Interrupta) And Eastern (Spilogale Putorius) Spotted Skunks: A Systematic Literature Review And Population Assessment In Kansas, Jenell De La Peña

Electronic Theses & Dissertations

The plains spotted skunk (Spilogale interrupta) has recently been recognized as a distinct species from the eastern spotted skunk (Spilogale putorius). While once abundant across the central and eastern United States, both species have experienced population declines, resulting in their review for listing under the Endangered Species Act (1973). In Kansas, the plains spotted skunk has suffered a particularly dramatic decline, the last detection in the state having occurred in 2020. Additionally, due to the recent taxonomic split, many past studies reporting on S. putorius ecology actually describe findings of two species, potentially complicating our understanding …

The Mojave Poppy Bee (Perdita Meconis) And A Primary Plant Host, The Las Vegas Bear Poppy (Arctomecon Californica): Status And Interactions, Sarit Chanprame

All Graduate Theses and Dissertations, Fall 2023 to Present

The Mojave Desert is one of the most biodiverse places in North America. A harsh environment with many species results in complex relationships between animals and plants. This study focuses on one bee-plant relationship, the Mojave poppy bee, and the Las Vegas Bear Poppy.

The Mojave poppy bee is rare and has only been collected from Las Vegas Bear Poppy, Dwarf Bear Poppy, and a few species of prickly poppies. A 1995 report suggested the bee was a major contributor of pollination for the Las Vegas Bear Poppy in Clark County, Nevada. More recently (2019), their local extinction in southwestern …

Ecological Correlates For Endemic And Threatened Amphibians In The Uluguru Nature Forest Reserve, Tanzania, Joseph M. Christopher, Wilirk Ngalason, John V. Lyakurwa

Tanzania Journal of Science

Information on habitat characteristics for endemic and threatened amphibians along the altitudinal gradient in the Uluguru Nature Forest Reserve (UNFR) is limited. We assessed habitat characteristics associated with the occurrence of endemic and threatened amphibians in the Uluguru Nature Forest Reserve between April and June 2022. Bucket pitfall traps, time-constrained audio-visual surveys, plots and opportunistic searching were used to study amphibians in 6 sites along elevational gradient from 600 m to 2100 m a.s.l. Eighteen amphibian species were recorded, thirteen of them being endemic to the Eastern Arc Mountains, two near-endemic and three widely distributed. Among the species recorded, seven …

The Florida Scrub-Jay, Emily Hill

PANDION: The Osprey Journal of Research and Ideas

Artist Statement

The Florida Scrub-Jay is a digital scientific illustration of Aphelocoma coerulescens, the only native bird species endemic to Florida. This piece celebrates the natural beauty of the Florida scrub-jay and its key features that allow it to thrive in scrub habitats. These habitats are threatened by anthropogenic activity and climate change, leading to the fragmentation, degradation, or eventual loss of these areas. Through this artwork, I hope to emphasize the importance of conservation and inspire viewers to appreciate and protect this bird species.

Every stroke and color choice were carefully considered to accurately depict the bird’s physical attributes. …

Lichens Of Iller Creek: A Checklist For The Iller Creek Unit, A Division Of Dishman Hills Conservation Area, Spokane Valley, Wa, Devin M. Mumey, Giovanna Bishop, Jessica L. Allen

2023 Symposium

The field of biodiversity documentation encompasses a broad range of research including new species discovery and description, compilation of species present in a given area, and investigation of interspecies interaction. In an era of increasingly devastating and rapid environmental change, documenting biodiversity has become increasingly important. Anthropogenic effects on urban-adjacent natural areas are especially significant, as they can cause numerous, often drastic, responses in ecosystems. Our objective here was to document the lichen biodiversity in a large urban-adjacent protected area: the Iller Creek Unit of the Dishman Hills Conservation Area in Spokane Valley, Washington. This unit encompasses a diversity of …

