Ecology and Evolutionary Biology Commons^™

How Individual Traits Predict Distribution Patterns And Community Convergence, Zachary K. Lange

Biology Dissertations - Archive

One of the fundamental questions in biology is whether natural conditions lead species and communities toward predictable outcomes. Answering this question requires understanding how traits of individual organisms are connected to species- and community-level patterns. In Chapter 2, I examined how thermal physiology and environmental temperatures interact to determine the distribution patterns of Anolis lizards on the Greater Antilles. I combined lab-measured thermal traits (critical thermal minimum: CT_min, critical thermal maximum: CT_max, thermal preference: T_pref) with occurrence and abundance data from 21 species of Anolis lizards collected from extensive mark-resight surveys of communities across …

Snake Venoms As Models For Understanding The Origins And Evolution Of Gene Regulatory Networks, Siddharth S. Gopalan

Biology Dissertations - Archive

Understanding the relationship between genotype and phenotype is a fundamental goal of biology. However, the vastly complex nature of eukaryotic gene regulation can make deriving precise relationships between genotype and phenotype challenging. The gene regulatory architecture of snake venom systems provide an opportunity to study this problem in a phenotypic system with immense variation in phenotypes and the underlying genetics. Using a set of integrated functional genomic approaches with snake venoms as a central model, in this dissertation, I provide several examples of the regulatory mechanisms by which diversity in phenotypes arises. Specifically, I identify how gene expression heterogeneity between …

The Evolution Of The Stress Response In The Trinidadian Killifish: Ecological Drivers And Maternal Mediation, Mikaela E. Feder

Biology Dissertations - Archive

Ecological variables can induce the stress response in organisms. Yet, few studies have tested for evolutionary shifts in stress responses across ecological gradients. In these studies, we used Trinidadian killifish found in sites with predators (high predation, HP) and sites where they are the only fish present (killifish only, KO). HP and KO populations differ in a suite of behavioral and life-history traits, making the Trinidadian killifish an excellent model to examine evolutionary physiology. My dissertation addresses the knowledge gap by examining: (1) how baseline cortisol differs in wild-caught Trinidadian killifish found in HP and KO sites, (2) the influence …

Diversification Of Avifauna In The Darién Highland Region: Ecological Niche Modeling, Phylogeography And Morphology To Explore Speciation In The Montane Species Myadestes Coloratus, Chlorospingus Tacarcunae And Margarornis Bellulus., Jorge L. Garzon Vasquez Mrs

Theses and Dissertations

Montane regions in the Neotropics are hotspots of endemism and biodiversity, yet their species are especially vulnerable to the impacts of climate change and geographic isolation. This thesis investigates the evolutionary and ecological dynamics of three bird species endemic to the Darién Highlands of eastern Panama: Myadestes coloratus, Chlorospingus tacarcunae, and Margarornis bellulus. Through an integrative approach combining ecological niche modeling, morphometric analysis, and genomic data from ultraconserved elements (UCEs) and mitochondrial DNA, the study explores the historical biogeography, current distribution patterns, population structure, and phenotypic differentiation of these montane taxa. Ecological niche models revealed that suitable habitat …

Using Rna Sequencing To Examine Encephalic Gene Expression In Cactus Mice, Sarah A. Nicholls

Honors Theses and Capstones

Many of the exact mechanisms by which desert-adapted animals avoid dehydration-induced complications are unknown, though there are likely ties to the general mammalian dehydration response, a multisystem process spearheaded by the brain. Peromyscus eremicus, the cactus mouse, can survive its whole life without intaking water and is commonly used as a model to study desert adaptations. In this study, we have used bulk transcriptomics to characterize the differential gene expression across hydrated and dehydrated P. eremicus in five major regions of the brain: the cerebral cortex (referred to throughout much of this paper as the cortex), hippocampus, thalamus, midbrain, …

