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Ecosystems around the world are seeing an unprecedented decline in biodiversity. However, to better prevent this decline we cannot only understand the drivers of biodiversity loss, but also the factors that support diversity. Traditional ecological hypotheses such as the Habitat Heterogeneity Hypothesis (HHH) and the Theory of Island Biogeography (TIB) have provided frameworks for understanding biodiversity drivers. However, recent research suggests a more nuanced relationship between heterogeneity, habitat size, and diversity than previously thought. This study looks to bridge existing research gaps by examining the ecologically and conservational important habitat of wetlands. Specifically, the study focuses on the plant diversity of freshwater forested wetlands in the Piedmont region of South Carolina. I hypothesize that in Piedmont wetlands, abiotic heterogeneity primarily drives plant biodiversity, regardless of habitat size. To test this hypothesis, three main objectives were outlined. First, is to characterize plant diversity patterns across wetlands. Secondly, to assess the relationship between abiotic heterogeneity and wetland size. Lastly, to determine the effects of both heterogeneity and size on various aspects of wetland plant diversity. Overall, the initial hypothesis was rejected, but clear trends still emerge. Chemical heterogeneity showed a positive relationship with species richness and phylogenetic diversity after correcting for the effect wetland size. Additionally, habitat size was positively correlated with beta diversity, but only with species richness after correcting for the effect of chemical heterogeneity. These results provide evidence that the best way to preserve plant diversity in Piedmont wetlands is to effectively manage habitat size reduction and preserve a heterogeneous chemical landscape.

Coastal forested wetlands are identified as some of the highest-priority ecosystems for climate change mitigation. Here, we present two studies conducted in these unique ecosystems. The first assessed changes in aboveground vegetative C stocks along the estuarine-riverine gradients of the Winyah Bay in South Carolina and the Savannah River in Georgia, using a space-for-time substitution to increase understanding of the impacts to upper estuarine forested wetlands from relative sea level rise. Standing C stocks on the Savannah River averaged 183.6 Mg C ha-1, while sites on the Winyah system averaged 162.3 Mg C ha-1. The largest aboveground C pools were found at sites furthest upriver, decreasing downstream as salinity rose. These data, alongside predicted sea-level rise suggest a marked decrease in future aboveground C stocks in forested wetlands situated in and around tidal estuaries. Our second study investigated the radial and azimuthal patterns of sap flow in species (baldcypress and water tupelo) common to the freshwater swamps of the southeastern US, suspecting that these diverse species may exhibit similar sap flow patterns under permanently flooded conditions. Granier-style thermal dissipation probes were used to measure daytime sap flux at 15 mm and 25 mm depths into the active xylem of both species to assess radial patterning and at each cardinal direction on the bole of each species to assess azimuthal patterning. Analysis of sub-daily time series data found significant (p < 0.05) effects on sap flux by time of day, month, species, and depth. We did not find any differences between the two depths with water tupelo (p > 0.5), but average baldcypress flux rates at 15 mm were significantly higher than those at 25 mm (p < 0.0001). Azimuthal patterns were not detected for either species, contradicting previous studies. This study supports the treatment of azimuthal sap flow variation as a random variable rather than one with predictable directionality, and demonstrates that common radial sap flow patterns may not be generalizable across diverse environmental settings. Because our study found temporal variation in sap flux rates, the inclusion of these temporal factors could improve modeling estimates of individual tree water use.

