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Browsing by Author "Hoke, Kim, advisor"

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    Diverse developmental trajectories of perineuronal nets during vertebrate nervous system construction
    (Colorado State University. Libraries, 2018) Edwards, Jacob, author; Hoke, Kim, advisor; Anderson, Charles, committee member; Garrity, Deborah, committee member; Mueller, Rachel, committee member
    In the central nervous system, aggregated extracellular matrix compounds known as perineuronal nets (PNNs) shape patterns of neural connectivity over development. Removing PNNs restores juvenile-like states of neural circuit plasticity and subsequent behavioral plasticity. Our current understanding of the role of PNNs in plasticity has resulted in promising therapeutic applications for many neurodegenerative diseases. To ensure safety and efficacy in such applications, we require a broad understanding of PNN function in the nervous system. The current data suggest that PNNs stabilize fundamental features of neural connectivity progressively in an ascending, or "ground-up", fashion. Stabilizing lower input processing pathways establishes a solid, reliable foundation for higher cognition. However, data on PNN development exists almost exclusively for mammals. Is, then, the ground-up model of circuit stabilization a general feature of PNNs across vertebrates? I found that developmental patterns of PNNs in fish (Poecilia reticulata), amphibians (Rhinella yunga), and reptiles (Anolis sagrei) follow diverse trajectories, often emerging first in higher forebrain processing pathways. Similarly, they associate with diverse cell populations and vary widely in structural characteristics both within and across species. While my data do not invalidate a ground-up model for mammal PNNs, they do suggest that this pattern may be an evolutionary innovation in this group, and that the broad roles of PNNs in circuit stability and neuronal physiology are complex and lineage-specific.
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    Genetic 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 member
    An 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.
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    The evolution of plasticity in the transcriptome of the Trinidadian guppy
    (Colorado State University. Libraries, 2023) Whedbee, Miles, author; Hoke, Kim, advisor; Sloan, Dan, committee member; Montgomery, Taiowa, committee member; Ben-Hur, Asa, committee member
    Phenotypic plasticity is a ubiquitous feature of all living systems, and there is much interest in how plasticity influences long term evolutionary trajectories. One of the major complications with modeling evolutionary trajectories is that plasticity itself is known to evolve. The evolution of plasticity has mainly been focused on at the level of the whole organism, and it is unclear if plasticity at all levels of biological organization evolve. Models that assume no generational change in plasticity may be overly simplistic; a more nuanced approach could incorporate the evolution of plasticity into the modeling. A first step towards this end is to determine what levels of biological organization plasticity evolves, and then to determine if there are predictable patterns of evolved plasticity. RNA is an intermediate to DNA and protein, that can undergo changes in response to environmental conditions, thereby modifying the genetic information passed on to non-coding RNAs, functional RNAs, and proteins. Responses to environment include both changes in abundance of RNAs, as well as changes to the composition of the molecules. This dissertation focuses on the evolution of plasticity within the transcriptome of Poecilia reticulata (Trinidadian guppy). One of the major known regulators of transcript abundance are small RNAs (sRNAs). Micro RNAs (miRNAs), are a specific type of sRNA that bind transcripts, typically leading to translational silencing. We investigated two forms of plasticity, an abundance measure of plasticity (miRNA differential expression), and a compositional measure of plasticity (A-to-I RNA editing). A-to-I RNA editing is the chemical nucleotide change from adenosine to inosine, catalyzed by the enzyme ADAR. We first produced a set of miRNAs in guppies, and confirmed the presence of key biogenesis pathway components, i.e. argonaute proteins in the genome. Tissue-specific miRNA expression patterns were identified for three tissues in Poecilia reticulata (Trinidadian guppy), brain, ovary and testis. We found most discovered miRNAs were located in intergenic regions of the genome. Some miRNAs matched known miRBase sequences, while others were considered novel guppy miRNAs. We observed miRNAs expressed from tandem clusters and analyzed piRNA distribution in ovary samples. This study provides important insights into guppy small RNA expression, laying the groundwork for future investigations into their regulatory roles. The 3rd chapter of this dissertation revealed many miRNAs with differential expression (DE), including population main effects, rearing condition, and their interactions. Population DE miRNAs showed a wide range of expression levels. Rearing condition main effects were (slightly) less common. We identified miRNAs with evolved expression plasticity, distributed across four categories: reversed, evolved plastic, assimilated, and accommodated. Both populations showed similar numbers of miRNAs exhibiting plasticity. In the final chapter of this dissertation we characterized the "editome" of guppies. The majority of the edits were consistent with A-to-I editing, with a smaller proportion of C-to-U edits. The intragenic edits were distributed among a number of genes. However, there were no significant differences in editing between populations, rearing conditions, or their interaction. This dissertation revealed significant miRNA expression differences and provided insights into A-to-I editing patterns in guppies.