The Theory Of Evolution, Alois Nicholas Wurst

Bachelors’ Theses

What is perhaps one of the most fascinating questions in the scientific and philosophical world today is the theory on the Decent of Man. We hear much concerning Evolution. New theories on the subject appear almost daily. Most of these seem to be hoaxes on the part of publicity hungry scientists. If a man would have his name in newspapers the world over, he must only say that he produced a living organism out of inanimate matter. Of course such a statement produces a sensation. But this sensation is short lived. Investigation usually exposes prevarication on the part of the …

A Geometric Morphometrics Analysis Of The Limb Morphologies Of Mosasaurs And Its Palaeoecological Implications, Zachary J. Herbert

Master's Theses or Doctor of Nursing Practice

Mosasaurs were a major component of Late Cretaceous marine ecosystems, being the last Mesozoic radiation of secondarily aquatic tetrapods into diverse niches.

To shed light on the diversity and evolution of limb morphology in this clade, geometric morphometrics analyses were performed on seven skeletal elements from the forelimb and hindlimb. This study tested the hypothesis tested that mosasaurs living in similar environments would exhibit similar morphologies.

After analyzing datasets containing 29 taxa, the observed patterns did not support the hypothesis that habitat was the primary variable influencing morphology. The recurrence of a pattern, the plotting of plioplatecarpine mosasaurs closer to …

Karyotyping As A Method To Verify Phylogenetic Relationships Among The Enneacanthus Species, Ophelia A. Anderson

Theses and Dissertations

The Enneacanthus genus consists of three species of freshwater fish endemic to eastern North America: E. obesus (Banded Sunfish), E. gloriosus (Blue Spotted Sunfish), and E. chaetodon (Black Banded Sunfish). Previous studies using molecular data suggest that E. obesus and E. gloriosus are more closely related, with E. chaetodon as the most distantly related species in the genus. This study investigates the phylogenetic relationship among the Enneacanthus species, using karyotype characteristics - chromosome number, morphology and fundamental number - as comparative metrics. Chromosome spreads were obtained from scale and gill epithelium samples collected between 1993 and 1994. Prepared slides …

A Mystery Of Microecology: Revealing The Ecological Relationship Between Allorhizobium Vitis And Missouri Native Grape Species, Hunter White

Graduate Theses/Dissertations

Crown gall disease can be very detrimental to grape and wine producers around the world by reducing vine vigor and yield. It is caused by the bacteria Allorhizobium vitis (A. Vitis) carrying a tumor inducing (Ti) plasmid. The A. vitis bacteria have been found in soil and cane tissues in vineyards around the world, and infect all cultivated grapes. However, there have been no reports of crown gall on native wild grapevines, and very little is known about the ecology of A. vitis in native ecosystems. I have sampled cambium tissues from three native wild grape species of …

Molecular Characterization Of Fungus-Arthropod Associations, Angie M. Martin

Graduate Theses, Dissertations, and Problem Reports (ETD)

Arthropods, or phylum Arthropoda, are the largest group of animals, accounting for over three quarters of all animal records on NCBI Taxonomy. And yet, only 40% of all deposited sequences on NCBI Nucleotide come from arthropods. Clearly, arthropods are an understudied group of animals: they are small, often drab, and lead lives very alien to our own. Arthropods have chitinous exoskeletons, segmented bodies, and jointed appendages, and include crabs, barnacles, insects, spiders, and millipedes. Since the era of DNA based studies took off in the 1980s, DNA and other small molecules have been integral to our understanding of the Earth …

Exploring Mating Patterns: The Interplay Of Genes, Environment, And Their Evolutionary Outcomes, Sanduni Talagala

Theses and Dissertations (Comprehensive)

There is great variation in the reproductive tactics exhibited both between and within different species, which is reflected in how individuals engage in mate assessment, mate choice and offspring production. It is therefore important to understand general mating patterns of populations, the factors that influence these mating patterns, and the consequences they carry, in order to get a more holistic understanding of mating systems. This doctoral research represents a multi-pronged investigation of the factors shaping mating patterns and their consequences, how environmental factors influence mating patterns, and how both genotypes and the environment interact to influence mate choice decisions and …

Epigenetic Potential Remains Stable Over 100 Years After Introduction, Danielle Dawkins

