Browsing by Author "Mims, Meryl C."

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    Adaptive evolution, sex-linkage, and gene conversion in the voltage-gated sodium channels of toxic newts and their snake predators
    Gendreau, Kerry (Virginia Tech, 2022-05-27)
    Understanding how genetic changes ultimately affect morphology and physiology is essential for understanding and predicting how organisms will adapt to environmental changes. Although most traits are complex and involve the interplay of many different genetic loci, some exceptions exist. These include the convergent evolution of tetrodotoxin resistance in snakes, which has a simple genetic basis and can be used as a model system to investigate the genetic basis of adaptive evolution. Tetrodotoxin is a potent neurotoxin used as a chemical defense by various animals, including toxic newts. Snakes have evolved resistance through mutations in voltage-gated sodium channels, the protein targets of tetrodotoxin, sparking an evolutionary arms race between predator and prey. In this dissertation, I describe how genomic rearrangements have led to sex-linkage of four of the voltage-gated sodium channel genes in snakes and compare allele frequencies across populations and sexes to make inferences about how sex linkage has influenced the evolution of resistance in garter snakes. By measuring gene expression in different snake tissues, I show that three of these sex-linked sodium channel genes are dosage compensated in embryos, adult muscle, and adult brain. In contrast, two channels show sexual dimorphism in their expression levels in the heart, which may indicate differences in dosage compensation among tissues. I then use comparative genomics to track the evolutionary history of tetrodotoxin resistance across all nine sodium channel genes in squamate reptiles and show how historical changes have paved the way for full-body resistance in certain snakes. Finally, I use targeted sequence capture to obtain the sodium channel sequences of salamanders and show evidence that tetrodotoxin self-resistance in toxic newts was likely accelerated through gene conversion between resistant and non-resistant sodium channel paralogs. Together, these results illustrate parallelism in evolutionary mechanisms and processes contributing to the appearance of an extreme and complex trait that arose independently in two distinct taxa separated by hundreds of millions of years.
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    Amphibian and reptile conservation in a changing environment: Case studies from the southeastern United States
    Chandler, Houston Cawthorn (Virginia Tech, 2023-05-22)
    The southeastern United States is a global biodiversity hotspot but has experienced severe declines of natural ecosystems. The southeast is currently facing widespread change, particularly from an increasing human population and climate change, that is likely to impact all remaining natural areas to some degree. In this work, I examine some of the challenges currently facing imperiled species of reptiles and amphibians in this region. The work is focused on two species, the Reticulated Flatwoods Salamander (Ambystoma bishopi) and the Eastern Indigo Snake (Drymarchon couperi) both of which are listed on the U.S. Endangered Species List. Chapter 1 used Light Detection and Ranging (LiDAR) data to measure wetland bathymetry (basin shape) in flatwoods salamander breeding wetlands. Bathymetry data were used to construct stage–area relationships for each wetland, and a history of water level monitoring data were applied to these relationships to build multi-year time series of flooded area metrics. These metrics were then combined with an assessment of vegetation characteristics to map potentially suitable habitat for flatwoods salamander breeding within each wetland. Chapter 2 focused on flatwoods salamander phenology (the timing of life history events) in response to climate change. I quantified flatwoods salamander movements into and out of breeding wetlands over a 10-year period (2010–2020), identifying temperature and precipitation patterns that were conducive to salamander movements. I then used future climate projections to forecast movement opportunities for flatwoods salamander from 2030–2099 and used an existing hydrologic model built on the same climate data to understand how phenology may interact with hydrology. Overall, only a small number of years are likely to have an ideal intersection of phenology and hydrology as has been observed during recent breeding seasons. Chapter 3 described the construction of a stochastic Integral Projection Model for flatwoods salamanders. I integrated the projections from Chapter 2 with the population model to estimate the viability of two flatwoods salamander populations from 2030–2099 under multiple climate change scenarios. The results indicated that approximately half of the examined scenarios resulted in a high probability (>0.5) of extinction when considering both wetland hydrology and salamander phenology. In Chapter 4, I described the creation of a stochastic Integral Projection Model for indigo snakes. I then demonstrated the utility of this model by examining the effects of initial population size, road density, and removal of individuals to support a captive colony on indigo snake populations. I found that high road densities and high collection rates would likely lead to population declines, although the rate of declines and extinction risk varied across scenarios. Taken together, these projects highlight some of the challenges currently facing herpetofauna in the southeastern United States, demonstrate the difficulty in conserving these often-overlooked species, and provide useful tools for ongoing conservation efforts focusing on these two imperiled species.
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    Amphibians in a changing world: assessing the effects of warming and drying on amphibian larvae and the relationships between larval survival, body size, and time to metamorphosis
    Shadle, Elizabeth Jane (Virginia Tech, 2020-12-17)
    Amphibians are influenced by climate change, but we do not have a clear understanding of how changes in temperature, precipitation, or both, may influence amphibian larvae in temperate regions. Do amphibian larvae have similar developmental responses to increased temperature and increased drying rates of wetlands - both plausible effects of climate change? What influence do the interactive effects of temperature and drying have on the relationships between the larval responses themselves (e.g., survival, body size, and time to metamorphosis)? To address these questions, we studied larval responses of two amphibian species, wood frogs (Lithobates sylvaticus) and spring peepers (Pseudacris crucifer), to simulated warming and drying in experimental ponds. Over 13 weeks, we manipulated temperature and water levels in ponds to produce 4 treatments: control, drying, warming, and drying + warming. Our manipulations created warming treatments that were on average 2 ° C higher than controls, and our drying treatments decreased in water depth by 2.5 cm each week compared to warming and control treatments that held a consistent amount of water. In both species, warming treatments resulted in significantly earlier timing of metamorphosis, and drying treatments resulted in significantly reduced body size. We saw a negative relationship between body size and time to metamorphosis (i.e., individuals that metamorphosed faster generally had larger body sizes), indicating an unexpected decoupling of the typical positive relationship between time to- and size at metamorphosis. The strength of the relationship between responses also varied by treatment for wood frogs but not spring peepers, indicating that the responses of larval amphibians to climate change may vary among species. Our study reveals complex relationships among larval survival, body size, and time to metamorphosis and highlights the need for considering not only the role of interacting climate-related pressures on amphibians but also the mechanisms underlying coupling of larval responses to these pressures. We encourage future research and discussion on a better understanding of why different climate pressures caused different responses, and if these patterns may be consistent in other aquatic species.
