Ecology and Evolutionary Biology Commons^™

Vertebrate Diversity In Cave Systems Of Colombia: An Approach Based On Environmental Dna Metabarcoding Analysis, Rita Daniela Martinelli Marín, Carlos Andres Lasso, Francesco Sauro, Susana Josefina Caballero

International Journal of Speleology

There is currently limited knowledge of the biological communities inhabiting cave ecosystems in South America. This study examines the vertebrate community composition of 21 caves across diverse subterranean ecosystems in Colombia using environmental DNA (eDNA) analysis. Water was collected from water bodies inside caves and subterranean systems in six of the eight speleological regions of Colombia in eight departments. Water was filtered manually through a 0.8 m pore size filter and preserved with Longmire solution. A 170-base pair (bp) fragment of the 12s mitochondrial gene specific for vertebrate identification was amplified by PCR and sequenced by Illumina (metabarcoding). Data corresponding …

Light-Driven Zonation And Community Structure Of Aerophytic Microalgae In A Tropical Limestone Cave (Gua Tempurung, Malaysia), Wan Maznah Wan Omar, Mohammad Basri Eshak, Luthfiana Aprilianita Sari, Zulaihat Hamza Abdullahi, Yusuf Abdullahi

International Journal of Speleology

Cave ecosystems host specialized phototrophic biofilms structured primarily by light availability, yet quantitative assessments of aerophytic microalgal community organization in tropical limestone caves remain limited. This study investigated spatial variation in the structure of aerophytic microalgal communities across four ecologically distinct zones (entrance, transition, penetration, and low light) of Gua Tempurung, Malaysia. Stratified sampling was conducted during three seasonal periods. Dominant phototrophic morphospecies were identified using microscopy, and community composition was analyzed in relation to key environmental variables. Twenty-three dominant microalgal morphospecies were recorded across the cave gradient. Cyanobacteria constituted the major component of both richness and abundance, followed by …

House Sparrow Invasion Success Across Ecological, Immunological, And Molecular Scales, Kailey Marie Mccain

USF Tampa Graduate Theses and Dissertations

Biological invasions offer natural experiments for studying how organisms cope with ecological novelty. Although invasion success is often attributed to enemy release, introduced organisms do not enter enemy-free environments. Instead, they enter heterogeneous landscapes in which some familiar enemies are absent, others remain, and entirely novel enemies may be encountered. The question, then, is how invaders (hereafter non-natives) are poised to respond to these threats? This dissertation examines whether successful invasions in house sparrows (Passer domesticus) is associated with shifts in pathogen exposure, immune dynamics in blood, gut physiology, and gene co-expression network structure.

Chapter 1 is at the population/ecological …

Assessing The Impact Of Lampenflora Growth On Invertebrate Distribution And Food Resource Use In Ryusen-Do Cave, Japan, Kazuhide Nakajima, Kanato Ando, Shuji Watanabe, Masuo Komukai

International Journal of Speleology

Subterranean spaces, such as caves with openings to the surface, represent unique environments characterized by limited resources derived from photosynthetic primary production. Consequently, organic inputs from organisms inhabiting above- and belowground habitats, such as bats, play a crucial role in maintaining cave ecosystems. However, in show caves converted into tourist attractions, environmental changes have progressed without sufficient ecological assessment. One important factor is the impact of photosynthetic organisms colonizing around artificial lights, known as lampenflora, on cave ecosystems. Lampenflora growth may influence invertebrate distribution and resource use; however, its impact on both aspects has been poorly evaluated. In this study, …

Invasion Risk Of Regal Demoiselle Following Lionfish Invasion In The Western Atlantic Ocean, Gulf Of Mexico, Bahamas, And Greater Caribbean, Shea L. Volkel

