Ecology and Evolutionary Biology Commons^™

Movement Behavior And Metapopulation Connectivity Of Stream Salamanders In Response To Disturbance Events, Kathryn M. Greene

Theses and Dissertations--Biology

Metapopulations are shaped by the dispersal between populations in a landscape. Disturbance events can disrupt this connectivity resulting in local population extinction. For my dissertation, I used a combination of empirical and theoretical techniques to examine dispersal in response to disturbance and assessed it’s population-level consequences. My research used capture-mark-recapture sampling techniques to evaluate stream salamander movement in response to (1) a supraseasonal drought and (2) mountaintop-removal-mining (MTR) and valley-filling (VF) and (3) agent-based simulation modeling to evaluate population extinction risk in response to varying dispersal and mortality rates.

First, I evaluated the effects of a supraseasonal drought, a severe …

Competition And Herbivory Influence The Survival, Growth, And Physiology Of Native Tree Seedlings In The Kentucky Inner Bluegrass Savanna-Woodland, James D. Shaffer

Theses and Dissertations--Biology

Terrestrial plant communities are shaped by competition for resources, herbivory, and abiotic processes. Savanna systems represent a dynamic coexistence of contrasting life forms (grasses and trees) shaped by competition and disturbance. The Kentucky Inner Bluegrass Savanna-Woodland (KIBSW) is described as an open woodland of shade intolerant species; however, climatic, and edaphic conditions can support closed-canopy forest. After European pioneer settlement (c1750-1800), over 99% of “savanna-woodlands” have been lost. KIBSW remnants are experiencing a recruitment failure, leading to a dominance shift in tree communities. I researched how tree-grass competition and mammalian herbivory influence KIBSW regeneration and maintenance. The KIBSW does not …

Variation In Behavioral Strategies For Coping With Environmental Uncertainty, Allison Mclaughlin

Theses and Dissertations--Biology

My dissertation investigates how animals behaviorally respond to environmental change, especially when there is limited information about that change. Uncertainty about the environment comes in various forms, including food resources which vary unpredictably and novel cues which present an unknown level of potential risk or benefit. Various behavioral strategies help animals cope with such uncertainty. Tactics to manage unpredictable variation in food include gathering information to reduce uncertainty (sampling) and strategically adjusting preference or aversion to variation in resources (variance-sensitivity). To manage the uncertainty of a novel cue, animals may generalize their previous experience with similar cues, or they may …

Parental Effects On Offspring Reaction Norms: Consequences For Complex Phenotypes In Variable Environments, Alexandra G. Cones

Theses and Dissertations--Biology

Organismal traits all exhibit some degree of environmental sensitivity, and both the strength and direction of these phenotypically plastic responses to the environment can evolve in adaptive ways. For example, parents can use information about their own environment to precondition the traits of their offspring so that they thrive in their future environment. This transgenerational plasticity can also alter the plasticity of offspring, but explicit investigations of this specific phenomenon are rare. I begin with a review of the literature and provide a quantitative genetic framework to investigate this phenomenon, which I then explore empirically using avian embryos. The metabolic …

Placing The Evolutionary History Of Desmognathus Salamanders In Context: A Phylogeographic Approach, Kara Jones

Theses and Dissertations--Biology

Patterns of genetic variation do not arise in a vacuum but are instead shaped by the interplay between evolutionary forces and ecological constraints. Here, I use a phylogeographic approach to examine the role that ecology played in lineage divergence in the Desmognathus quadramaculatus species complex (Family: Plethodontidae), which consists of three nominal species: D. quadramaculatus, D. marmoratus, and D. folkertsi. Previous phylogenetic studies have shown that individuals from these species do not form clades based on phenotype. My approach to reconciling phylogenetic discordance was two-fold, using (1) genome-wide markers to provide insight into the …

Multilevel Phenotypic Integration Of Metabolism And Behavior In House Sparrows And Mice, Tim Salzman

Theses and Dissertations--Biology

Patterns of multilevel variation in behavior, both within and among individuals, raise challenging questions about underlying mechanisms and the selective pressures acting on them. One intriguing hypothesis is that physiology shows parallel multilevel variation, and so might represent a latent trait that integrates multilevel behavioral responses. For example, foraging acquires the fuel needed to maintain metabolism, and in turn, an individual’s metabolism affects expression of foraging, and other, behaviors. Metabolism and behavior thus might coevolve to become integrated traits. Despite the appeal of this hypothesis, numerous investigations into the link between metabolism and behavior have yielded largely equivocal results.

