Biology Commons^™

Signatures Of Selection, Gene Flow, And Genetic Drift On The Genomes Of A Recent Avian Radiation, Flor Brigitte Hernandez Camacho

Open Access Theses & Dissertations

Speciation is not a discrete event but rather a gradual process that occurs along a continuum. Initially, populations remain genetically and reproductively connected, but they become reproductively isolated as the process of speciation progresses. Advances in DNA sequencing technology has helped our understanding of the processes that contribute to changes in the genetic composition of populations over the progression of speciation, also known as drivers of evolution (i.e. genetic drift, mutation, selection, and gene flow). Among them, hybridization, or the interbreeding between distinct lineages, is increasingly recognized as a natural process that can have significant consequences to the speciation process. …

An Exploration Of The Drivers Of Intraspecific Variation In Arthropod Phenotypes, Jamie Phelps

LSU Doctoral Dissertations

Herein we explore the various forces that drive phenotypic variation in arthropods focusing on spatial and temporal differences as well as sexual dimorphism. We use both marine, Tigriopus californicus, and terrestrial, Melitaeini, organisms to investigate these forces.

Tigriopus californicus and Heat Hardening: The study explores how Tigriopus californicus, a copepod, adapts to thermal variation along the North American Pacific Coast. Researchers investigated intraspecific variation in heat hardening, measuring differences in upper lethal limits (ULLs) and potential fecundity costs across five populations. We found a cost of heat hardening: the size of the first brood produced after heat shock …

Seed Dispersal By Martu Peoples Promotes The Distribution Of Native Plants In Arid Australia, Rebecca Bliege Bird, Douglas Bird, Christopher T. Martine, Chloe Mcguire, Leanne Greenwood, Desmond Taylor, Tanisha M. Williams, Peter M. Veth

Faculty Journal Articles

Commensal relationships between wild plants and their dispersers play a key ecological and evolutionary role in community structure and function. While non-human dispersers are often considered critical to plant recruitment, human dispersers have received much less attention, especially when it comes to non-domesticated plants. Australia, as a continent historically characterized by economies reliant on non-domesticated plants, is thus a key system for exploring the ecological role of people as seed dispersers in the absence of agriculture. Here, we utilize a controlled observation research design, employing ecological surveys and ethnographic observations to examine how seed dispersal and landscape burning by Martu …

Records Of The Red-Bellied Snake (Storeria Occipitomaculata) In Central And Northeastern Nebraska, Taylor Lowe, Sarah M. Bailey, Dan D. Fogell, Keith Geluso

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Red-bellied Snakes (Storeria occipitomaculata) are a distinctive, small species that live in moist woodlands throughout much of eastern North America. In the Great Plains, isolated populations exist in South Dakota, Wyoming, and Nebraska. In Nebraska, the only known extant population occurs in wooded riparian habitats along the Big Bend Reach of the Platte River in southcentral parts of the state. Herein, we report on new county records of Red-bellied Snakes in Nebraska, with two observations from Merrick County along the Platte River adjacent to known populations and two observations of a new population in the extreme northeastern part …

Microplastic Accumulation In The Marsh Periwinkle (Littoraria Irrorata), Sarah Keaton, Hannah Lukhard, Eli Windy, Manar Hasan

DePaul Discoveries

Contamination of oceans by microplastics (mm) currently poses a major threat to aquatic and terrestrial ecosystems worldwide. Recent attention towards this issue has raised questions about the extent to which microplastics have accumulated in the environment, and has led to an increase in studies on the effects of microplastics in various organisms. However, levels of contamination in protected natural areas are still largely unexplored, yet can offer an important empirical perspective on the issue. In addition, little is known about the potential effects of microplastics on behavior in the field. This research was conducted within the protected ACE Basin National …

Sexually Antagonistic Coevolution Of The Male Nuptial Gift And Female Feeding Behaviour In Decorated Crickets, Samuel Burns-Dunn, Tassie Mortys, Clarissa M. House, Christopher Mitchell, Kristin R. Duffield, Bert Foquet, Ben M. Sadd, Scott K. Sakaluk, John Hunt