USF Tampa Graduate Theses and Dissertations

Indo-Pacific lionfish (Pterois volitans and P. miles) and regal demoiselle(Neopomacentrus cyanomos) are reef-associated fishes that have invaded the Western Atlantic Ocean, Gulf of Mexico, Bahamas, and Greater Caribbean. While invasive lionfish are established mesopredators with documented impacts on native reef communities, regal demoiselle are at an earlier stage of invasion, and their ecological risks are unclear. Because lionfish consume regal demoiselle in their invaded range, interactions between these species, particularly predation, may influence regal demoiselle invasion success. This dissertation assessed the invasion risk of regal demoiselle, focusing on predator-prey interactions among these species. The objectives were to 1) identify areas …

Improving Coral Restoration Outcomes Through Novel Molecular Applications, Matthew H. Gamache

USF Tampa Graduate Theses and Dissertations

Coral reef ecosystems are declining globally from numerous stressors, including localized pollution, disease, and marine heatwaves induced by climate change. To preserve these ecosystems, it is critical to identify corals that can withstand stressors—primarily future marine heatwaves—and prioritize them for coral restoration efforts until these stressors are mitigated. Coral responses to thermal stress can be influenced by several partners, including mutualistic microalgae and a vast prokaryotic community. Here, I use advanced molecular techniques to examine which partners (coral host, algal symbiont, and microbial communities) are associated with coral health, how they contribute to holobiont physiology, and their potential to increase …

Using Rattlesnake Venom To Model Complex Trait Evolution Across Ecological And Evolutionary Scales, Samuel R. Hirst

USF Tampa Graduate Theses and Dissertations

A central challenge in evolutionary biology is understanding how genetic variation leads to phenotypicdiversity, particularly for complex traits that strongly influence fitness. Traits form the substrate of natural selection, but it is genes, that are inherited across generations. To fully understand the evolutionary process, we must therefore connect the molecular basis of trait variation with the evolutionary outcomes of such traits.

For relatively simple traits, the genotype–phenotype relationship is well understood. Classic systems, such as coat color in beach mice or toxin resistance in garter snakes, have provided effective examples of how relatively few loci underlie conspicuous adaptive differences across …

Abiotic Factors Influencing Anuran Occupation Of Neotropical Brazilian Caves, Vinícius F. Sperandei, Willian Vaz-Silva, Tejerina-Garro L. Francisco

International Journal of Speleology

Despite increasing research on the Neotropical underground environment, anurans remain poorly understood in this habitat. It was analyzed scientific literature records of anurans in Brazilian natural caves and performed a redundancy analysis (RDA) to identify the environmental, taxonomic, geographic, geological and land-use variables that influence their cave occupancy. It was examined a total of 247 literature records, encompassing 83 species/morphospecies, which revealed distinct cave-dwelling tendencies. Some anuran species occupy caves at altitudes between 5 to 21 meters above sea level (m asl), in areas characterized by rocky outcrops and grassland. Others are associated with caves surrounded by forest, savanna, pasture …

Using Stomach Content Analysis To Determine The Trophic Ecology Of Omosudis Lowii, A Deep-Sea Predator In The Gulf Of Mexico, Claire De Noyo

USF Tampa Graduate Theses and Dissertations

Little is known about the feeding dynamics of deep-sea communities, despite their significant ecological importance. Deep-pelagic communities contribute to marine biodiversity and ecosystem stability while directly offsetting climate change via carbon sequestration. Omosudis lowii is an understudied, deep-sea fish found in temperate and tropical waters worldwide, including the Gulf of Mexico. Omosudis lowii have large jaws and distensible stomachs, allowing them to capture prey items larger than their body size. The present seminal study used stomach content analysis to quantitatively describe the O. lowii trophic ecology, providing baseline data regarding diet composition, feeding selectivity, and factors that impact prey selection. …

Bat Occurrence And Microclimatic Conditions Of The Sima Del Órgano Cave, Mexico, Luis A. Hernández, Jaime E. Gómez, Cyntia Reyes