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    Assessing placement bias of the global river gauge network
    Krabbenhoft, Corey A.; Allen, George H.; Lin, Peirong; Godsey, Sarah E.; Allen, Daniel C.; Burrows, Ryan M.; DelVecchia, Amanda G.; Fritz, Ken M.; Shanafield, Margaret; Burgin, Amy J.; Zimmer, Margaret A.; Datry, Thibault; Dodds, Walter K.; Jones, C. Nathan; Mims, Meryl C.; Franklin, Catherin; Hammond, John C.; Zipper, Sam; Ward, Adam S.; Costigan, Katie H.; Beck, Hylke E.; Olden, Julian D. (Nature Portfolio, 2022-07)
    Hydrologic data collected from river gauges inform critical decisions for allocating water resources, conserving ecosystems and predicting the occurrence of droughts and floods. The current global river gauge network is biased towards large, perennial rivers, and strategic adaptations are needed to capture the full scope of rivers on Earth. Knowing where and when rivers flow is paramount to managing freshwater ecosystems. Yet stream gauging stations are distributed sparsely across rivers globally and may not capture the diversity of fluvial network properties and anthropogenic influences. Here we evaluate the placement bias of a global stream gauge dataset on its representation of socioecological, hydrologic, climatic and physiographic diversity of rivers. We find that gauges are located disproportionally in large, perennial rivers draining more human-occupied watersheds. Gauges are sparsely distributed in protected areas and rivers characterized by non-perennial flow regimes, both of which are critical to freshwater conservation and water security concerns. Disparities between the geography of the global gauging network and the broad diversity of streams and rivers weakens our ability to understand critical hydrologic processes and make informed water-management and policy decisions. Our findings underscore the need to address current gauge placement biases by investing in and prioritizing the installation of new gauging stations, embracing alternative water-monitoring strategies, advancing innovation in hydrologic modelling, and increasing accessibility of local and regional gauging data to support human responses to water challenges, both today and in the future.
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    Biology and conservation of the endangered Bahama Swallow (Tachycineta cyaneoviridis)
    Wilson, Maya (Virginia Tech, 2020-01-02)
    In order to prevent species extinctions, conservation strategies need to incorporate the identification and mitigation of the root causes of population decline with an assessment of vulnerability to genetic and stochastic factors affecting small populations. Species or populations with small ranges, such as those on islands, are particularly vulnerable to extinction, and deficient knowledge of these species often impedes conservation efforts. The Bahama Swallow (Tachycineta cyaneoviridis) is an endangered secondary cavity-nester that only breeds on three islands in the northern Bahamas: Abaco, Grand Bahama, and Andros. I investigated questions related to population size and distribution, genetic diversity and population structure, breeding biology, and ecological interactions of the swallow, with the goal of informing the conservation and management of the species. Using several population survey methods on Abaco, I found that swallow site occupancy and density is higher in southern Abaco, especially near roads and pine snags. Future research should prioritize identifying the causes of variable and low population densities in parts of the swallow's range. I used microsatellite markers and morphometrics to assess differences between populations on Abaco and Andros. We found a lack of genetic differentiation (G'ST = 0.03) between populations, but differences in morphology suggest that gene flow might be low enough to enable traits under selection to diverge. By locating and monitoring nests, I found that swallows rely on woodpecker-excavated cavities in pine snags and utility poles, and that swallows nesting in pine snags had higher fledging success (92%) than those nesting in utility poles (50-62%). Using a cavity nest-web approach, I assessed how swallows interact with cavity-nesting birds and resources on Abaco. Hairy Woodpeckers (Dryobates villosus) primarily excavated pine snags, while West Indian Woodpeckers (Melanerpes superciliaris) excavated utility poles in non-pine habitat. Only swallows and La Sagra's Flycatchers (Myiarchus sagrae) used nest sites in the pine forest. Swallows in non-pine habitat face competition for cavities with American Kestrels (Falco sparverius), and non-native House Sparrows (Passer domesticus) and European Starlings (Sturnus vulgaris). These results highlight the importance of pine forest and the Hairy Woodpecker for the persistence of the swallow.