To …

Context-Dependency And Sex-Specificity Of Dispersal Syndromes, Allyssa Kilanowski

Theses and Dissertations--Biology

For populations in landscapes with increasingly heterogeneous and fragmented habitat patches (e.g., metapopulations), dispersal is an important behavior that leads to gene flow and connectivity among isolated patches. Because dispersal is a complex process, there are many traits involved. When suites of morphological, behavioral, physiological, and life-history traits covary with dispersal (e.g., a dispersal syndrome), the correlated traits can assist dispersing individuals through the complex process. Furthermore, once dispersal is completed, the correlated traits can influence the fitness of those dispersed individuals. Dispersal syndromes will likely interact with the local environment to produce ecological and evolutionary feedbacks on the metapopulation. …

The Social Behavior Of Pine Sawflies In The Genus Neodiprion, John W. Terbot Ii

Theses and Dissertations--Biology

Group living is found across the animal kingdom ranging from temporary mating aggregations to complex, eusocial lifestyles. A particularly common form of group living found among insects are larval or nymphal herds. This lifestyle consists of immature insects living together and results in several proposed costs and benefits. Benefits of this lifestyle include improved ability to regulate a group’s microenvironment, more efficient use of their host, and the ability to engage in collective predator defenses. Offsetting these benefits are costs resulting from living in close proximity to conspecifics which include increased competition, greater visibility to predators, and heightened disease risks. …

Limb Development In Salamanders: An Evolutionary Perspective To The Tetrapod Limb, Sruthi Purushothaman

Theses and Dissertations--Biology

Vertebrate limb is an ideal model to study growth, patterning and morphogenesis and the interplay between these processes. The developing limb bud is a three-dimensional structure and its outgrowth depends on the interaction between 2 important signaling centers: the Apical Ectodermal Ridge (AER) at the junction of the dorsal and ventral halves of the limb bud and the Zone of Polarizing activity (ZPA) in the posterior mesenchyme. These centers produce their respective key molecules and the close interplay between them specifies structures along the anterior-posterior (thumb to pinky), proximal-distal (shoulder to fingertips) and dorsal-ventral (knuckle to palm) axes.

Developmental biologists …

Landscape Ecology And Population Genomics Of Two Sympatric Pitviper Species Across A Fragmented Appalachian Landscape, Thomas Maigret

Theses and Dissertations--Biology

Understanding the link between landscape patterns and ecological and evolutionary processes is an important prerequisite for informed wildlife conservation and management, especially in rapidly changing landscapes. Until recently, the inaccessibility of spatial and genomic data sets of sufficient resolution limited our ability to incorporate the impacts of landscape patterns into predictions of ecological and environmental outcomes. In this dissertation, I utilized several high-resolution spatial and genomic data sets to address ecological questions in a rapidly fragmenting landscape in southeastern Kentucky. Overall, my results indicate that large-scale surface coal mining is causing widespread homogenization of landforms, resulting in a uniquely permanent …

Predicting Patterns Of Gene Family Evolution In Taxa With Similar Ecological Niches, Kim Vertacnik

Theses and Dissertations--Biology

To fully understand the genetic basis of adaptation, we need to know its predictability—the extent to which specific selective pressures and contexts can yield corresponding genetic changes. In particular, the repeated colonization of similar, specialized environments by different taxa is ideal for assessing the frequency of reoccurring changes in the same genes or functions. But compared to a growing body of literature on the convergent evolution of individual genes, far less is known about the repeatability of gene family evolution, where families (defined here as groups of genes that share sequence and functional similarity from common ancestry) can expand (gain …

From Genes To Species: Ecological Speciation With Gene Flow In Neodiprion Pinetum And N. Lecontei, Emily E. Bendall