International Journal of Speleology

Caves represent an important type of shelter for many species of bats, particularly in karstic regions. In Mexico, about 60 bat species regularly use caves as roosts. The microclimate of a cave is a key component of the overall cave ecosystem. So, an adequate microclimate can minimize the energetic costs of bats associated with thermoregulation, gestation, embryonic development, parental care, lactation and social interaction. Cave environments are among the least known and most threatened on the planet, which is why we aimed to determine the monthly occurrence of bat species in the Sima del Órgano Cave, estimate the population size …

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 …

Species Distribution Modeling With Environmental Time Series Data And Deep Learning, Austin M. Smith

USF Tampa Graduate Theses and Dissertations

Species distribution models (SDM) are frequently used to gain ecological understanding and guide conservation decisions. These models are developed with a wide variety of procedures - from regression-based approaches to more modern machine learning algorithms - but a requirement almost all share is the use of predictor variables that strongly simplify the temporal variability of driving factors. These static features are chosen by the user, which can incorporate unnecessary bias into a study. Additionally, current data preparation techniques often remove variables from the process entirely, which inherently removes information that may still be of importance. Conversely, novel architectures of deep …

Spatiotemporal Dynamics Of Coastal Nekton Metacommunities In The Western Atlantic, Jonathan A. Peake

USF Tampa Graduate Theses and Dissertations

The processes of diversification, selection, dispersal, and stochastic drift can combine in many ways to assemble ecological communities. A key focus in ecology is to describe and quantify the relative influences of these processes for different systems and explain the mechanisms by which these processes produce patterns of community structure. To accomplish this goal, ecologists have developed several frameworks that seek to integrate processes that occur locally andregionally. The metacommunity concept treats local communities as pieces of a broader landscape that are connected through dispersal of their constituent organisms. Empirical studies have generally lagged behind the development of metacommunity theory. …

Exploring Biosignatures And Biogeochemical Processes In Lanzarote Lava Tubes: Implications For Martian Analog Research, Vera Palma, Ana Z. Miller, Francesco Sauro, Bogdan P. Onac, José M. De La Rosa, Sara Gutiérrez-Patricio, Beatriz Cubero, José A. Gonzalez-Perez, Jesus Martínez-Frías, A Teresa Caldeira

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Emerging Contaminants In Extreme Environments: Microplastics Monitoring In Karst Springs Of Montenegro, Marko Nikolic, Djuradj Milosevic, Ana Manovic, Vladimir Pesic, Melita Mustafic, Dragana Asceric, Milica Nikolic, Dimitrija Savic-Zdravkovic

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Deciphering Above-Treeline Vegetation Greenness Trends: Insights From The Carpathian Mountains, Pavel Dan Turtureanu, Arthur Bayle, Nicoud Baptiste, Olimpiu Traian Pop, Mihai Pușcaș, Philippe Choler

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

High Mountain Ecosystems And Snow Cover In A Changing Climate: For Better Or For Worse, Philippe Choler

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Exploring Pristine Microbial Ecosystems From The Uninhabited Volcanic Selvagens Islands, Pedro N. Jiménez-Morillo, Sara Gutiérrez-Patricio, Vera Palma, Ana Teresa Caldeira, Nicasio Tomás Jiménez-Morillo, Ana Z. Miller

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Insights Into Past Extreme Environments Through Ancient Biomolecules, Ioana Nicoleta Meleg, Magdalena Năpăruş-Aljancic, Yuichi Naito, Hervé Bocherens, Axel Barlow

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Populations Of The Stygobiotic Amphipod Palearcticarellus Pusillus (Martynov, 1930) Maintain Genetic Connectivity Between The Mountain Springs And The Deep Bottom Habitats Of Lake Teletskoye (Altai Mountains, Russia), Ivan Marin, Liubov Yanygina, Svetlana Ostroukhova, Dmitry Palatov