The microorganisms found in marine subseafloor sediment play a vital role in global carbon and nitrogen cycles, with an estimated 2.9×1029 cells, accounting for about 0.6% of Earth’s total living biomass. These microbes grow at a very slow rate, with carbon turnover occurring over the course of years to thousands of years, about six orders of magnitude slower than sulfate reducing bacteria in pure culture. These slow metabolic rates suggest that the enzymes they produce must also have extended lifespans in order to be effective over such long periods of time. As a result, these enzymes are likely to be highly stable. The central question of my thesis is: "Do subsurface microbes have more stable proteins compared to other organisms?". I tested this hypothesis by examining various Carbohydrate-Active enzyme (CAZy) families within sediment samples obtained from the Baltic Sea at two distinct depths (25 cm and 15 meters below the seafloor). previous research suggested a distinction in the stabilities of proteins belonging to two distinct families, GH29 and GH109. I investigated the stability of proteins by using Gibbs free energy of folding ∆Gfold. Some prokaryotic proteins intended for export have an N-terminal signal peptide that directs them to the secretion pathway. Having this signal peptide signifies a substantial environmental change, therefore I conducted a comparative analysis of protein pairs, ensuring both pairs either contained signal peptides or lacked them, revealing a significant stability difference, with higher stability noted at greater depth. Also, the stability is notably higher in protein pairs lacking signal peptides in deep samples compared to surface samples, predominantly among pairs from the glycoside hydrolase (GH) family. Contrary to our expectations, our investigation revealed no significant difference in the stability of extracellular proteins between deep and surface samples. This outcome does not align with our initial hypothesis, indicating that the environmental depth may impact the stability of these proteins. This suggests that the presence of a signal peptide may play a role in the environmental adaptability and stability of proteins, providing a specific area of interest for further research to understand the protein stability across different environments.

Freshwater crayfish constitute one of the most-threatened taxonomic groups in North America. Invasion by other crayfish species as well as habitat degradation through alteration of natural flow regime are two of the most prominent threats to crayfish persistence. Additionally, extreme weather events like droughts can amplify threats posed by other stressors on crayfish populations and are expected to increase in frequency, magnitude, and/or duration in the future, which may negatively influence narrow-ranged endemic crayfish populations typical of the Southeast. The Mammoth Spring Crayfish, Faxonius marchandi, is a narrow-ranged endemic that occurs in the Spring River drainage of Arkansas and Missouri where it is both geographically and genetically isolated. Additionally, F. marchandi populations may be faced with a spreading invader, F. neglectus chaenodactylus, the Gap Ringed Crayfish. This dissertation sought to examine the influence of invasion and drying on F. marchandi growth and survival using mescosm experiments, the desiccation tolerance of the invader versus F. marchandi using experimental chambers, the influence of stream permanence and drying on crayfish density, occupancy, detection, colonization, and extinction using a multi-season dynamic occupancy model, and the predicted extinction risk and population viability of F. marchandi under future invasion and drought scenarios using a stage-based demographic metapopulation model. In the mesocosm experiment, there was a significant negative interspecific competition effect on change in length, and the experimental chamber experiment found differential tolerance to desiccation for all populations, with larger individuals tending to live longer. Additionally, the population models found negative effects under severe invasion and only under severe drought. These results indicate F. marchandi may show resilience when faced with F. neglectus invasion and drying will likely not play a part in their dynamics. The dynamic occupancy results showed context-dependent differences in density, detection, colonization, and extinction. This dissertation shows how crayfish may respond to environmental changes and invasive species in the coming years and gives potential implications about their persistence.

Mountain lions (Puma concolor) have been studied extensively throughout their wide geographic distribution in the Western Hemisphere, but most research has been conducted at relatively small spatial scales. We used GPS telemetry data contributed by researchers in 16 study areas throughout California to advance understanding of mountain lion spatial ecology. First, we investigated multi-scale resource selection of mountain lions relative to spatially varying risk of intentional human-caused mortality associated with livestock depredation management. We show that individuals that proactively avoided mortality risk when selecting home ranges were able to relax their avoidance of risk when making resource selection decisions within their home ranges. Our analysis also demonstrates that functional responses in resource selection provide a quantitative link between coarse and fine-scale resource selection decisions made by individual animals. Second, we evaluated movement-based resource selection of subadult mountain lions during dispersal, which is the primary mechanism that maintains gene flow between populations. Our results support the hypothesis that anthropogenic landscape features act as barriers to movement that limit demographic and genetic connectivity between populations, elucidating behavioral mechanisms underlying the observed genetic structure between California mountain lion populations. However, our results also suggest that preservation of even relatively small patches of natural habitat and implementing road-crossing infrastructure should enhance connectivity. Third, we investigated intrinsic, ecological, and anthropogenic factors influencing home range size of mountain lions along a statewide gradient of landscape productivity and human disturbance. Our results indicate that home range size is influenced by the abundance and distribution of prey in relatively undisturbed landscapes, whereas anthropogenic features create fragmentation and barrier effects that influence home range size in developed regions. Our work advances understanding of responses of mountain lions to mortality risk from the leading mortality cause in California, behavioral mechanisms of reduced connectivity between populations, and the influence of natural and anthropogenic factors on space use. Management and conservation informed by empirical research will contribute to promoting long-term viability of mountain lions in Southern California and along the Central Coast, which face challenges similar to those of large carnivores around the globe associated with human-wildlife conflict, habitat loss, and fragmentation. Advisor: John F. Benson