Faculty Publications – Biological Sciences

The evolution of nuptial gifts has traditionally been considered a harmonious affair, providing benefits to both mating partners. There is growing evidence, however, that receiving a nuptial gift can be actively detrimental to the female. In decorated crickets (Gryllodes sigillatus), males produce a gelatinous spermatophylax that enhances sperm transfer but provides little nutritional benefit and hinders female post-copulatory mate choice. Here, we examine the sexually antagonistic coevolution of the spermatophylax and the female feeding response to this gift in G. sigillatus maintained in experimental populations with either a male-biased or female-biased adult sex ratio. After 25 generations, males …

The Influence Of Resource Patch Condition And Size On Social Interactions, Reproductive Behaviors, And Oviposition In A Fungivorous Beetle, Lillian J. Fornoff , '21, C. A. Stahlmann Roeder, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Variation among resource patches can structure spatial patterns of social behavior. Individual preferences and requirements for heterogeneous resources can lead to differences in where behaviors take place and which kinds of individuals interact. In this study we examined whether properties of habitat patches predict presence of and interactions among wild forked fungus beetles (Bolitotherus cornutus). B. cornutus use shelf-like fruiting bodies of wood decaying fungi (brackets) as social arenas, courtship and mating sites, oviposition locations, and food sources. Brackets on a single log vary in size and condition and represent a dynamic resource as individual brackets decay over …

Scientific Note: An Incursion Of The Widely-Cultivated Katsura (Cercidiphyllum Japonicum, Cercidiphyllaceae) In Pennsylvania, Kayleigh R. Long, Melody P. Sain, Elizabeth H. Williams, Christopher T. Martine

Faculty Journal Articles

Cercidiphyllum japonicum (katsura) is a dioecious tree native to China and Japan. Although imperiled in parts of its natural distribution, the species has become quite common as a cultivated tree in temperate North America. The species is noted as occasionally escaping cultivation in the eastern United States, but few records of established incursions (and the conditions under which they might recruit) exist in the literature. We here report an incursion of C. japonicum in central Pennsylvania, along with notes on seedling recruitment on the Bucknell University campus.

New Insights On Hybridization In Potamogeton Floridanus (The Florida Pondweed), Kaitlyn R. Sampson

Graduate Theses and Dissertations (2019 - present)

Freshwater ecosystems are some of the most important and highest threatened habitats in the world, and aquatic plants play an important, but often-overlooked, role in maintaining them. Potamogeton is a diverse and ecologically important aquatic plant genus well known for taxonomic difficulty and rampant hybridization. lbis study aimed to 1) test the hypothesis that Potamogeton jloridanus (Florida pondweed) is a hybrid between P. oakesianus and P. pulcher, and 2) to investigate correlations in ecological conditions for the focal species. This study revealed the discovery of a new population of P. jloridanus in Big Coldwater Creek in Santa Rosa Co., FL, …

The Ecological Applications Of Δ17O: Validating A Novel Technique For Assessing Animal Metabolism And Water Intake, Zachary Taylor Steele

Biological Sciences Theses & Dissertations

Animals obtain water via different processes such as drinking, consuming food, and through metabolic processes like at the end of the electron transport chain when atmospheric oxygen is combined with hydrogen to form ‘cytochrome oxidase water’. Assessing animal water flux and metabolism has mainly been conducted via stable isotope analysis (SIA) of biological samples using hydrogen (²H) and oxygen isotopes (¹⁶O, ¹⁷O, and ¹⁸O; Δ¹⁷O), typically using enriched isotope tracers. However, natural abundance isotope modeling offers an approach for conducting SIA of biological samples that differs because it relies on the unique, …

Climate And Shared Evolutionary History Drive Trait Variation Among Species Of Neotropical Understory Monocots, Eleinis Ávila-Lovera, Oscar M. Vargas, Jennifer L. Funk, Kathleen M. Kay, Gregory R. Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Environmental variation commonly drives functional trait diversity within species, among species, and across communities. Climate and shared evolutionary history can both influence trait–environment relationships. We studied variation in plant functional traits among closely related Costus species occurring across environmental gradients, the extent to which this variation occurs within single species, and how that variation may be influenced by shared evolutionary history. We measured leaf, aboveground stem, rhizome, and fine root traits of 17 species of Costus in eight sites in Costa Rica and Panama, which varied in elevation, temperature, and precipitation. We then assessed the relationships among traits and environmental …