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    Bog Turtle Distribution in Virginia: Assessing Proposed Methods for Finding New Localities and Examining Movement Between Wetlands
    Barron II, Joseph Charles (Virginia Tech, 2021-07-13)
    Freshwater turtles are among the most threatened groups of taxa globally, and the bog turtle, Glyptemys muhlenbergii is among the most imperiled in North America. In Virginia, USA, bog turtles are restricted to occupying Appalachian Mountain fens. Fens are naturally small and fragmented wetlands characterized by elevated water tables and an open canopy. Although there is a strong need to document and monitor populations of bog turtles, efforts to do so are often limited by the low detection of the species. The first objective of this thesis was to assess proposed methodologies for locating populations of turtles on the landscape. My first chapter assessed a previously-developed habitat distribution model for bog turtles using an occupancy modeling approach. I conducted 216 surveys of 49 discretely predicted patches of habitat, recording conditions such as weather, size of wetland and time of year, hypothesized to affect detection during each survey. In addition, I assessed factors including stream entrenchment, grazing presence and surrounding impervious surfaces for each surveyed patch to identify data sources that could improve future models or better assess sites. I found that sites with larger total wetland area had higher detection per survey, possibly due to larger sites having higher densities of turtles (among other explanations), and that sites with higher amounts of impervious surfaces within their drainage were less likely to be occupied. In addition to the bog turtle, several plant species also occur in mountain fens. These species usually have a locally rare distribution or are disjuncts from a more northern latitude. Because of these traits, a high diversity of specialist plants may be indicative of a fen with a robust hydrology that has historically been less disturbed. Past site quality analyses have proposed using indicator diversity to assess sites, but no study has found if these species to tend to co-occur. My second chapter examines this hypothesis. I first chose a list of plant species that would most likely have habitat requirements similar to those of turtles. Then, at 12 sites, 6 with turtles and 6 without, I conducted a complete floral inventory. I first tested community-wide differences between the floral communities of these sites and found no difference, but when I narrowed my analysis to examining occurrence patterns of plant species determined a priori to be fen specialists and Glyptemys muhlenbergii, a pattern of co-occurrence was found. This lends support to the idea that indicator plants could be used as a tool to better evaluate sites that may have bog turtles. My last chapter investigated movement of bog turtles in a landscape impacted by anthropogenic development. Movement of turtles between adjacent sites is critical to maintaining genetic diversity and maintaining metapopulation integrity. Despite this importance, records of long distances movements among wetlands are scarce in the literature, likely due to the lack of long-term studies for areas with multiple adjacent sites. In Virginia, mark recapture monitoring has been done intermittently in a cluster of sites for over 32 years. To determine the prevalence of movement among sites for bog turtles, I examined the dataset for all instances of turtles found at sites different from their last capture. I calculated the straight-line distance for each recorded movement. I also examined the sex of the turtle to test whether sex influences movement the frequency and distance of movements. For a subset of movements, I calculated least-cost pathways to identify possible barriers to movement using a previously published resistance model. I found 21 instances where a turtle was caught at a different site than its last capture over 32 years of monitoring. Neither sex was more likely to move farther than the other. Although the study's observed rate of movement may appear low, it is likely an underestimate when detection and asymmetric sampling are taken into account. The least cost pathways analysis suggested that roads or driveways were likely crossed for a significant portion of movement events. Finally, to examine how movement may be affecting the current distribution of bog turtles, I described a method to test whether adjacency to known populations influences the probability of a new site being occupied by turtles. I prove the utility of the method by applying it to a map of bog turtle occurrences collected over this study and show that it can account for habitat differences and barriers to movement between sites as well. In spite of plausibility of the method, limitations in how occurrence data are currently collected prevent its immediate application. Together, this thesis will help managers not only find and assess wetlands on the landscape, it will also provide information about the network of connected patches on the landscape. Knowing where bog turtles are and what wetlands or sub-populations are potentially connected will allowed for a more directed and informed regional management strategy.
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    Disentangling the influence of dispersal on community assembly and stability
    Cathey, Sara Elizabeth (Virginia Tech, 2023-01-31)
    With the introduction of metacommunity theory, the field of community ecology expanded its scope to include patterns and processes beyond the scale of local communities. Dispersal, or the movement of organisms between sites, can play an influential role in generating patterns of community assembly and stability. However, little is known about the role of dispersal in structuring and stabilizing freshwater communities. For my dissertation, I conducted a literature review of dispersal in stream metapopulations and metacommunities. Our current knowledge of the movement of freshwater taxa is limited due to difficulties in accurately monitoring dispersal. We have inferred the role of dispersal based primarily on organismal-based and graph-based proxies, although the body of work in modeling and experimental research is growing. Future research should incorporate innovative methods to directly monitor dispersal at finer spatial and temporal scales. To address this knowledge gap, we experimentally manipulated dispersal mode (aerial and drift) alongside the magnitude of dispersal (network location as a proxy) to investigate the role of these components of dispersal in community assembly and multiple metrics of stability. The results of my experiment suggest both factors may play a role in community assembly and stability patterns in stream metacommunities. Lastly, I conducted a mesocosm experiment with zooplankton mesocosms to investigate if biodiversity can generate asynchronous patterns of community dynamics that contribute to stability. There was a positive biodiversity-asynchrony relationship that, in turn, generated higher levels of stability. This effect was strongest in communities connected via dispersal. Overall, my dissertation demonstrates that dispersal plays a role in the assembly and stability of freshwater communities.