Theses and Dissertations--Biology

My dissertation focuses on how differences accumulate across the genome during ecological speciation with geneflow. To do this I used two species of Neodiprionpine sawflies, which are plant-feeding hymenopterans with high host specificity. I used experimental crosses to measure both intrinsic and extrinsic postzygotic isolation and to understand the contribution of specific traits to reproductive isolation. Despite substantial genetic divergence and haploid males in which all recessive incompatibilities should be expressed, I found surprisingly little evidence of intrinsic postzygotic isolation. Recombination in hybrid males may reconstitute viable genotypes and counteract the effects of haploidy in males. Nevertheless, hybrids have …

From Organisms To Ecosystems: Impacts Of Limb Loss And Regeneration On Crayfish Behavior, Luc Arnaud Dunoyer

Theses and Dissertations--Biology

The ability of some organisms to regenerate tissues and organs has fascinated naturalists since antiquity, dating back to the earliest accounts of scientific inquiry with Aristotle in Ancient Greece. Then, Darwin’s theory invigorated some scientists’ dream of stimulating (or reactivating) regenerative capacities in human beings by showing that we are related to highly regenerative organisms. More recently, a renewed interest in discovering the molecular and genetic basis for organ and tissue regeneration has led biologists to focus more specifically on a restrictive set of model organisms.

Although the process of limb regeneration is different between invertebrate and vertebrate organisms, it …

Ecology, Monogamy, And The Evolution Of Animal Families, Jacqueline Rae Dillard

Theses and Dissertations--Biology

Family-living has been recognized as a necessary prerequisite for the evolution of advanced cooperative societies, yet the evolutionary and ecological processes that drive the coupling of different forms of cooperation in family-based societies are still poorly understood. In my dissertation, I investigate the correlated evolution of parental care, monogamy, and cooperative breeding in a variety of family-based taxa. I explore the mating and social behavior of family-living beetles with incipient cooperation to better understand the factors driving these social traits. Specifically, I evaluate different causes of extra-pair mating in socially monogamous beetles, the potential benefits that young adult offspring may …

Intraspecific Variation In Dehydration Tolerance: Insights From The Tropical Plant Marchantia Inflexa, Rose A. Marks

Theses and Dissertations--Biology

Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition, …

The Role Of Sociality And Disturbance In Shaping Elk (Cervus Canadensis) Population Structure, Brittany L. Slabach

Theses and Dissertations--Biology

Investigating how and why individuals interact is an important component to understanding species ecology. The type and patterning of relationships (social structure) provides pertinent insight into how ecological factors such as spatial heterogeneity of resources and predation influence associations between individuals. Many taxa exhibit temporally fluid association patterns, where individuals associate with a variety of others at different rates. Ungulate species exhibit prime examples of highly fluid grouping patterns and individuals form both temporary and long-term associations. The effects of human disturbance on ungulate behavior are well documented and these changes are further exacerbated during the hunting season. Species such …

Sexual Dimorphism In The Moss Bryum Argenteum And Its Implications For Sex Ratio Bias, Jonathan David Moore Iii

Theses and Dissertations--Biology

In dioecious plants, selection due to sex function differences has produced sex-specific life histories, morphologies, and physiologies. In many dioecious seed plants, dimorphisms and population sex ratios have been plausibly linked, but similar links are not yet apparent in dioecious bryophytes. Population sex ratio bias is often expected to favor the sex with lower investment in sexual reproduction, especially in resource-poor environments. Unlike in seed plants, bryophyte males may have higher average reproductive investment than females, which typically have low offspring production rates due to sperm limitation. However, traits aside from reproductive investment such as shoot and leaf arrangement may …

Mitochondrial And Nuclear Patterns Of Conflict And Concordance At The Gene, Genome, And Behavioral Scales In Desmognathus Salamanders, Justin D. Kratovil

Theses and Dissertations--Biology

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns …

Invasion Dynamics Of The Exotic Liana Euonymus Fortunei (Turcz.) Hand.-Mazz. (Wintercreeper), Todd J. Rounsaville

Theses and Dissertations--Biology

Elevated atmospheric CO₂ has been implicated as a driver of increased liana abundance worldwide. Known as disturbance creators and beneficiaries, lianas possess the potential to significantly influence forest ecosystems. I investigated the early-invasion dynamics of Euonymus fortunei (wintercreeper), an evergreen liana that is invading forests in eastern North America, disrupting native plant communities and ecosystem functions.