College of Graduate Studies: Theses & Dissertations

Introduced species provide important insights into organismal behavioral responses. Epigenetic mechanisms are one of the various ways in which behaviors can be modified, particularly through DNA methylation. Through such mechanisms, phenotypic changes can occur in response to environmental changes, allowing an organism to be more plastic. Epigenetic potential (EP) represents the capacity for an organism to be epigenetically modified, and can be measured by counting CpG motifs; cytosine adjacent to guanine within a DNA sequence. Phenotypic plasticity as it relates to EP has been studied extensively in the house sparrow (Passer domesticus), a globally introduced songbird. It is …

Distribution And Ecology Of The Cedar Keys Mole Skink (Plestiodon Egregius Insularis), Kevin M. Enge, Louis A. Somma, Paul E. Moler, Travis M. Thomas, Matthew T. Fedler, John M. Matter, Dennis C. Haney

Papers in Herpetology

We conducted surveys for the Cedar Keys Mole Skink, Plestiodon egregius insularis (Mount), during 1989– 1999 and 2015–2024, examined museum vouchers, and compiled personal observations from others to determine the status and distribution of this subspecies, which has the smallest geographic distribution of the five subspecies and is being considered for federal listing. We observed Cedar Keys Mole Skinks on Airstrip Island, Atsena Otie, Cedar Point, Deer Island, North Key, Scale Key, Seahorse Key, Snake Key, and possibly Dog Island. We have anecdotal reports of Mole Skinks on Way Key, which contains the most potential habitat and is the main …

Précis Of The Edge Of Sentience: Risk And Precaution In Humans, Other Animals, And Ai, Jonathan Birch

Animal Sentience

We often face grave practical decisions that seem to hinge on whether a system is sentient. This family of cases includes invertebrate animals, people who are unresponsive after brain injury, fetuses, neural organoids, and now AI technologies. We must decide what to do despite ongoing disagreement about the nature of sentience. In our state of uncertainty, we should pragmatically transform the question from “Is it sentient?” to “Is it a sentience candidate, an investigation priority, or neither?”. When a system is a sentience candidate, it is negligent to fail to consider precautions. We should instead evaluate precautions for their proportionality …

Genomic Differences And Parentage In West Virginia's Reintroduced Elk (Cervus Canadensis), Adam A.V. Cook

Graduate Theses, Dissertations, and Problem Reports (ETD)

Elk (Cervus canadensis) reintroductions have been common in the 20th and 21st centuries, yet 40% have failed to establish self-sustaining elk populations due to a lack of post-reintroduction demographic monitoring. Elk were reintroduced to West Virginia in 2016 following more than a century of absence after the species was extirpated in 1875. Elk were translocated to West Virginia from Land Between the Lakes National Recreation Area (LBL) in eastern Kentucky and from Arizona. The two groups of elk differ in their subspecies, physiology, reintroduction history, connectivity, and habitat. Reintroductions create genetic risks such as the founder effect and …

Endocrine Responses To Two Distinct Foraging Contexts In The Bonobo (Pan Paniscus), Lauren Mitchell

Master's Theses

In gregarious animals, a social structure characterized by female dominance is relatively rare. However, bonobos (Pan paniscus), one of the two species most closely related to humans, are characterized by partial female dominance, with females forming close social bonds. In contrast, chimpanzees (Pan troglodytes), a close relative of the bonobo, are characterized by strong male-male bonding and social dominance with female chimpanzees lacking close social bonds. There is a lack of consensus concerning the reasons for these behavioral differences in Pan, specifically, the physiological processes responsible for female dominance in bonobos. The role of hormones …

What Is It Like To Be A Diplomat? Reflections On Donald Griffin And Emotion, Oliver H. Turnbull

Animal Sentience

This commentary addresses three aspects of Donald Griffin’s work: (1) his thoughts beyond cognition, on emotion; (2) his views on the earliest origins of mind, including primitive forms of consciousness; and (3) his diplomatic use of memorable phrases to facilitate change.