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    Three-dimensional reconstruction and finite element modeling of anuran middle ear biomechanics
    (Colorado State University. Libraries, 2021) Fleming, Rachel C., author; Hoke, Kim, advisor; Mueller, Rachel, committee member; Bangerth, Wolfgang, committee member
    The ancestors of modern-day amphibians were the first vertebrates to evolve a middle ear for land-based hearing. Today's amphibians retain a simple and effective middle ear structure similar to those of their ancestors, and the fundamental mechanisms of these ears may reflect those that served as foundations of hearing in terrestrial vertebrates. Understanding amphibian hearing mechanisms can therefore offer insights into the evolution of the more sophisticated hearing we observe in land-dwelling vertebrates today. Although the anatomy of the amphibian middle ear has been thoroughly described, it is not known to what extent various anatomical properties, such as material properties or shape and size of ear structures, influence middle ear movement and sound transduction. To achieve this, I created 3D finite element models of the middle ears of Rhinella marina and Arthroleptis tanneri, two anuran species with different ear geometry. To create these models, I segmented middle ear parts from the scan, processed them into volumetric FE models, and set up finite element simulations. I subjected both models to harmonic response simulations at a range of frequencies and measured the sensitivity of the model to changes in various parameters to determine their effects on sound transmission. This study presents a hypothesis-generating tool for ear mechanics research and a better understanding of the biomechanics of how variation in the middle ear affects sound transmission. Additionally, this study may inform future work on the fundamental principles of hearing in terrestrial vertebrates.
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    What in your right mind would make you do that?? Proximate and ultimate mechanisms of plasticity in mating strategies by the Trinidadian guppy (Poecilia reticulata)
    (Colorado State University. Libraries, 2020) Dolphin, Kimberly, author; Hoke, Kim, advisor; Mueller, Rachel, committee member; Seger, Carol, committee member; Ghalambor, Cameron, committee member
    All animals must make decisions every day and often these decisions are directly linked to fitness outcomes, meaning better decisions are expected to be associated with higher fitness. Rapid decisions between alternative strategies allow animals to behave more appropriately for their environment. Thus, selection will shape not only how animals will respond to cues at different timescales, but also what cues they respond to at different timescales. Neural substrates of decisions are a vital component for our understanding of how experiences on different timescale influence decision-making strategies. The sensitivity of sensory systems to specific cues is tuned by genetics and then subsequently refined through developmental neural plasticity. The goal of this dissertation is to fill in gaps in understanding how experiences across multiple timescales influence neural mechanisms and behavioral strategies. I chose to address this question with the alternative mating strategies of male Trinidadian guppies (Poecilia reticulata), a sexually dimorphic tropical fish native to the island of Trinidad. In chapter two we compared how ancestral predation pressures influenced sensitivity to developmental exposure to predator cues and how those two timescales interacted to shape activity and reproductive behaviors when males were in different social contexts. Evolutionary history shaped how developmental contexts influence the resulting behavioral phenotypes across multiple acute contexts. However, the influence of experiences across timescales were not consistent between behaviors. We then extended our study further in chapter three to investigate how developmental experiences with conspecifics influenced males' later abilities not only to respond to virgin and recently mated females, but also to refine mating strategies in response to the female behaviors over multiple exposures. Social experiences during developmental timescales also had distinct influences on the expression of the two reproductive strategies in chapter three. We showed that males modulated and refined mating strategies relatively independently of each other in relationship to their rearing experiences. We concluded with an investigatory probe into the cellular identities of neurons that are responding to a reproductive context in chapter four using a phosphoTRAP RNA-seq protocol. Chapter four provides evidence that several neuromodulatory pathways respond to cues in a reproductive context, which could point to constraints on evolution. In sum, this dissertation used an integrative approach to understand how experiences across multiple timescales influence decisions. We bridged several fields that can help provide insight into the evolution of decision-making processes and allow us to make future hypotheses about influences of multiple experiences with complex cues.