Wintercreeper is widely cultivated as an ornamental groundcover, frequently invading natural areas via asexual stem growth. Invasion of remote natural areas is dependent upon seed transport and may occur less frequently. I examined the mechanisms of seed dormancy by conducting a ‘move-along’ experiment …

Genetic Perspectives On Biodiversity In Rocky Mountain Alpine Streams, Scott Hotaling

Theses and Dissertations--Biology

In alpine regions worldwide, climate change is dramatically altering ecosystems, affecting biodiversity across habitats and taxonomic scales. For streams, the associated recession of mountain glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, and basal resources – often threatening the very existence of some habitats and biota. Globally, alpine streams harbor particularly substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity: however, anthropogenic warming threatens to homogenize habitats through the reduction of the cryosphere, thereby reducing biodiversity from micro- to macroscopic organisms and genes to communities. Still, alpine stream biodiversity, …

Examining The Role Of Host Use On Divergence In The Redheaded Pine Sawfly, Neodiprion Lecontei, Across Multiple Spatial Scales, Robin Kimberly Bagley

Theses and Dissertations--Biology

Phytophagous insects make up over one quarter of described species on Earth, and this incredible diversity seems directly linked to feeding on plants. Comparative studies of sister groups have shown shifts to herbivory are consistently associated with increased species diversity in insects, but the reasons for this diversification remain unclear. While other explanations, such as decreased extinction rates or influences on population structure, exist, one prominent hypothesis suggests shifts and subsequent adaptation to novel host plants can lead to the evolution of reproductive barriers.

Given their extreme specialization on host plants in the genus Pinus and intimate, life-long association with …

Using Genomics To Understand Population Demographics In The Context Of Amphibian Conservation, Schyler O. Nunziata

Theses and Dissertations--Biology

Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Large single nucleotide polymorphism datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of both model and non-model species. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography, in both simulation and empirical settings. Here, I used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (N_e) in Wright-Fisher populations over the course of stable and declining population trends, and distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Overall, my results reveal that demographic inference using genome-wide data can be successfully applied to estimate N_e, and the detection of population-size declines. Next, I assess these methods in an empirical study from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and …

Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales, Paul Michael Hime

Theses and Dissertations--Biology

Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in …

Population Genetic Structure Of Necturus Maculosus In Central And Eastern Kentucky, Mason Owen Murphy

Theses and Dissertations--Biology

Population structure is influenced by extrinsic factors, such as landscape architecture and dispersal barriers. Lotic network architecture is known to constrain ecological, demographic and evolutionary processes, including population genetic structure. I assessed the population structure of a widespread aquatic salamander, Necturus maculosus, across three river basins in central and eastern Kentucky. I examined the role of network architecture, anthropogenic barriers, and spatial scale on patterns of population structure. I also provided a review of N. maculosus capture methods and offer an improved trap design. I identified significant structuring between the combined Licking/Kinniconick basin and the Kentucky River basin, with …

Context-Dependent Individual Variation In Foraging Behaviour And Parental Care In House Sparrows, David Moldoff

Theses and Dissertations--Biology

Behaviors can exhibit a wide degree of plasticity depending on the environmental context in which they are expressed. Despite this, repeatable differences have been found among and within individuals across a wide range of taxa. For my thesis, I investigated individual differences in foraging and parental care. In the first experiment, I assessed house sparrows (Passer domesticus) for domain-generality among neophobia, habituation and associative learning as they are all responses to novelty. While the results of the study find individual differences in each of these contexts the conclusion supported separate mechanisms for each response (domain-specificity). In the second experiment, I …