Scorpiops Reini Sp. N. From Yunnan, China (Scorpiones: Scorpiopidae), Victoria Tang

Euscorpius

Scorpiops reini sp. n. is described from Yingjiang County (Dehong Prefecture, Yunnan Province) based on an adult pair. It can be readily discriminated from all of its congeneric geographic neighbors in Yunnan, namely S. jendeki Kovařík, 1994, S. shidian (Zhu et al., 2005), S. tongtongi Tang, 2022, and S. zhangshuyuani (Ythier, 2019). Within Yunnan, it resembles S. validus (Di et al., 2010) and S. yangi (Zhu et al., 2007) most, but can be identified by its large median ocelli (relative to the width of ocular subislet), pedipalp chelal finger morphology and pectinal tooth count. Beyond Yunnan, it shows the highest …

Hidden Markov Model For Identifying Local Variants In Human Genomes Using Simulated Data, Scott Mccallum

Electronic Theses and Dissertations

Identifying adaptive mutations in genetic data is challenging due to the low frequency of occurrence of such events, and because signatures of selection are intertwined with the footprints of various other evolutionary forces that shape our genomes. Even when a larger region appears to be under selection, genomic sites that are linked to adaptive mutations have similar statistical signals, and thus can obfuscate the identification of the actual adaptive mutation. The new method described here uses a Hidden Markov Model that allows for classification of neutral, linked, and sweep (adaptive mutation) genomic sites. This model is general and can be …

Star-Studded Stingers: Fluorescent Sensilla On The Scorpion Aculeus (Arachnida: Scorpiones), Graeme Lowe

Euscorpius

The aculeus of the scorpion telson was studied by UV fluorescence microscopy. Numerous brightly fluorescent punctae were observed on the non-fluorescent distal aculeus, including the tip region. The punctae were identified as aculear sensilla coeloconica (ASC), and were connected to fluorescent canals running through the cuticle. ASC were present in both sexes, and in adults and immatures as early as the second juvenile instar, but were absent from the first instar. The distal aculeus was found to be encased in a thick, non-fluorescent dark exocuticle (DX), covering an underlying thin, fluorescent hyaline exocuticle (HX). Fluorescent ASC were recorded from 183 …

Scorpions Of The Horn Of Africa (Arachnida: Scorpiones). Part Xxxiv. Four New Species Of Neobuthus From Somaliland (Buthidae), František Kovařík, Hassan Sh A. Elmi, František Šťáhlavský

Euscorpius

New information about taxonomy and distribution of the genus Neobuthus Hirst, 1911 is presented, based on material recently collected in Somaliland. Four new species are described, N. dhobo sp. n., N. opatovae sp. n., N. osoli sp. n., and N. verae sp. n. (Somaliland). An updated distribution map of the genus Neobuthus is provided.

Testing Vivo-Morpholino Mediated Gene Knockdown Of Stat6, Spi1b, And Hnf4Α In Adult Threespine Stickleback, Stella Dipippo

Honors Scholar Theses

The fibrotic immune response to the cestode parasite, Schistocephalus solidus, varies among threespine stickleback populations. Fibrosis suppresses parasite growth but has costly effects on the fish. Previous genomic studies in stickleback have suggested potential roles of Spi1b, STAT6, and HNF4α in modulating fibrosis severity, but there is presently no evidence for this in-vivo. We used antisense vivo-morpholino oligonucleotides (MOs) to attempt to knockdown the expression of each gene in the liver, spleen, and intestine of adult stickleback. Vivo-MOs have been proven effective in other species of teleost fish, as well as in mice and humans, but …

Analyzing Head Morphology Trends With Increasing Population Density In A Jamaican Lizard Species, Lillian Durand

2024 Fall Honors Capstone Projects - Archive

Anolis lizards are model organisms for studying natural selection and evolutionary processes. One trait that is hypothesized to be advantageous for males is head size, as larger heads lead to stronger bite forces and increased likelihood in outcompeting other males for mates. To better understand how linked head size and intraspecific competition are, the head morphology of male A. lineatopus was analyzed among Jamaican populations with varying levels of population density. Population densities were determined using standardized plot surveys and mark resight models. Head dimensions and body condition for individual lizards were measured at each site. My study found that …

