Parasitic manipulation of host behavior lies at the intersection of disease, animal behavior, and coevolutionary processes. In many of these interactions, the underpinning biology is brought into sharp focus as they are obligate relationships, under strong selection to bring about specific changes in host behavior that determine if the parasite will transmit or die. However, experimental and molecular techniques to understand these interactions are still developing and identification of the mechanisms of manipulation is a primary goal in the field. As such, we investigated host-parasite interactions between Camponotus floridanus (Florida carpenter ant) and Ophiocordyceps camponoti-floridani (Florida zombie ant fungus) from multiple molecular perspectives. By combining genome, gene expression, protein-interaction, and metabolite data from multiple experiments, we analyzed parasitic manipulation in a multiomic framework. We considered the most robust hypotheses of how parasitic manipulation occurs to be those supported by multiomic data. Two major avenues of parasitic influence on host behavior appear to be direct interference with neurotransmission and dysregulation of core cellular pathways that affect behaviors. For example, heightened expression of host dopamine synthesis enzyme genes, predicted binding of secreted parasite proteins to dopamine receptors, and reduced dopamine precursor abundance during displays of manipulated behavior all correlate the dysregulation of dopaminergic processes to manipulation phenotypes. We discuss numerous possible hypotheses, many with multiomic support, some without. We predict that modification of host behavior is a complex and multi-layered process that integrates multiple mechanisms we propose here.

Sea turtles are long-lived, globally distributed animals with a complex life-history. Individuals from different populations often share the same foraging areas (mixed stock aggregations). Understanding patterns of dispersal and connectivity between reproductive populations and mixed stock aggregations is fundamental for the development of effective conservation plans. Recently, green sea turtle (Chelonia mydas) populations in several reproductive areas have increased, providing an opportunity to evaluate how demographic changes in reproductive areas impact dispersal to, and the composition of, mixed stock aggregations. In this dissertation, I evaluated how dispersal from reproductive populations in the Greater Caribbean to mixed stock aggregations may have changed over time (Chapter 2). I analyzed mitochondrial DNA haplotypes from samples collected from nesting females captured at Melbourne Beach, Florida, USA, and in-water juveniles from two mixed stock aggregations in central Florida (Indian River Lagoon and Trident Basin) over two time periods. Over a 15-year period there were small variations in the composition of the mixed stocks, without a clear relationship to the recent growth in reproductive populations. I developed a modification to the established "many-to-many" mixed stock model to use the distance between source populations and mixed stock aggregations to weight model estimates. In Chapter 3 I created a simulation to understand how sample size and the level of similarity in relation to haplotype frequency between source populations can impact mixed stock model estimates. I determined that a minimum of 150 samples from each mixed stock aggregation is required to accurately estimate contributions from source populations to mixed stock aggregations for most cases using data currently available in the literature. Improving the resolution of the genetic marker used (i.e., increasing the distinction of haplotype frequencies between source populations) can produce similar results using a smaller number of samples. Finally, in Chapter 4 I evaluated genetic structure of green turtle populations in the Greater Caribbean using a next-generation sequencing approach. I used the same sampling scheme as Chapter 2, with samples from a nesting beach (Melbourne Beach, FL) and two mixed stock aggregations (Indian River Lagoon and Trident Basin, Florida). I identified 4 distinct populations within the samples, and similar to the mtDNA assessment in Chapter 2, the genomic approach also showed small variations in the composition of mixed stock aggregations over a 15-year period. I used a coalescent model to evaluate how these populations diverged from one another, and found strong support for current gene flow among all 4 populations. Results from my analyses reiterate the complexity of sea turtle's dispersal dynamics, and the level of connectivity among populations in the Greater Caribbean. Future studies using mixed stock analysis should consider sample size with more than 150 samples per mixed stock aggregation and the use of more refined genetic markers. Also, genomic assessments of across multiple reproductive aggregations are required for a deeper understanding of other aspects of their ecology.