Removal As A Control Method For Trachemys Scripta Elegans And The Response Of Chrysemys Picta Bellii, Jacob Swanson

University Honors Theses

The red-eared slider is considered one of the most ubiquitous freshwater turtles globally. Several key ecological advantages and life history traits of this species jointly impact growth rates and survivorship of native freshwater turtles where sympatry occurs. Evaluation of current management actions for red-eared slider turtles is limited, resulting in a paucity of information to guide management for the species and conservation of declining native freshwater turtles. We used previously collected mark-recapture and removal sampling data from sites with sympatric populations of red-eared slider and western painted turtles. We examined the effects of control (trapping and removal) of red-eared sliders …

Evolution And Adaptation To Temperature In Thermotogota, Anne Amelia Farrell

Dartmouth College Ph.D Dissertations

Life thrives across incredibly diverse environmental conditions, yet most organisms are restricted to growing within a narrow range around their optimum growth temperature (OGT). The evolutionary events leading to changes in OGT are poorly understood, and it is uncertain if specific genes are required to thrive at a particular temperature. The bacterial phylum Thermotogota is an excellent model for the evolution of OGT. It comprises mesophilic, thermophilic, and hyperthermophilic members that collectively grow between 20°C and 90°C.

In this work, I analyze the history of OGT in the Thermotogota phylum and show how horizontal gene transfer contributes to the evolution …

Fisheries Occasional Publication No.147 - Aquaculture Development Zones – Policy Position Relating To Permitted Alternative Species, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Occasional Publications

The purpose of this policy is to set out considerations relevant to the assessment of aquaculture proposals within Aquaculture Development Zones (ADZ) for species distinct from the group of species for which the ADZ was initially established (Alternative Species).

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

Dissertations

Understanding how indigenous plant species respond to arid environmental stressors is critical for biodiversity preservation and the development of sustainable agricultural practices in the United Arab Emirates (UAE). This study investigated the morphological and physiological aspects of the germination and early growth stages, along with the adaptation strategies of three indigenous plant species—Senna italica, Prosopis cineraria, and Tephrosia nubica. The controlled chamber experiments aimed to subject the three selected indigenous species to elevated CO2 (400 ppm ambient to 800 ppm) and temperature (35°C ambient to 50°C) for simulating future atmospheric carbon dioxide (CO2) and temperature scenarios. …

The Stability Of Epigenetic Variants That Can Act As Loci Causing Phenotypic Change, Raul Faburrieta

Biology Theses

Epigenetic variations are a possible source of heritable phenotypic variation. In this study I focus on phenotypic alterations seen in epigenetic Recombinant Inbred Lines (epiRILs) of Arabidopsis thaliana. These epiRILs allow me to study the effects differentially methylated regions (DMRs) have on phenotypic variance. In a study performed in 2014 by Cortijo et al., they found that DMR’s affect flowering time and root length when grown under greenhouse conditions. In this study, I replicated the Cortijo et al. (2014) study, with some changes, to see whether the same significant eQTL regions are found. I found that, some of the eQTLs …

Maturation Of An Off-Channel Habitat Concept To Conserve Native Fishes In The Lower Colorado River, Paul C. Marsh, Thomas E. Dowling, Thomas F. Turner, Megan J. Osborne, Brian R. Kesner

Monographs of the Western North American Naturalist

Two endemic, “large river” fishes of the Colorado River basin of western North America, bonytail Gila elegans and razorback sucker Xyrauchen texanus, are among several critically endangered species in the system. Wild populations of bonytail are gone, and there are no self-sustaining populations of razorback sucker anywhere; reproduction occurs but recruitment does not. Both species have been under intensive management in the Lower Colorado River since the 1980s. Today, with the single exception of Lake Mead, remaining populations are composed entirely of repatriated individuals that depend on stocking for their continued existence. In 2003, a conceptual off-channel habitat (OCH) …

Spawning Ecology And Spawning Site Fidelity Of Alligator Gar, Atractosteus Spatula, In The Fourche Lafave River: Implications For River-Floodplain Management And Alligator Gar Conservation, S. Reid Adams, Thomas E. Inebnit, Lindsey C. Lewis, Christopher J. Naus, Edward Kluender, Geoffry G. Spooner