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    Downstream Dilemma: Navigating Microplastic's Impact on Freshwater Symbiosis in the Anthropocene
    Braswell, Cameron Bryce (Virginia Tech, 2024-06-27)
    Annually, it is estimated that 82 million tons of global plastic waste is either mismanaged or littered, bypassing waste management practices. This mismanagement causes the permeation of plastic debris into the environment, which then undergoes natural degradation processes. These degradation processes result in the proliferation of miniscule plastic particles known as microplastics. Due to the inherent proximity to sources of anthropogenic waste, concerns of microplastic pollution and its impact on freshwater ecosystems have recently increased. Until recently, microplastic research has primarily been focused on the toxicological affects felt by an individual organism rather than the intricate interactions that occur between taxa. Only focusing on the individual toxicological impact turns a blind eye on the communities that maintain ecosystem health and stability. To that end, our experiment was unique as it will be the first study assessing the impact of a freshwater symbiosis, as symbioses in the scope of toxicokinetic studies have primarily been dominated by that of terrestrial and marine relationships. This knowledge gap is a serious concern as its argued freshwater systems are more contaminated, than that of other aquatic habitats. To address this knowledge gap, we conducted mesocosm-based exposure-response assays, exposing the crayfish-branchiobdellidan symbiosis to microplastics of fibrous, microsphere, and tire wear particle morphologies while varying symbiont densities. We used the crayfish-branchiobdellidan model system in our study due to its amenability to laboratory monitoring and manipulation. The crayfish C. appalachiensis, common in the Virginia New River Basin, served as hosts to obligate ectosymbiotic annelids in the order Branchiobdellida. Previous research, using the crayfish-branchiobdellidan symbiosis demonstrated that the interaction is a cleaning symbiosis, where hosts benefit from reduced gill fouling while symbionts benefit from increased resource availability. We observed the physical and behavioral changes of the crayfish-branchiobdellidan symbiosis over a 172-day chronic exposure assay. Our results show, crayfish hosts with higher symbiont densities experienced decreased physical growth when exposed to microplastics compared to the control. This alteration in host growth was the result of increased antagonistic symbiont behavior in the form of gill tissue consumption. Our results suggest microplastics caused a reduction in epibiont abundance, thus decreasing symbiotic resource availability. This reduction in resources resulted in a shift of context dependency, thus increasing parasitic symbiont behavior. This study demonstrates microplastics have the capability to shift symbiotic context from a mutualism to a parasitism.
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    From genes to species: Characterizing spatial and temporal variation in frog and toad multidimensional biodiversity
    Moore, Chloe Ellen (Virginia Tech, 2023-05-15)
    Biodiversity is a complex concept encapsulating the variation that occurs within and among levels of biological organization. It is positively linked to ecosystem persistence, adaptability, and function. Biodiversity loss, driven by global change and human activities, is one of the most prominent threats to ecosystems. Characterizing the variation of and processes driving biodiversity is a critical step in understanding the causes, consequences, and magnitude of biodiversity loss. However, characterizing biodiversity comprehensively requires understanding multiple dimensions, or types, of diversity, such as genetic, taxonomic, phylogenetic, and life history diversity, that encompass both ecological and evolutionary processes varying across space and time. In this dissertation, I investigate spatial and temporal variation in frog and toad (order Anura) biodiversity to understand the effects of how diversity is measured on biodiversity characterization and the underlying processes driving biodiversity. In my first chapter, I examined the spatial and temporal variation of genetic diversity and other population genetic metrics to understand the effects of multi-year sampling on population genetic inference in an anuran metapopulation (Arizona treefrog, Hyla (Dryophytes) wrightorum). I found that a single sample year captures global, but not local, population genetic dynamics, as there is considerable temporal variation in genetic metrics within individual populations. In my second chapter, I developed a tool to improve the characterization of anuran life history diversity using species traits. Traits are the measurable attributes of species, and a suite of species traits is used to distinguish ecological strategies found among species. I collated trait data from 411 primary and secondary sources for 106 anuran species found in the United States to develop an anuran traits database for use in conservation, management, and research. In my third chapter, I investigated spatial variation within and among taxonomic, phylogenetic, and life history anuran diversity in the United States and examined the abiotic relationships behind observed patterns. To do this, I developed species distribution models at a 1 km2 resolution for the majority of the native US anurans. I identified relationships among diversity metrics for improved, comprehensive biodiversity characterization and potential ecological and evolutionary processes underlying biodiversity. Spatial variation in multidimensional relationships highlights regional needs for multiple metrics of diversity to comprehensively characterize biodiversity. This spatial variation is driven by temperature, elevation, and water availability, likely related to the biological limits for anurans. Collectively, these chapters highlight the considerable variation that exists within and among species of a broad and diverse biological. Furthermore, these chapters call attention to the importance of measuring multiple biodiversity dimensions for effective conservation in a rapidly changing world.
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    Functional and geographic components of risk for climate sensitive vertebrates in the Pacific Northwest, USA
    Mims, Meryl C.; Olson, Deanna H.; Pilliod, David S.; Dunham, Jason B. (2018-12)
    Rarity and life history traits inform multiple dimensions of intrinsic risk to climate and environmental change and can help systematically identify at-risk species. We quantified relative geographic rarity (area of occupancy), climate niche breadth, and life history traits for 114 freshwater fishes, amphibians, and reptiles in the U.S. Pacific Northwest. Our approach leveraged presence-only, publicly available data and traits-based inference to evaluate area of occupancy, climate sensitivity (i.e., climate niche breadth), and a Rarity and Climate Sensitivity (RCS) index of all species across multiple geographic extents, grain sizes, and data types. The RCS index was relatively stable across extents, grains, and data types, with climate sensitivity differentiating species with otherwise similar areas of occupancy. We also found that species with sensitivity-associated traits (e.g., long generation time, low fecundity) were not necessarily the same species identified as at-risk with geographical approaches (small range size, small climate niche breadth). Many multispecies assessments using coarse-scale data (e.g., entire range maps or convex-hull approaches) often focus on a single dimension of intrinsic risk; others rely on data-intensive models only applicable to a few well-studied species. What remains is a need for an approach that enables multispecies, multidimensional assessment efforts. This is particularly true at regional scales, where management needs require assessments that are intermediate to coarse- and fine-scale approaches. We demonstrate that by considering multiple dimensions of intrinsic risk to climate change (range size, climate sensitivity, and traits), site-specific locality data may offer a pathway for ensuring vulnerable, understudied species do not go overlooked in conservation.