Parasitoid wasps are ecologically and economically important as biological control agents. However, little is known about the diversity, distribution and biology of most hymenopteran parasitoids due to their small size, morphological conservatism, and complex life styles. The focus of my PhD research was to investigate the evolution and speciation of euphorine braconid wasps, using a combination of multilocus phylogenetics and population genomic techniques combined with traditional taxonomy. The three data chapters of my dissertation are divided into different taxonomic ranks of euphorine braconids, focusing on genera, species, and populations. For chapter 2, I built a multilocus phylogeny of the tribe Euphorini with extensive taxa sampling around the globe. I confirmed the monophyly of Peristenus and Leiophron, two important biological control agents, and provided updated generic concepts and identification resources to aid applied researchers. In Chapters 3 and 4, I focused on cryptic species within the Peristenus pallipes complex in North America. I used an integrative taxonomic approach to resolve the taxonomic confusion within the Nearctic Peristenus pallipes complex (Chapter 3), then I used ddRADSeq to examine their evolutionary relationships with their Lygus hosts (Chapter 4). My dissertation provided a comprehensive analysis of Peristenus at multiple taxonomic ranks using phylogenetics and population genomics, providing insights into their evolutionary history that can be extrapolated into other groups of parasitoid wasps. The results from these studies also advanced our understanding of this group of animals of theoretical, economical, and conservation importance.

Small populations, specifically those that are isolated from others, are more prone to extinction than larger inter-connected populations. The risks that these small isolated populations face include loss of genetic diversity due to founder effects and inbreeding due to population bottlenecks, as well as demographic uncertainty due to fluctuating fecundity and mortality rates and impacts of external environmental factors. Ex situ populations, including those managed as conservation breeding programs with species recovery aims, as well as those that do not have reintroduction goals but are managed for long term population sustainability, suffer from the same extinction risks as small and isolated natural populations. Using three separate avian species which have different life histories and population structures, I investigated impacts of multiple genetic and demographic management strategies on these ex situ populations. I examined the use of molecular genetic datasets including microsatellites and single nucleotide polymorphisms (SNPs) to determine their utility for reconstructing pedigrees, examining individual relatedness within populations, and compared results of measuring genetic diversity through theoretical methods verses those obtained from a molecular dataset. These methods can then ultimately be applied to improve future management including improving studbook datasets and to measure actual loss of genetic diversity. I also used analytical strategies including population viability analysis to determine how management practices influence demographic parameters and determine the future probability of population extinction. The genetic and demographic analyses of both the historic management of an ex situ population, and its current status, are a first step in hypothesizing the potential directions for future management and understanding the likelihood of survival of an ex situ population.

The Y-chromosome and mitochondria (containing mtDNA) appear entirely dissimilar, the former being a sex chromosome found in the nucleus and the latter an organelle with thousands of copies in the cytoplasm. However, both experience uniparental inheritance, with Y-chromosomes being patrilineal and mitochondria matrilineal. This leads to various other similarities including haploidy, high mutation rates, and limited or lack of genetic recombination. Moreover, the low number of protein-coding genes contained on both led to the belief that neither contributes significantly to the adaptive evolution of complex traits. However, recent studies show the Y-chromosome and mitochondria both influence roughly 10% of male transcripts, greatly increasing their evolutionary reach. The nature of the mitochondria's influence is clear – maternal inheritance leads to the accumulation of male-deleterious mutations that negatively impact autosomal and X-linked transcripts (termed mother's curse). However, the nature of the Y-linked variation is less clear, but may impact the manifestation of mother's curse, the evolution of sexual dimorphism, or even act as a constraint on adaptive evolution. In Chapter 2, we explore the potential for Y-chromosomes to influence sexual dimorphism by examining the nature of Y-linked genetic variance. If this variance is additive, it may facilitate the evolution of sexual dimorphism by allowing male traits to be shaped independently of female traits despite males sharing a genome with females. However, if this variance is epistatic, it may slow population level responses to strong selective pressures such as climate change or novel diseases. To date, previous works suggest that Y-linked variation is predominately epistatic. To address our objective, we compare fruit fly populations with and without Y-linked variance and measure the heritability of male and female morphological traits. Surprisingly, we find more heritable variance in populations with Y-linked variance, suggestive of Y-linked additivity. In Chapter 3, we examine whether Y-linked variation can counteract mother's curse. Theoretically, compensatory mutations could evolve on the autosomes, X-chromosome, or Y-chromosome. However, Ys appear best suited to host these mutations as there can be no counter-selection from females due to the Y's uniparental inheritance. To test this, we placed coevolved and non-coevolved Ys and mitochondria into an isogenic background that shared no coevolutionary history with either genetic element. We find that the Y-chromosome has the potential to compensate for mother's curse for at least one trait, male longevity. In Chapter 4, we address a potential limitation in our previous test for Y-linked compensation in Chapter 3: the non-coevolved nuclear background. Theoretically, Ys may compensate for mitochondrial mutations by interacting with the autosomes. Thus, having a coevolved Y and autosomal background may be critical to compensation. To this end, we repeated our experiments from Chapter 3 with the inclusion of a coevolved nuclear genome. We again find Y-chromosomal compensation for mother's curse for longevity, but only when coevolved autosomes are used. This suggests that using non-coevolved backgrounds (as all previous studies have done) may be unreliable and create misleading results.