Evaluating The Roles Of Pollinators In Shaping The Floral Color Variation Of Phacelia Dubia, Katherine Riddle

All Theses

Floral color variation within a species is a common occurrence and its maintenance has been a long-standing question in evolutionary biology. Differences in flower color between populations can be shaped by pollinator-mediated selection. Pollinators can exhibit innate and learned preferences for color that may influence floral color variation. These preferences may be molded by the visual environment in which pollinators forage. Most current understanding of how pollinators shape floral color variation involves dramatic differences in dominant pollinators between populations (e.g., hawkmoth vs. bee) and most behavioral work utilized model pollinators like honeybee and bumble bee. However, less is known about …

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 …

To Be Conscious Or Not To Be, Bjørn Grinde

Animal Sentience

Carolyn Ristau has done a fine job summarizing the work and life of the zoologist Donald Griffin. Most scientists now accept the existence of animal sentience, but identifying which species possess consciousness remains controversial. Griffin defined consciousness as "the subjective state of feeling or thinking about objects and events.” Nonconscious processes are faster and more energy-efficient, however, and often drive behavior. Consciousness probably evolved for complex decision-making, shaped by evolutionary continuity, with feelings as a common currency for evaluating outcomes. Its survival advantage may be limited, and its presence across species varies depending on evolutionary trajectories.

Tityopsis Rolandoi Sp. N. (Scorpiones: Buthidae) From Cuba, František Kovařík, Mark Stockmann, František Šťáhlavský, Sheyla Yong

Euscorpius

A new species Tityopsis rolandoi sp. n. is described from Cuba, fully illustrated with color photos showing its morphology and habitus. T. rolandoi sp. n. is the only species of the genus with a combination of two characters: movable finger shorter than carapace and chela length/width ratio 3.6 in male. This species also has a characteristic shape of a median smooth patch of sternite V, which is almost oval in male. In addition to morphology, we present the information about the karyotype of T. rolandoi sp. n. (2n=20) and T. sheylae (2n=22).

Communication In Noise Is The Window On Cognition, R. Haven Wiley

Animal Sentience

As Griffin surmised, communication is the window on cognition, but as shown here, only if it is noisy. This commentary is an invitation to consider the full implications of the evolution of noisy communication. A combination of Information Theory, Signal Detection Theory, and Natural Selection, in a unified theory of the evolution of communication, reveals that noise is inevitable. All organisms are thus decision makers. Perception, thought, freedom of decision, self-awareness, metabolism, and natural selection all share the consequences of signals in noise. A full understanding of each requires attention to the errors of receivers. Griffin’s hunch is correct with …

Understanding The Welfare Of Aquarium Fish, Paul Rose

Animal Sentience

Bony fishes (Osteichthyes) are prevalent in public and domestic aquaria, yet evidence-based welfare practices exist for only a limited number of species. Oldfield & Bonano’s (O&B’s) target article highlights critical questions about the wellbeing and sociality of Osteichthyes. Advancing research on their biology, physiology, psychology, and behavior is essential to develop and validate welfare measures, ensuring guidelines for welfare-focused housing and husbandry.

Structural Molecular And Developmental Evidence For Cell-Type Diversity In Cnidarian Mechanosensory Neurons, Julia Baranyk, Kristen Malir, Miguel A.P. Silva, Sakura Rieck, Gracie Scheve, Nagayasu Nakanishi

Biological Sciences Faculty Publications and Presentations

Deploying a conserved mechanosensory neuron known as the concentric hair cell, cnidarians have evolved diverse mechanoreceptors from hydroid filiform tentacles to jellyfish statocysts. However, it is unknown whether cnidarian mechanoreceptor evolution has relied solely on repurposing a single ancestral mechanosensory neuron type. Here we report evidence for cell-type diversity of mechanosensory neurons in sea-anemone cnidarian Nematostella vectensis. Uncovered in the ectoderm of feeding tentacles are conventional type I hair cells and previously unrecognized type II hair cells differing in the structure of apical sensory apparatus and synapses. Moreover, we identify TRP channel-encoding gene polycystin-1 as a type-II-hair-cell-specific essential mediator of …