International Journal of Speleology

The diversity of underground fauna is often associated with the presence of karst areas, which have extensive underground cavities and connecting channels. Non-karst areas, however, make up a larger portion of the planet’ surface, and our understanding of the distribution and dispersal abilities of underground fauna in these areas currently remains limited. During a recent study of the diversity of stygobiotic crustaceans in the mountain streams of the Kurai Mountain Range (Altai, Russia), a small-sized species of crangonyctid amphipod, Palearcticarellus pusillus (Crustacea, Amphipoda, Crangonyctidae) was found in high-altitude springs. This species has been previously known only from deep-water habitats in …

Modeling Pelagic Feeding In The Gulf Of Mexico With Implications For Ecosystem-Based Fisheries Management, Rebecca L. Scott

USF Tampa Graduate Theses and Dissertations

The focus of this dissertation was simulating trophic dynamics in the pelagic Gulf of Mexico (GOM) with an emphasis on ecosystem-based fishery management (EBFM) strategies for large pelagic species. Fisheries management in the United States largely utilizes single-species assessments, although managers are increasingly interested in EBFM approaches to better account for ecosystem effects on stocks such as predator/prey dynamics. Production in the surface layer of the pelagic zone is variable with environmental conditions and prey is often concentrated in patches by hydrodynamic features. Production is also transported vertically via diel vertical migration, during which deep-sea species provide potentially key forage …

The Polyaneuploid Cancer Cell State And Therapeutic Resistance: Eco-Evolutionary Dynamics In Structured Populations, Anuraag Bukkuri

USF Tampa Graduate Theses and Dissertations

In this dissertation, I develop and apply eco-evolutionary modeling techniques to understand how the polyaneuploid cancer cell (PACC) state, entered when aneuploid cells exit the cell cycle after S phase and undergo a whole genome duplication, contributes to therapeutic resistance. Since resistance remains one of the primary causes of treatment failure in cancer patients, it is critical to understand how such demographic state transitions allow for acclimatization of cancer cells to therapeutic stressors and how they interact with evolutionary processes to promote irreversible resistance.

In Chapters Two and Three, I lay the foundation for this work. In Chapter Two, I …

Thermal Ecology And Swimming Performance Of Native Tadpoles Dryophytes Femoralis In Central Florida, Jessalyn Aretz

USF Tampa Graduate Theses and Dissertations

Urbanization and climate warming have contributed to global amphibian declines in recent decades. Amphibians are particularly vulnerable to climate and urban-induced warming because their physiological processes are dependent on temperature across all life stages, but few studies have been done on tadpole responses to warming in comparison to adult responses. The study objective was to determine how the thermal ecology and swimming performance of a native Florida tadpole varied with rearing temperature and urban level, and whether these traits are plastic or adaptive. We collected eggs from wild populations of pine woods treefrog (Dryophytes femoralis) tadpoles at an urban and …

Metatranscriptomic Insights Into The Interaction Between Microcystis Blooms And Hydrogen Peroxide, Taylor L. Hancock

USF Tampa Graduate Theses and Dissertations

For this dissertation I studied the interactions of hydrogen peroxide and cyanobacterial harmful algal blooms (cHABs) dominated by Microcystis in the Caloosahatchee River, FL. Specifically, I examined how taxonomic and functional succession relates to both natural hydrogen peroxide dynamics and hydrogen peroxide added to the environment as a cHAB treatment. Chapter 2 investigated how taxonomic succession and gene expression patterns relate to blooms and associated elevated hydrogen peroxide concentrations. The results showed that gene expressions related to cyanobacterial growth were positively correlated with hydrogen peroxide. The genes identified included enzymes capable of hydrogen peroxide generation which were expressed by blooming …

Exploring The Swimming Behavior Of A Hydromechanical Copepod In The Context Of Positive Density Dependence, Eva J. Muir