Living organisms exhibit daily rhythms as a way to anticipate predictable fluctuations in their environment. Such daily rhythmicity is the phenotypic outcome of oscillating genes and proteins, driven by an endogenous biological clock. Clock-controlled behavioral rhythms are inherently "flexible" since their phase, amplitude, and period can change throughout an animal's life hallmarked by changes in so-called chronotype. How this inherent plasticity of clock-controlled rhythms is linked to plasticity of behavior is still an open question in biology. Characterizing the various mechanistic links between plasticity of the animal clock and behavioral state will not only shed light on the molecular underpinnings of animal behavior, but also lead to novel chronotherapeutic interventions to treat human disorders that affect the behavioral state such as bipolar disorder and Alzheimer's. While clock-controlled behavioral plasticity is crucial to a species' survival and fitness, it has also been hypothesized to be a target for manipulative parasites that need to induce timely changes in host behavior to facilitate growth and transmission. Using the Florida carpenter ant Camponotus floridanus as a model, this dissertation attempts to bridge some of the existing knowledge gaps in sociobiology, chronobiology, and parasitology. In the first chapter, we have identified a mechanistic link between plasticity of the C. floridanus clock and its behavioral state. Subsequently, in chapter two, we have provided evidence showing that Ophiocordyceps camponoti-floridani, a fungal parasite that induces timely changes in C. floridanus behavior targets the pre-existing links between host behavior and chronobiological plasticity we have found in chapter one. In the final chapter, we characterize how the clock of O. camponoti-floridani functionally differs from the clock of a non-manipulating fungal parasite, Beauveria bassiana, and put forward a regulatory mechanism via which the manipulating parasite's clock might be inducing timely changes in host behavior.

Amazonian freshwaters host the most diverse ichthyofauna in the world but the ecological mechanisms that generate and regulate this diversity are poorly known. I performed the first comparison of spatial and temporal patterns of fish community diversity among the four primary aquatic habitats of the Amazon (major rivers, floodplains, lowland terra firme streams, and upland shield streams) and among the three distinct chemical water types in Amazon river-floodplain systems (low-nutrient blackwaters and clearwaters, and high-nutrient whitewaters). To minimize confounding influences of geographical variation in species ranges, my study targeted one of the few parts of Amazonia (near Santarém, Brazil) where all four habitats and all three river-floodplain water types occur in close proximity. In the first of three chapters, I compare diversity and biomass between blackwater, clearwater, and whitewater rivers and floodplains. My results provide the first support for positive species-energy and biomass-energy relationships across multiple aquatic habitat types from the same biome and region. In Chapter 2 I compare patterns of temporal beta-diversity, and beta-deviations from null model simulations, to demonstrate that species turnover is positively correlated to seasonality and hydrological connectivity among the four Amazonian habitats types but is uninfluenced by water type. In Chapter 3 I compare up-river transects from the common confluence of a blackwater, Clearwater, and whitewater river to infer that abrupt gradient of water chemistry act as major barriers to fish dispersal. My results have important implications for biodiversity monitoring and conservation planning in the increasingly threatened aquatic habitats of the Amazon basin.