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    Global change effects on ant-mediated seed dispersal
    Burt, Melissa Ann (Virginia Tech, 2024-05-20)
    Seed dispersal mutualisms, including seed dispersal by ants, are critical to the assembly of communities and the function of ecosystems. However, the consequences of human-caused global change factors, such as habitat fragmentation and climate change, for the future of these mutualisms are not fully understood. My dissertation consists of five chapters that investigated the effects of habitat fragmentation and climate change on ants and their seed dispersal mutualisms. Chapter 1 is an introduction that provides background information on habitat fragmentation and anthropogenic climate change and their impacts on biodiversity. In Chapter 1, I also introduce my study system of ant-mediated seed dispersal mutualisms, myrmecochory. My next two chapters (Chapters 2 and 3) explored the effects of reconnecting fragmented habitat patches with corridors in restored longleaf pine savanna systems in South Carolina. We used a landscape scale experiment to investigate how reducing isolation affects the assembly of ant communities over time (Chapter 2) and seed dispersal of the myrmecochorous forb, Piriqueta cistoides (Chapter 3). For Chapter 2, we found evidence that both habitat connectivity and edge effects underly the effects of corridors on ant communities over time. We found that connected patches accumulated ant species faster than isolated patches over time suggesting that corridors function by facilitating colonization. We also found evidence that edge effects play a role with greater ant functional group diversity in patches with higher edge than patches with lower edge amounts. For Chapter 3, we also found evidence of corridor and edge effects with ants dispersing seeds of P. cistoides longer distances in patches connected via corridors than isolated patches, but only in the center of patches. In Chapter 4, we investigated the effects of predicted climate change scenarios for seed dispersal mutualisms in eastern deciduous forests. For this chapter, we conducted a mesocosm experiment in which we crossed temperature with altered precipitation magnitude and frequency. Our mesocosms contained a common spring ephemeral wildflower, Sanguinaria canadensis, and whole colonies of their mutualist seed disperser, Aphaenogaster rudis. This design allowed us to collect high-resolution data on how ants interacted with seeds under different climate change scenarios that incorporated warming temperatures and altered precipitation. We found that warming effects depended on the precipitation treatment with negative effects of warming on the collection of seeds by ants under historical precipitation regimes and positive effects of warming under simulated precipitation conditions altered under predicted climate change. Finally, Chapter 5 describes my general conclusions from this body of work. Taken together, the research making up my dissertation provides valuable insights into how changing environmental conditions under habitat fragmentation and climate change may alter ant seed dispersal mutualisms. Importantly, we often found that the impacts of global change were context dependent and that our experiments were important tools in disentangling that context dependency. Further, this work demonstrates the value of understanding the basic ecology of the interactions among organisms. Understanding the natural history of organisms across changing environmental conditions will benefit the ways in which we conserve and restore ecosystems in a fragmented and warmer world.
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    Host-pathogen interactions and conservation implications of snake fungal disease over broad geographical scales
    Blanvillain, Gaelle Jh (Virginia Tech, 2024-06-27)
    Emerging infectious diseases represent a threat to biodiversity, posing significant challenges to wildlife conservation globally. Infectious diseases can cause population declines, local extirpations and, in rare cases, complete species extinction. Among emerging pathogens, pathogenic fungi have been responsible for drastic declines in several high-profile vertebrate taxa, such as Batrachochytrium dendrobatidis causing chytridiomycosis in many species of amphibians worldwide. Recently, an emerging infectious disease, 'snake fungal disease' (SFD), caused by the fungal pathogen Ophidiomyces ophidiicola, is affecting the health of snake populations in North America by causing skin infections which can be fatal. Given the potential impact of this disease on snake biodiversity worldwide, compounded by the pressure of anthropogenic stressors that already jeopardize the viability of many snake populations, there is a clear need for ecological research in this understudied system. This dissertation is comprised of 4 data chapters focusing on the disease dynamics of snake fungal disease in Europe, and the factors resulting in differential infection. In chapter 2, I develop a large field-based data collection in 10 countries in Europe to investigate the presence of disease hotspots and the variation of disease prevalence across host species, and to examine the pathogen genotypes that are present on the landscape. I found isolated areas of disease hotspots, and models including an interactive effect of host species and which pathogen clade are present on the landscape were best at explaining disease prevalence. In chapter 3, I perform a virulence challenge assay using 120 corn snakes (Pantherophis guttatus) and 7 strains of O. ophidiicola (3 collected from Europe, 4 from the USA). This experiment reveals that pathogen genotypes associated with higher disease prevalence in Europe also have higher pathogen virulence, and that different strains from the USA show variation in virulence. These results also match both physiological host responses measured in the lab and landscape patterns of disease. In chapter 4, I explore two mitigation-driven snake translocation projects in Europe that were complicated due to O. ophidiicola outbreaks. One snake species, N. tessellata, appears highly susceptible to SFD, indicating that under stressful conditions, O. ophidiicola can cause mortality regardless of pathogen genotype, and that this snake species may be important in pathogen maintenance. Finally in chapter 5, I report the presence of a different fungal pathogen in Spain, Parannannizziopsis sp., never reported in wild snakes in Europe before. Broadly, my dissertation demonstrates coevolutionary relationships between hosts and pathogens and has important implications to snake conservation over large scales.