Dna Barcoding Of Springsnails (Mollusca, Gastropoda, Caenogastropoda) Endemic To The Trans-Pecos Region Of Texas (Usa), Kathryn E. Perez, Vanessa Saenz, Natalia Salazar-Lozano, Benjamin F. Schwartz, Benjamin T. Hutchins

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

In desert environments, unique communities depend on groundwater from springs, including a diverse radiation of small (<5 >mm) snails found in the desert across the southwestern United States. Nearly all springsnail species are considered critically imperiled with their existence depending on maintenance of spring-flows in regions of declining water availability. Extant, endemic springsnails in the Trans-Pecos region of Texas include one species of Pseudotryonia Hershler, 2001, five nominal Tryonia W. Stimpson, 1865 (Cochliopidae) and seven Pyrgulopsis Call & Pilsbry, 1886 (Hydrobiidae). Four of these are classified as endangered under the US Endangered Species Act. Surveys for springsnails were conducted at …

Population Physiology, Demography, And Genetics Of Side-Blotched Lizards (Uta Stansburiana) Residing In Urban And Natural Environments, Spencer B. Hudson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Wildlife populations across the globe are poised to lose their natural habitat to urbanization, yet there is limited information on how different species handle living in cities. Animals in urban environments are often susceptible to novel stressors, which can threaten their individual health and population viability. The physiological characteristics of animals, such as those related to metabolic hormones, oxidative stress, and immunity, are expected to be important for survival in this context. If so, animals persisting in urban areas may demonstrate physiological differences from their natural counterparts, perhaps due to evolutionary change. These potential outcomes have been documented in birds …

Monitoring The Effects Of Poultry Waste On Fishes And Macroinvertebrates In The Sabine River, Karley R. Parker

Biology Theses

Freshwater is a vital resource that provides life and sustainability for almost all organisms on Earth. It is important to maintain its health and protect it from emerging pollutants that pose a threat to the organisms that use it. Pollution continues to threaten the well-being of the environment’s freshwater sources all around the world that could lead to damaging effects in the future. The Sabine River is a major freshwater resource in the east Texas and western Louisiana areas that provides a habitat for thousands of organisms as well as other domestic uses for humans. In 2019, a waste discharge …

Variability In Billfish Vertical Distribution And Fishing Interactions Driven By Environmental Conditions In The Eastern Tropical Pacific Ocean, H. E. Blondin, D. E. Haulsee, Ryan Logan, Mahmood Shivji, E. R. Hoffmayer, J. H. Walker, J. M. Dean, E. L. Hazen, L. B. Crowder

Biology Faculty Articles

Blue marlin (Makaira nigricans) and sailfish (Istiophorus platypterus) are ecologically important predators and valuable species throughout the world’s recreational, commercial, and subsistence fisheries. Comparing multi-species vertical habitat use can inform ecological uncertainties such as inter-species competition, as well as relative vulnerabilities to fishing activities. In this study, we identified key differences in both depth use and which environmental variables drive these selections, which highlights the variability in the catchability both as target species in recreational fisheries and bycatch in commercial fisheries. To understand these two species’ vertical habitat use, we examined depth profiles from 26 sailfish …

Characterizing Effects Of Non-Point Runoff On Subwatersheds Of The Middle White River In Arkansas, Rainee Nicole Lynn Deroin

Student Theses and Dissertations

The Middle White River Watershed located in northeastern Arkansas is part of the larger White River drainage area that flows into the Mississippi River. The watershed has been on the 303(d) list for impairments such as pathogens, turbidity, total suspended solids, and dissolved oxygen. This study monitored water quality and potential toxicity in four subwatersheds of the Middle White River to inform management and regulation downstream conditions. During the three years of weekly sampling from 2019 to 2022, the subwatersheds violated state standards for pathogens, turbidity, and dissolved oxygen. Aquatic and sediment toxicity testing conducted on the four subwatersheds using …