- ItemOpen AccessEnrichment as a conservation tool to enhance behavior, morphology, gene expression, and survival in Arkansas darters(Colorado State University. Libraries, 2023) Kopack, Christopher J., author; Angeloni, Lisa, advisor; Fetherman, Eric, advisor; Ghalambor, Cameron, committee member; Kanno, Yoichiro, committee memberConservation practitioners often rely on captive breeding programs to supplement wild populations at risk of extinction. While population augmentation has been successful for some taxa, the use of hatchery fish to supplement wild populations can be severely impacted by predation. Elevated predation on hatchery fish may arise because hatchery environments often differ starkly from wild environments, constraining the ability of hatchery fish to phenotypically match the environments in which they are targeted for release. Phenotypic mismatch caused by differences between hatchery and wild environments can limit efforts to conserve fish species at risk of extinction when hatchery-reared fish are used to augment wild populations. Phenotypes adapted to or induced by hatchery environments are thought to be maladapted for life in the wild. Thus, enriching the hatchery environment (abiotically and biotically) to make it more similar to the wild may induce phenotypes, including behavior, morphology, and gene expression profiles, that are better suited to the environments fish will experience after release. Chapter One explores how hatchery-reared fish respond to novel predators and whether those responses can be enhanced to improve survival. Identifying the presence of innate predator recognition and the capacity for learning to recognize predators can inform conservation management practices. We assessed antipredator behavior (time spent moving and distance from a predator) and the efficacy of predator training for three populations of a species of conservation concern, the Arkansas darter (Etheostoma cragini), which is vulnerable to predation by esocid predators like the introduced northern pike (Esox lucius). Arkansas darters demonstrated an innate ability to recognize and respond to a novel esocid predator. Their behavior also changed in response to predator cues (training), though the direction of response to cues was opposite our prediction. Populations differed in their response to the predator treatment, highlighting the potential value of managing populations separately. Our results suggest that antipredator behavior is innate and that exposure to predator cues does affect behavior. This study demonstrates the importance of evaluating enrichment practices and incorporating behavioral observations into conservation programs to guide population-specific management decisions. In Chapter Two, we used a factorial approach to assess whether abiotic enrichment and biotic enrichment (predator recognition training) increase survival of Arkansas darters during encounters with a novel predator. We also assessed the effects of abiotic enrichment on the expression of behavioral and morphological phenotypes across three populations. Morphology and behavior differed among populations and between abiotic treatments, and populations responded differently to the abiotic treatments. Furthermore, we found that in combination with predator training, abiotic enrichment increased the probability of surviving a first encounter with a predator. We therefore recommend conservation practitioners incorporate abiotic enrichment and predator recognition training in the hatchery, as any increase in survival is expected to benefit efforts to conserve this species. In Chapter Three, we took a molecular approach (TagSeq) to elucidate how abiotic enrichment and biotic enrichment impacts the whole-brain gene expression of Arkansas darters, comparing the effects in two hatchery populations to a wild reference population. Although, we found no effect of biotic enrichment on gene expression, we did find that abiotic enrichment has the potential to reduce phenotypic mismatch between hatchery and wild fish, indicating that enrichment may aid current conservation efforts. Overall, these studies suggest a potential role for enrichment in the conservation of imperiled fish, and they highlight the value of a phenotypic approach to managing populations.