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    The Influence of Reduced Forest Cover and Dissolved Oxygen on the Viability of Eggs from Eastern Hellbenders (Cryptobranchus alleganiensis)
    Funkhouser, Holly Ann (Virginia Tech, 2024-11-18)
    Riparian deforestation is a significant threat to freshwater riverine ecosystems and sensitive fauna that depend on clean water. Sensitive aquatic species are vulnerable to the destruction of riparian forest cover which diminishes protection from pollutants, sedimentation, and solar radiation, while also depleting dissolved oxygen. In this thesis, I explore the influence of degraded riparian forest cover and its effect on dissolved oxygen on the embryonic viability of a sensitive freshwater habitat specialist, the Eastern hellbender. Hellbenders are a large-bodied, long-lived amphibian that inhabits fast flowing, cold mountain streams in the eastern United States. Over the last several decades, hellbender populations have experienced declines that are associated with low riparian forest cover, a geriatric population age structure, and high rates of nest failure. Adult male hellbenders normally provide extensive paternal care to embryos and larvae over an 8-month period. However, researchers have recently discovered that in degraded populations, hellbender nests are failing due to whole-clutch filial cannibalism by adult males. The underlying mechanism that triggers males to eat their young remains unknown, but one possibility is that eggs are not developing properly and as a result the attending male ceases to provide care. However, the embryonic viability of clutches developing in habitats with low riparian forest cover is unknown. Given the limited research on hellbender embryonic viability, I first sought to examine whether embryo viability is associated with a forest cover gradient. To accomplish this, I inherited two years of laboratory and field data, and I conducted a final third year of data collection for the study. Over these three years of data collection, I simultaneously evaluated embryo viability in a controlled captive rearing system while classifying nest failure due to whole-clutch cannibalism of sibling embryos in the field. I found significantly lower hellbender embryo viability, faster hatching times, and higher rates of underdeveloped hatchlings in hellbender populations with degraded riparian forest cover. However, I found no relationship between embryonic viability and whole-clutch filial cannibalism. I concluded that elevated specific conductance of water (i.e., dissolved ions) associated with loss of forest cover may affect the embryonic development of hellbenders, but this hypothesis has yet to be tested. To further explore the impact of degraded riparian forest cover on hellbender embryonic viability, I designed a study to evaluate the influence of depleted dissolved oxygen on embryonic development. To accomplish this, I designed and implemented a dissolved oxygen manipulation system to rear sibling embryos in high, medium, and low dissolved oxygen concentrations. I found that hellbender embryos are vulnerable to relatively modest reductions in dissolved oxygen (i.e., 5 mg/L), comparable to those found to affect embryos of some of the most sensitive species examined to date. Nests reared in low dissolved oxygen had a lower percentage of viable hatchlings, lower hatching success, higher rates of underdeveloped hatchlings, and smaller morphometrics compared to those reared at higher dissolved oxygen concentrations. I concluded that hellbenders may be particularly susceptible to reductions in dissolved oxygen because of their high degree of specialization for well oxygenated streams, and I suggest prioritizing additional research on dissolved oxygen to advance hellbender conservation. Taken together, my research established a foundation of knowledge on the sensitivities of hellbender embryos to degraded water quality caused by low riparian forest cover. Further, my work underscored the importance of riparian forest conservation for hellbender populations and for other freshwater biodiversity. Protection of riparian forest will also be critical to build resilience in streams against the existential threat of climate change.
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    Invasive Hosts and their Context Dependent Relationships with Native Symbionts
    Lockett, Cameron St. John (Virginia Tech, 2024-06-11)
    Symbiotic relationships display plasticity through time, depending on a variety of factors that include host properties, symbiont densities, and environmental conditions. Invasive species can affect symbiotic relationships by introducing invasive symbionts, reducing the population of native symbionts, or competing for native symbionts as a resource. There is an established symbiotic relationship between crayfish and annelid worms in the order Branchiobdellida. Branchiobdellidan worms can have a mutualistic cleaning symbiosis with crayfish, or at times become parasitic and feed on crayfish gill tissue if nutrients on the host are low. With the introduction of invasive crayfish in the Southern Appalachians in Virginia, branchiobdellidan worm populations have sharply declined due to invasive crayfish being less competent hosts for the symbionts. However, degree of competency as a host may differ among invasive species to, as invasive hosts have their own unique context-dependent symbiotic relationships. To investigate how symbiotic relationships differ between invasive hosts, I encouraged symbiotic relationships between invasive hosts Faxonius virilis and Faxonius cristavarius and native symbionts Cambarincola ingens. In two experiments spanning several months, I observed changes in growth rates of hosts and damage to gill tissues over varying levels of symbiont exposure. One species of invasive host, F. cristavarius, had increased growth rates when exposed to native symbionts at low symbiont densities, while for the other invasive host, F. virilis, growth rates and gill chamber damage was not impacted by the presence of symbionts. I also compared an invasive host F. cristavarius to a native host Cambarus appalachiensis to measure the response of growth rate, symbiont damage to gills, and behavior of worms across a gradient of symbiont exposure. The native host's growth rates increased over time, but not due to an effect of symbionts. However, the invasive host exhibited effects from parasitism when symbiont densities were high. My findings suggest that invasive hosts can have their own unique context-dependent relationship with native symbionts. Because there is no one-size-fits-all rule for invasive hosts, when invasive hosts enter a region, new symbiotic relationships can be formed that are beneficial for invasive hosts and native symbionts. Invasive hosts or native symbionts could also be rejected by the other which may lead to decreases in either of their populations.