USF Tampa Graduate Theses and Dissertations

This dissertation investigates the swimming behavior and population dynamics of the marine copepod, Acartia tonsa. This copepod is of interest as it utilizes hydromechanical signals within the environment to navigate its surroundings, resulting in a distinctive hop/sink swimming pattern. This adaptive trait serves several purposes including searching for mates, obtaining food, and detecting predators, however the evolution of this unique swimming style has not been explored. To address this knowledge gap, the first chapter of this dissertation explores the swimming characteristics and escape responses of captive-reared and wild-caught A. tonsa. When reared in aquaculture, A. tonsa populations experience higher populations …

Book Review: Habitantes De La Obscuridad (Fauna Ibero-Balear De Las Cuevas) – Inhabitants Of The Darkness (Ibero-Baleric Fauna Of Caves), Oana Teodora Moldovan

International Journal of Speleology

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Red Mangrove (Rhizophora Mangle) Recruitment And Retention Dynamics On Eastern Oyster (Crassostrea Virginica) Reefs In A Subtropical Estuary, Noreen Selma Mathews

USF Tampa Graduate Theses and Dissertations

Mangroves are invading oyster reefs in areas no longer impacted by winter freezes and completely transforming them into mangrove islands. The mechanisms influencing the transition between these two habitat states remain unclear. Here, I test experimentally whether oyster reef (Crassostrea virginica) structure directly facilitates red mangrove (Rhizophora mangle) propagule capture via differences in propagule retention and successful mangrove establishment. In addition to oyster reef structure, I compared physical reef features of size, elevation, and wind-wave exposure to uncover whether these traits influenced mangrove retention. Recently- abscised red mangrove propagules were inserted onto 21 oyster reefs across 5 sites in Tampa …

Spatial Structure Of Germination And Seed-Associated Fungi In Tropical Pioneer Seeds, Daniela Varon Garcia

USF Tampa Graduate Theses and Dissertations

Negative density-dependent regulation is the process by which host-specific natural enemies reduce the survival of seeds and seedlings of conspecifics near adult trees, favoring heterospecific recruitment, and ultimately increasing local diversity. Negative density-dependent regulation by fungal pathogens has been consistently reported to promote plant diversity in the tropics, even though they tend to be multi-host and host-specificity is rarely reported. Nevertheless, evidence suggests that host-generalist fungi can have host-specific effects that produce disproportionate negative effects on some plant species but not others, promoting regional diversity. However, such studies have not tested for both host-specificity and distance-dependent effects in fully replicated …

Geoarchaeology Of Estuarine Seascapes In Tampa Bay, Florida., Kendal R. Jackson

USF Tampa Graduate Theses and Dissertations

This dissertation investigates the geological, ecological, and archaeological histories of Tampa Bay, Florida’s largest open-water estuary system. Previous geoscientific and archaeological work has studied the evolution of Florida’s estuaries as ‘pre-anthropogenic’ ecosystems and conceptualized Indigenous maritime societies as mostly passive inhabitants of dynamic ‘natural’ environments. Further, the environmental legacies of more recent, industrial-scale estuary modification attending Florida’s 20th-century population boom have been understudied—leading to popular and scientific confusion about historical conditions. The work composing this dissertation research seeks to reconceptualize Tampa Bay as a complex mosaic of cultural seascapes that have been variously altered and modified by human societies across …

Ecohydrology, Cultural Perceptions, And Recovery Of Freshwater Wetlands In A Heavily Managed Urban Aquifer, Jessica Ashley Balerna

USF Tampa Graduate Theses and Dissertations

Freshwater wetlands provide essential ecosystem services that influence, and are influenced by, human perceptions and behaviors. I explore these feedbacks in the Tampa Bay region, which hosts numerous freshwater wetlands subjected to population increases, economic growth, and shifting management policies. These wetlands are embedded in urban and residential areas, where people can observe and respond to changes in wetland condition over time. I utilized long-term (1991–2018), high sample size (n=152) datasets to assess how wetland inundation responds to the interactive effects of climate variation and shifts in water conservation policies primarily related to cutbacks in groundwater extraction. As wetland ecosystem …