Recent work indicates that the Y-chromosome of the fruit fly Drosophila melanogaster can influence gene regulation on the autosomes and X chromosome. This newly discovered function of the Y has the potential to dramatically shape the regulatory evolution of numerous genes that reside throughout the genome; even for genes that code for both male and female traits. Given that the mechanism underlying the Y-linked influence on gene expression in D. melanogaster appears to exist in other independently evolved heterogametic sex chromosomes, the evolutionary implications of Y-linked regulatory variation (YRV) deserves to be explored. These implications include the potential for Y-chromosomes to facilitate the adaptive evolution of sexually dimorphic gene expression, and the potential for the Y to constrain evolutionary rates in both males and females (depending on the nature of the YRV effect). Unfortunately, the evolutionary implications of this potentially widespread and significant phenomenon have yet to be explored. My dissertation addresses this knowledge gap by determining the influence YRV has on the evolution of autosomally coded traits in D. melanogaster. First, we address the potential for selection to shape YRV by determining if YRV (i) exists within natural populations (i.e. where natural selection operates), and (ii) has any influence on male fitness-related autosomal traits. Second, we address if YRV can facilitate the adaptive evolution of sexually dimorphic gene expression by testing for the presence of Y-linked additive genetic variation. To this end, we investigate the physiological properties of select Y-chromosomes across multiple genetic backgrounds. Third, we address if YRV can constrain adaptive evolution for autosomally coded traits by employing artificial selection on replicate populations that contain either multiple Y-chromosomes (i.e. contain YRV) or only a single Y-chromosome (no YRV). The following studies present evidence that YRV does exist within populations where natural selection operates. We show significant levels of YRV on X-linked and autosomal immune gene expression in wild caught D. melanogaster from a single natural population. Furthermore, YRV effects on immune related genes show a significantly positive correlation to a male fly's ability to fight an immune challenge (an important aspect of organismal fitness). Estimated physiological properties of YRV support previous interpopulation studies showing strong non-additive effect dependent on the autosomal genetic background with which Y-chromosome's are paired with. Physiological epistasis can manifest as additive genetic variation on a population level, but our experimental evolution study suggest that YRV constrains rather than facilitates the evolution of the autosomal coded geotaxis behavior. Ultimately, this dissertation provides evidence that YRV has the potential to influence how autosomal traits evolve and that population level studies of YRV indicate a potential constraint to the adaptive evolution of autosomal traits. If these trends are common and YRV is a wide spread phenomenon, Y-chromosomes have the potential to influence how autosomal traits evolve.

The Florida manatee (Trichechus manatus latirostris) was recently downlisted federally from "endangered" to "threatened" despite acknowledgments of remaining threats to long term population persistence. Challenges to future manatee conservation include, but are not limited to, increases in frequency of harmful algal blooms, intensifying anthropogenic disturbance, and loss of warm-water habitat. The goals of this dissertation were 1) to assess threats to the manatee via a comprehensive, long-term (1973-2016), retrospective analysis of the manatee rescue and rehabilitation partnership (MRRP) and 2) to use seascape genetics analysis to examine whether abiotic, biotic, or anthropogenic seascape variables could significantly describe genetic distance patterns in space for this genetically depauperate population. Results from the MRRP analysis revealed that anthropogenic threats were the most significant reason for manatees to be rescued and rehabilitated. Manatees rescued due to watercraft injuries spent long periods in recovery before succumbing or being released resulting in significant expense to the rehabilitation system. Additionally, the seascape genetics analysis indicated that watercraft activity best explained spatial genetic patterns in the manatee population. It is established that anthropogenic use of watercraft negative affects manatees through the mechanisms of sub-lethal injury and mortality, and these results suggest there may be further negative impacts via the disruption of population genetic connectivity. Future management practices should seriously consider manatee/vessel interactions as watercraft strikes are costly for management, place pressure on the manatee population, and could disrupt population gene flow with potentially dire consequences. Mitigating anthropogenic impacts on the Florida manatee population is critical for future conservation and should be a primary focus.

Animals that co-occur in sympatry with multiple closely-related species use reproductive mate attraction signals not only to assess the quality of a potential conspecific mate (sexual selection), but also to discriminate conspecifics from heterospecifics (species recognition). However, the extent to which sexual selection and species recognition may interact, or even conflict, is poorly known. Neotropical electric fish offer unrivaled opportunities for understanding this problem. They generate simple, stereotyped mate attraction signals that are easy to record and quantify, and that are well-understood from the neurobiological perspective. Additionally, they live in electrically-crowded environments, where multiple congeners live and reproduce in close proximity. This dissertation reports an investigation of electric signal diversity and reproductive life history in a nine-species assemblage of the electric fish genus Brachyhypopomus from the upper Amazon. A year-long quantitative sampling program yielded a library of electric signal recordings from >3,000 individuals and an accompanying collection of preserved specimens from which suites of informative life history traits were measured. These data were used to understand basic reproductive biology, and to describe sexually dimorphic and interspecific diversity in electric signals. By integrating approaches from ecology, physiology, and evolutionary biology, novel perspectives are provided on: 1. how sexual selection and species recognition interact to shape signal diversity and the occupation of signal space in multi-species animal communities; 2. how extreme seasonal variation in Amazonian ecosystems influences trade-offs in the allocation of reproductive resources – including mate attraction signals, and; 3. how environmental variation shapes general life-history traits in a diverse tropical animal assemblage.