Identifying Sources Of The Tragedy Of The Commons In Root Competition: A Spatially Explicit Simulation Model And Plants Grown In Transparent Growth Medium, R Deric Leith Miller

Theses and Dissertations--Biology

Existing research shows that plants produce less root when growing alone than when growing in competition with other plants. When plants under root competition over-allocate resources to roots at the cost of reproduction, it represents a Tragedy of the Commons. I constructed simulation models to determine the circumstances likely to give rise to a Tragedy of the Commons, and explore mechanisms by which plants may solve it. I grew plants in nutrient-rich transparent gel, allowing me to quantify root growth and development without destructive sampling. My plants responded positively to additional space and the presence of a competitor at full …

A Plant Trait-Based Approach To Evaluate The Ability Of Native C3 And C4 Grasses To Restore Functionality To A Remnant Bluegrass Savanna-Woodland In Kentucky, Usa., Jann E. Fry

Theses and Dissertations--Biology

Temperate Midwestern oak savannas are considered imperiled ecosystems with < 1 % remaining since the time of European settlement and are identified as critical areas for preservation. Restoration of Midwestern oak savannas is challenging due to the lack of accurate historical data, few intact remnants remaining to study, and lack of restoration ecology studies. A plant trait-based approach was used to evaluate the ability of six C₃ and three C₄ native bunchgrasses to restore functionality to a remnant savanna–woodland of the Bluegrass Region of Kentucky. The response and effect framework was used to assess the response of the nine native grasses according to the habitat filters of interannual precipitation, inter- vs. intra-specific competition, and simulated grazing. The effect traits associated with plant-soil nitrogen and carbon cycling were also assessed. The response traits of interannual competition and inter- vs. intra-specific competition along with the effect traits plant-soil nitrogen and carbon cycling were measured in a monoculture experiment …

The Causes And Consequences Of Individual Variation In Parental Care Behavior, Daniel P. Wetzel

Theses and Dissertations--Biology

Behavioral traits can be remarkably flexible depending on the conditions in which they are expressed, yet, in spite of this flexibility, persistent differences between individuals appear to limit the potential expression of behaviors. For example, despite evidence that parents provide variable amounts of parental care in response to changing environmental conditions, they also differ in the overall level of care they provide. I used a behavioral reaction norm approach to study individual variation in parental care behavior in free-living house sparrows (Passer domesticus). I investigated the nature of this variation by studying the relationship between different forms of …

Axolotl Paedomorphosis: A Comparison Of Juvenile, Metamorphic, And Paedomorphic Ambystoma Mexicanum Brain Gene Transcription, Carlena Johnson

Theses and Dissertations--Biology

Unlike many amphibians, the paedomorphic axolotl (Ambystoma mexicanum) rarely undergoes external morphological changes indicative of metamorphosis. However, internally, some axolotl tissues undergo cryptic metamorphic changes. A previous study examined interspecific patterns of larval brain gene expression and found that these species exhibited unique temporal expression patterns that were hypothesized to be morph specific. This thesis tested this hypothesis by examining differences in brain gene expression between juvenile (JUV), paedomorphic (PAED), and metamorphic (MET) axolotls. I identified 828 genes that were expressed differently between JUV, PAED, and MET. Expression estimates from JUV were compared to estimates from PAED and …

Factors Influencing The Establishment And Survival Of Native Hardwood Tree Seedlings Of The Kentucky Inner Bluegrass Blue Ash-Oak Savanna-Woodland, James D. Shaffer

Theses and Dissertations--Biology

Historically, the Kentucky Inner Bluegrass blue ash-oak savanna-woodland was the primary ecosystem of the Inner Bluegrass Region (IBR) of Kentucky. After European settlement, the majority (>99%) of Bluegrass savanna was converted to agricultural and urban land uses. Currently remnant savanna tree species are failing to recruit. Therefore, a long-term restoration ecology project researching competition and disturbance on seedling establishment, survival, and growth has been established at Griffith Woods (the largest remaining savanna in Kentucky) in Harrison Co., KY. Fourteen native hardwood tree species (a total of 6,168 seedlings) have been experimentally planted. Light, soil, surrounding vegetation, and herbivory, factors …