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    Limitations of trait‐based approaches for stressor assessment: The case of freshwater invertebrates and climate drivers
    Hamilton, Anna T.; Schäfer, Ralf B.; Pyne, Matthew I.; Chessman, Bruce; Kakouei, Karan; Boersma, Kate S.; Verdonschot, Piet F. M.; Verdonschot, Ralf C. M.; Mims, Meryl C.; Khamis, Kieran; Bierwagen, Britta; Stamp, Jen (Wiley, 2019-09)
    The appeal of trait-based approaches for assessing environmental vulnerabilities arises from the potential insight they provide into the mechanisms underlying the changes in populations and community structure. Traits can provide ecologically based explanations for observed responses to environmental changes, along with predictive power gained by developing relationships between traits and environmental variables. Despite these potential benefits, questions remain regarding the utility and limitations of these approaches, which we explore focusing on the following questions: (a) How reliable are predictions of biotic responses to changing conditions based on single trait–environment relationships? (b) What factors constrain detection of single trait–environment relationships, and how can they be addressed? (c) Can we use information on meta-community processes to reveal conditions when assumptions underlying trait-based studies are not met? We address these questions by reviewing published literature on aquatic invertebrate communities from stream ecosystems. Our findings help to define factors that influence the successful application of trait-based approaches in addressing the complex, multifaceted effects of changing climate conditions on hydrologic and thermal regimes in stream ecosystems. Key conclusions are that observed relationships between traits and environmental stressors are often inconsistent with predefined hypotheses derived from current trait-based thinking, particularly related to single trait–environment relationships. Factors that can influence findings of trait-based assessments include intercorrelations of among traits and among environmental variables, spatial scale, strength of biotic interactions, intensity of habitat disturbance, degree of abiotic stress, and methods of trait characterization. Several recommendations are made for practice and further study to address these concerns, including using phylogenetic relatedness to address intercorrelation. With proper consideration of these issues, trait-based assessment of organismal vulnerability to environmental changes can become a useful tool to conserve threatened populations into the future.
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    Long-term fish assemblages of the Ohio River: Altered trophic abundances with hydrologic alterations and land use modifications
    Pyron, Mark; Mims, Meryl C.; Minder, Mario M.; Shields, Robert C.; Chodkowski, Nicole; Artz, Caleb C. (PLOS, 2019-04-24)
    Long-term monitoring of species assemblages provides a unique opportunity to test hypotheses regarding environmentally induced directional trajectories of freshwater species assemblages. We used 57 years of lockchamber fish rotenone and boat electrofishing survey data (1957-2014) collected by the Ohio River Valley Water Sanitation Commission (ORSANCO) to test for directional trajectories in taxonomy, trophic classifications, and life history strategies of freshwater fish assemblages in the Ohio River Basin. We found significant changes in taxonomic and trophic composition of freshwater fishes in the Ohio River Basin. Annual species richness varied from 31 to 90 species and generally increased with year. Temporal trajectories were present for taxonomic and trophic assemblages. Assemblage structure based on taxonomy was correlated with land use change (decrease in agriculture and increase in forest). Taxonomic assemblage structure was also correlated with altered hydrology variables of increased minimum discharge, decreased fall rate, and increased rise rate. Trophic composition of fish catch correlated with land use change (decrease in agriculture and increase in forest) and altered hydrology. Altered hydrology of increased minimum discharge, increased fall discharge, decreased base flows, and increased number of high pulse events was correlated with increased counts of herbivore-detritivores and decreased counts of piscivores and planktivores. We did not find directional changes in life history composition. We hypothesized a shift occurred from benthic to phytoplankton production throughout the basin that may have decreased secondary production of benthic invertebrates. This may also be responsible for lower trophic position of invertivore and piscivore fishes observed in other studies.
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    Measuring and modeling the effects of temperature on the amphibian chytrid fungus and assessing amphibian skin bacterial communities
    Gajewski, Zachary John (Virginia Tech, 2021-08-17)
    Emerging infectious diseases are a threat to wildlife populations and conservation efforts. One example of this is the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis and has been linked to amphibian populations declines worldwide. There have been numerous attempts to mitigate the effects of Bd on amphibians, all with mixed results. Two factors that have previously been found to correlate with Bd infection intensity and prevalence are the amphibian skin bacterial communities and environmental temperatures. Some naturally occurring bacteria on the skin of amphibians and warmer temperatures can limit Bd infection. For my dissertation research, I aimed to 1) assess the amphibian skin bacterial communities across species, developmental stage, infection status, and different local environments, and 2) understand and predict the effect of a natural, varying temperature regime on the growth of Bd from constant temperature data. In Chapter 1, I reviewed the amphibian chytrid fungus and the effects of varying temperature on organisms' performance or trait rates. In Chapter 2, I sampled bacterial communities on ranid tadpoles and three ranid frog species at Mianus River Gorge Preserve in Bedford, New York, USA. I found that tadpoles had significantly different bacterial alpha diversity measurements than adult frogs, with higher Faith's phylogenetic diversity, Shannon diversity, and amplicon sequence variant (ASV) richness. Bacterial communities between the three different adult frogs species were not different. Additionally, infected frogs did not have significantly different bacterial communities than uninfected frogs. In Chapter 3, I predicted Bd growth in three varying temperature environments with Bayesian hierarchical models assuming different thermal performance curves. My predictions overestimated the growth of Bd in varying temperature environments, and the choice of thermal performance curve used in the models strongly impacted the predictions by altering the implied relationship between Bd's growth rate and temperature. In Chapter 4, I aimed to improve modeling methods for predicting in vitro Bd growth in varying temperature environments by adding additional features to the model based on observed biological phenomena, specifically a temperature-dependent delay period for Bd development. However, the model parameters were unidentifiable with this added complexity when only optical density data are available to quantify growth, highlighting the need to match the appropriate data to the complexity of the model. In Chapter 5, I created a mechanistic model that was parameterized by a combination of optical density, MTT assays (a metabolic assay), and zoospore count data to learn more about Bd growth dynamics. I also examined how many days of zoospore count data are needed to fit the mechanistic model. By combining these three data sources, I increased the ability to estimate most model parameters. My dissertation added to both the amphibian skin bacterial community literature, supporting differences between tadpoles and adult frog bacterial communities, and added new data from a previously unsurveyed area. Attempts are being made to use bacterial communities to limit diseases in many wildlife populations, through a probiotic. To use skin bacterial communities, factors that shape these communities need to be understood to ensure the successful application of a probiotic. My dissertation also added to the thermal ecology literature, showing that current methods and my optical density Bayesian hierarchical model do not accurately predict performance in varying temperature environments. As temperatures are changing around the world and temperature variability is expected to increase in many places, predicting how organisms will perform in new thermal environments is becoming increasingly important.