Southeastern Fishes Council Proceedings

We studied the spawning ecology of Alligator Gar, Atractosteus spatula, in the Fourche LaFave River (FLR) of Arkansas to better understand their reproductive ecology and spawning resource requirements. Evidence of spawning was only observed in floodplain tributary habitats, particularly the small, adventitious headwater stream West Fork Mill Creek (WFMC). A mid-May to mid-June spawning season was observed for Alligator Gar in the FLR that corresponded with rising water levels (mostly due to backflooding from the Arkansas River) and increased water temperatures (> 20°C). Direct spawning observations at WFMC were made on 17 June 2007, 15 June 2008, 23 May …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

Unraveling The Paradox Of The 'Great Speciators': Evolutionary Dynamics Of A Geographic Radiation Of Island Kingfishers (Todiramphus), Jenna Merle Mccullough

Biology ETDs

The paradox of the ‘Great Speciators’ describes a biogeographic pattern in which geographically widespread lineages have strong overwater dispersal capabilities, yet exhibit genetic and phenotypic divergence between islands, suggesting limited dispersal and cessation of gene flow. In my dissertation, I leveraged whole genomes and two comprehensive trait datasets of dispersal ability and plumage coloration of all described diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic ‘Great Speciators.’ Chapter 1 reveals that whole genome datasets do not outright solve the evolutionary relationships of this clade and that widespread incomplete lineage sorting (ILS) and gene flow are sources of …

Comparative Functional And Computational Analyses Of Primate Seminal Proteins: Insights Into Sexual Selection And Hiv/Siv, Emine Feride Kahveci

Electronic Theses and Dissertations

Male reproductive protein-coding genes are among the most rapidly evolving genes across many animal taxa, commonly attributed to sexual selection; however, pathogen defense mechanisms might also be contributing factors. This study aimed to both computationally and experimentally investigate the selective pressures responsible for the rapid evolution of seminal proteins. In the first part, the research focused on sexual selection in the form of post-copulatory sperm competition as a driving force behind the evolution of kallikrein related peptidase 3 (KLK3), also known as prostate-specific antigen (PSA), a key prostatic seminal protein. KLK3 is responsible for the liquefaction of semen coagulum through …

Greening The Edge: Investigating Riparian Buffer Restorations In A Pastoral Setting And Their Effects On Soil Carbon And Microbial Community Composition., Seth Mccullough

Masters Theses, 2020-current

Riparian buffer restoration represents a critical strategy for enhancing ecosystem health and resilience in agricultural landscapes. This study investigates the effects of riparian buffer restoration on soil properties, microbial communities, and carbon dynamics in Rockingham County, VA. Through a comprehensive field study, we assessed the physicochemical properties of soil, microbial biomass, community composition, and soil carbon storage in restored and unrestored riparian buffers. Our findings reveal significant improvements in soil physical properties in restored buffers, including increased soil moisture (p < 0.05) and decreased bulk density (p < 0.01), indicating enhanced soil structure and water retention capacity. While no significant differences were detected in soil pH or cation exchange capacity, restored buffers exhibited higher soil carbon stocks (p < 0.05) and carbon-to-nitrogen ratios, suggesting potential differences in nutrient cycling processes and organic matter decomposition rates. Moreover, restored buffers showed increased microbial biomass (p < 0.01), potentially driven by improved habitat conditions and shifts towards a fungal-dominated microbial community.

Although no significant differences were found in overall microbial community composition between restored and unrestored sites, specific shifts in bacterial …

Crossing The Ocean: The Importance Of Gene Flow In Island Evolution, Ethan F. Gyllenhaal

Biology ETDs

Islands have long been a critical arena for the development of ecological and evolutionary theory, particular due to persistent open-water gaps between them. In this dissertation I demonstrates how these caps are permeable, which can be leveraged to understand evolution on islands and more broadly. The first chapter develops this connection between ongoing, overwater gene flow and island biogeographic theory, and tests it on an archipelago species. The second take a three-pronged approach in demonstrating how over-water gene flow can bias phylogenetic inference, and how many phylogeographic metrics in islands are likely shaped by long-term gene flow. The final two …