- ItemOpen AccessGenetic background and experience affect courtship behavior in male Trinidadian guppies (Poecilia reticulata)(Colorado State University. Libraries, 2023) Phipps, Nathan M., author; Hoke, Kim, advisor; Angeloni, Lisa, committee member; Kanno, Yoichiro, committee memberAn animal's behavior may be shaped by its genetics and life experience, but the extent to which each of these factors contributes to determining behavioral phenotypes is an outstanding question in biology. Mating behaviors are of particular interest due to their importance in determining fitness. We sought to investigate the genetic architecture of mating behaviors and their plasticity in response to mating experience. Trinidadian guppies (Poecilia reticulata) occur in streams with either high or low predation rates. This genetic background has shaped the evolution of many behavioral phenotypes, including those involved in male courtship strategy. We observed male guppies from high predation, low predation, and intercross populations in their first encounter with a female, then later repeated the encounter to observe how experience affects mating behaviors. We recorded occurrences of three behaviors – sigmoids, forced copulation attempts, and gonopodial swings – to determine how they are affected by sexual experience and genetic background. We found that the frequencies of sigmoids and gonopodial swings vary depending on genetic background and experience. Our findings support existing literature demonstrating that mating behaviors respond plastically to experience. We also found that intercross guppies matched the gonopodial swing and sigmoid frequency phenotypes of the QH genetic line, suggesting that these behaviors may be controlled by loci that are dominant in the high-predation population.
- ItemOpen AccessEvolutionary increase in genome size drives changes in cell biology and organ structure(Colorado State University. Libraries, 2022) Itgen, Michael Walter, author; Mueller, Rachel Lockridge, advisor; Sloan, Daniel B., committee member; Hoke, Kim L., committee member; Zhou, Wen, committee memberThe evolution of large genome size has been associated with patterns of phenotypic change in cell and organismal biology. The most fundamental of these is between genome size and cell size, which share a strong positive and deterministic relationship. As a result, increases in cell size alter the structure and function of the cell. Genome and cell size, together, are hypothesized to produce emergent consequences on development and physiology at the cellular and organismal level. My dissertation aims to better understand these patterns and identify potential mechanisms underlying these phenotypic changes. I test for the effects of genome and cell size on cell function, cellular physiology, and organ morphology by leveraging the natural variation in genome size found in salamanders (Genus: Plethodon). First, I show that transcriptomic data supports the predictions that large genome and cell size has functional consequences on cell biology. I also reject the hypothesis that large cell size is functionally linked to lower metabolic rate at the cellular level, but I provide transcriptomic evidence that cell size alters the metabolic state of cells. Finally, I show that genome and cell size drives morphological change in organ-specific ways in the heart and liver. I conclude that large cell size does not lower metabolic rate in salamanders. As an alternative, I propose that the evolution of low metabolic rate lifts the constraint of cell size, thus permitting the evolution of genome gigantism.
- ItemOpen AccessSelenium accumulation in plants and implications for human health: a survey of molecular, biochemical, and ecological cues(Colorado State University. Libraries, 2022) Lima, Leonardo Warzea, author; Pilon-Smits, Elizabeth, advisor; Schiavon, Michela, committee member; Pilon, Marinus, committee member; Antunes, Mauricio, committee member; Paschke, Mark, committee memberTo view the abstract, please see the full text of the document.
- ItemOpen AccessParalogy or reality? Exploring gene assembly errors in a target enrichment dataset(Colorado State University. Libraries, 2022) Rosén, Austin, author; Simmons, Mark P., advisor; Ackerfield, Jennifer, committee member; Richards, Christopher, committee member; Stewart, Jane, committee memberDe novo gene assembly of short read data is inherently difficult – similar to the process of assembling a jigsaw puzzle. I describe three errors that occurred with the assembly of target enrichment data in the genus Cirsium (Asteraceae): inconsistent contig selection, artificial recombination, and inconsistent intron determination leading to over-alignment of non-homologous nucleotides. These errors occurred in 39% of loci in the dataset and were often a by-product of undetected paralogs: assembled loci that likely contained paralogous or homoeologous sequences but did not trigger default paralog warnings by the assembly program, HybPiper. Default HybPiper thresholds for identifying paralogy during the assembly process were insufficient to filter such loci. A custom target file was created in which putative paralogs were separated into independent loci. The custom target file was successful in reducing, but not eliminating, assembly errors in the dataset. A final iteration of quality control was performed to create a dataset largely free of assembly errors. However, phylogenetic inferences applied to this final cleansed dataset were unable to resolve the taxonomic relationships between the sampled specimens. Rather, these results affirm that Cirsium is a taxonomically problematic genus and may require population-level genetic data or integrative taxonomy approaches to delimit species boundaries.