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    Mismatch between conservation status and climate change sensitivity leaves some anurans in the United States unprotected
    DuBose, Traci P.; Moore, Chloe E.; Silknetter, Sam; Benson, Abigail L.; Alexander, Tess; O'Malley, Grace; Mims, Meryl C. (Elsevier, 2022-12-21)
    Species vulnerable to climate change face increased extinction risk, but many sensitive species may be overlooked due to limited data and exclusion from vulnerability assessments. Intrinsic sensitivity, or the inherent risk of species to environmental change due to biological factors, can be assessed with widely available data and may address gaps in multispecies vulnerability assessments. Species that exist in few places (geographically rare) and in fewer climates (smaller realized climate niche breadth) have high intrinsic sensitivity to environmental change. Using point occurrences, we systematically evaluated intrinsic sensitivity based on geographic rarity and realized climate niche breadth for 90 species of frogs and toads native to the United States using over 140,000 occurrence records. To relate sensitivity to perceived extinction risk, we compared intrinsic sensitivity to conservation status at state, federal, and international levels. We found no relationship between intrinsic sensitivity and federal or state conservation status, and some intrinsically sensitive species (i.e., those with small areas of occurrence and narrow climate specificity) were not listed as at risk at any level. Intrinsic sensitivity analysis can serve as an early warning system for species that may be currently at risk and overlooked
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    Pervasive changes in stream intermittency across the United States
    Zipper, Samuel C.; Hammond, John C.; Shanafield, Margaret; Zimmer, Margaret; Datry, Thibault; Jones, C. Nathan; Kaiser, Kendra E.; Godsey, Sarah E.; Burrows, Ryan M.; Blaszczak, Joanna R.; Busch, Michelle H.; Price, Adam N.; Boersma, Kate S.; Ward, Adam S.; Costigan, Katie; Allen, George H.; Krabbenhoft, Corey A.; Dodds, Walter K.; Mims, Meryl C.; Olden, Julian D.; Kampf, Stephanie K.; Burgin, Amy J.; Allen, Daniel C. (2021-08)
    Non-perennial streams are widespread, critical to ecosystems and society, and the subject of ongoing policy debate. Prior large-scale research on stream intermittency has been based on long-term averages, generally using annually aggregated data to characterize a highly variable process. As a result, it is not well understood if, how, or why the hydrology of non-perennial streams is changing. Here, we investigate trends and drivers of three intermittency signatures that describe the duration, timing, and dry-down period of stream intermittency across the continental United States (CONUS). Half of gages exhibited a significant trend through time in at least one of the three intermittency signatures, and changes in no-flow duration were most pervasive (41% of gages). Changes in intermittency were substantial for many streams, and 7% of gages exhibited changes in annual no-flow duration exceeding 100 days during the study period. Distinct regional patterns of change were evident, with widespread drying in southern CONUS and wetting in northern CONUS. These patterns are correlated with changes in aridity, though drivers of spatiotemporal variability were diverse across the three intermittency signatures. While the no-flow timing and duration were strongly related to climate, dry-down period was most strongly related to watershed land use and physiography. Our results indicate that non-perennial conditions are increasing in prevalence over much of CONUS and binary classifications of 'perennial' and 'non-perennial' are not an accurate reflection of this change. Water management and policy should reflect the changing nature and diverse drivers of changing intermittency both today and in the future.
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    The power, potential, and pitfalls of open access biodiversity data in range size assessments: Lessons from the fishes
    Smith, Jennifer A.; Benson, Abigail L.; Chen, Ye; Yamada, Steffany A.; Mims, Meryl C. (Elsevier, 2019-11-14)
    Geographic rarity is a driver of a species’ intrinsic risk of extinction. It encompasses multiple key components including range size, which is one of the most commonly measured estimates of geographic rarity. Range size estimates are often used to prioritize conservation efforts when there are multiple candidate species, because data for other components of rarity such as population size are sparse, or do not exist for species of interest. Range size estimates can provide rankings of species vulnerability to changing environments or threats, identifying rare species for future study or conservation initiatives. However, range sizes can be estimated by several different metrics, and the degree of overlap in the identification of the rarest or most common species across methodologies is not well understood. This knowledge gap compromises our ability to prioritize correctly rare species, and presents a particularly difficult challenge for stream-dwelling organisms with distributions constrained to river networks. We evaluated the relationship of multiple range size estimates of a subset of freshwater fishes native to the United States to determine the degree of overlap in rarity rankings using different data sources and grain sizes. We used publicly available, open access data from the Global Biodiversity Information Facility (GBIF) to calculate extent of occurrence (minimum convex polygons) and area of occupancy (total area occupied, measured across various grain sizes). We compared range sizes estimated using GBIF data with the best available estimates of current distributions described by publicly available digital maps (NatureServe) to evaluate the efficacy of GBIF data in assessments of range size. We found strong correlations between range size estimates across analytical approaches and data sources with no detectable bias of taxonomy. We found that variation among rarity rankings was highest for species with intermediate range sizes indicating that the approaches considered here generally converge when used to identify the rarest or the most common species. Importantly, our results show that the rarest, and perhaps the most vulnerable, species are consistently identified across common methodological approaches. More broadly, our results support the use of open access biodiversity data that include opportunistically collated and collected point occurrence records as a complement to coarse-grain (e.g., whole range map) approaches, as we observed no systematic bias or deviation across data sources in our analyses. This indicates databases such as the GBIF may help fill important fundamental and applied knowledge gaps for many poorly understood species, particularly in a broad-scale, multispecies framework.