Lmpact Of Salmonella Enterica Effector Proteins On Plant Physiology And Immunity, Sara Qader

Honors Theses

Salmonella enterica serovar Typhimurium are primarily recognized as pathogens associated with foodborne illnesses in humans. Salmonella also can colonize plant tissue effectively. The pathogen relies on type III secretion systems (T3SS) to infect mammals and plants successfully and counteract the immune response. Understanding the molecular mechanisms underlying Salmonella’s interactions with plants is essential for developing effective strategies to reduce its impact on human health and agriculture. Effector proteins, known for their role in modulating host-pathogen interactions, have been implicated in the virulence and pathogenicity of Salmonella. However, their specific functions and contributions to Salmonella’s interactions with plants remain largely unknown. …

Beating The Heat: The Use Of Coral-Benefitting Bacteria For Heat-Stressed Anemones And Inspiring Future Biologists, Navah Eshraghi

Undergraduate Honors Theses

The warming of ocean temperatures has caused mass coral-bleaching events characterized by the expulsion of vital algal symbionts from coral tissues. However, the possibility of algal reuptake and existence of bacteria that support coral-algal symbiosis are two avenues of potential restoration efforts. Using the sea anemone Exaiptasia diaphana as a model for corals, I tested whether the coral-benefitting bacterium Endozoicomonas montiporae could enhance algal uptake under ambient (27°C) and heat-stressed (32°C) conditions. I then turned acquired results into an article modeled after National Geographic Kids to introduce the experiment to younger ages. While temperature was a larger determinant of algal-uptake …

The First Draft Genome Of Cold-Water Octocoral Anthothela Grandiflora, The Great Flowerbud Coral, Laurel Humphrey

Honors Scholar Theses

Cold-water corals are important sources of ocean biodiversity, yet populations are increasingly threatened by human activity and climate change. Soft octocorals may endure higher ocean acidification levels in comparison to stony hexacorals, although the mechanisms of octocoral biomineralization are less understood. Building genomic resources for cold-water octocorals could help to close information gaps by elucidating the evolutionary history of octocoral calcification and provide a reference for future studies of adaptation to acidified waters. This report describes the first reference genome for the cold-water octocoral species Anthothela grandiflora found throughout the Atlantic Ocean. Sequencing using Oxford Nanopore Technologies generated 43.6 Gb …

West Coast Rock Lobster Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed by the Department of Primary Industries and Regional Development (DPIRD, the Department) to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act …

Random-Effects Substitution Models For Phylogenetics Via Scalable Gradient Approximations, A. F. Magee, A. J. Holbrook, J. E. Pekar, Itzue W. Caviedes-Solis, F. A. Matsen Iv, G. Baele, J. O. Wertheim, X. Ji, P. Lemey, M. A. Suchard

Biology Faculty Works

Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate …

Chemical-Mediated Mate Attraction In Clover Root Curculio (Sitona Hispidulus F.), A Belowground Pest Of Forage Crops, Kristin Leutgeb

Undergraduate Honors Capstone Projects

Curculionid beetles are well known for their production of semiochemicals, including contact (e.g. cuticular hydrocarbons) and volatile pheromones that mediate conspecific attraction and mating. Clover root curculio (CRC; Sitona hispidulus) in particular is an emergent, soil-borne pest of significant concern to producers of alfalfa and other leguminous crops in the United States. Producers have few control options for CRC and a greater understanding of chemical-mediated attraction in this species can potentially improve the sustainability of its management. To examine which chemical cues are important for affecting the behavior of CRC and whether there are sex-based differences in response, I …

Cross-Pollination: Building A Co-Taught Course To Examine Art And Sex Through The Lens Of Botany, Christopher T. Martine, Diamanda A. Zizis, Anna K. Kell

Faculty Journal Articles

Driven by overlapping interests in plants, art, and diversity in sex expression, Anna Kell (Department of Art and Art History) and Chris Martine (Department of Biology) developed a course that integrates the perspectives of a visual artist and a botanist. Art & Sex Through the Lens of Botany seeks to impart the importance of making connections across disciplines and the value of visual literacy across academic lines. The course introduces foundational concepts in each field and encourages students to integrate and explore these different systems of knowledge and their intersections. In addition to developing fluencies related to both general botany …