Diatom assemblage reconstruction from the Valles Caldera sediment core (VC-3) was utilized to infer climatic and aquatic changes during a 50-thousand-year [ka] period in the Mid-Pleistocene (435-385 ka). This 50 ka interval spans most of Marine Isotope Stage 11 (MIS 11) – one of the most prominent interglacials of the past 500 ka – and is widely considered an analog for the Holocene and future climate regimes. Nearly all records from MIS 11 are either marine or ice-core based, making VC-3 unique among lacustrine sediment records as it captures insolation variations and climatic changes during the mid-Pleistocene. Analysis of the diatom community assemblages shows rapid shifts between benthic (bottom-dwelling) and planktonic (free-floating) taxa, indicating the lake that occupied the Valle Grande within the Caldera experienced variable lake-levels. Autecology of dominant species (>10% relative abundance) allowed for the interpretation of water conditions and lake bathymetry during the mid-Pleistocene: taxa that thrive in cold, oligotrophic occur in abundance before Glacial Termination V; species indicative of higher nutrient-flux characterize transgressional and regressional events in the Lake’s history; dominance of taxa that prefer shallow, eutrophic conditions occur coeval to mega-drought conditions; and low-density samples overlap with two ash-layer deposits (~397.2 and ~394.0 ka)

Embryophytes have undergone numerous re-invasions to aquatic habitats, impacting their morphological evolution. Despite the prominence of these transitions, their phylogenetic implications and morphological adaptations are just beginning to be investigated, especially as molecular methodologies become more accessible. We investigate these phenomena using the genus Fissidens, a diverse group of mosses encompassing both terrestrial and aquatic species. Our study integrates phylogenetic methods with morphological analyses to elucidate the evolutionary patterns within Fissidens and explore correlations between habitat transitions and morphological traits. Through extensive taxon sampling from herbarium specimens, DNA extraction, and sequencing, we construct robust phylogenetic trees using concatenated and coalescence methods. Our results reveal the non-monophyly of historically defined subgroups within the genus Fissidens, challenging prior classifications. Furthermore, ancestral state reconstructions suggest there have been multiple independent transitions to aquatic environments within the genus. Morphological analyses indicate that although variations in leaf length correlated with habitat moisture, phylogenetic relatedness diminishes this correlation. These findings better our understanding of the complexity of evolutionary transitions in embryophytes and emphasizes the need for further studies to refine taxonomic classifications and better understand morphological changes in response to ecological shifts. This study contributes to wider discussions on the evolutionary dynamics of aquatic transitions in both bryophytes and, more broadly, embryophytes and their ecological significance.

With an increase in wind energy development and continued deforestation and habitat degradation, eastern red bats (Lasiurus borealis; LABO) and other migratory foliage roosting bats (hoary bat [Lasiurus cinereus; LACI], silver-haired bat [Lasionycteris noctivagans; LANO]) are at risk of severe population declines, potentially leading to the need for protection under the Endangered Species Act. While studies have been done examining the ecology of these species, there is still a lack of research on winter roosting and foraging behaviors. This research aims to fill some of those knowledge gaps by 1) Examining roost use (i.e., trees vs. litter) and determining roost fidelity of LABO in forest stands during late fall, winter, and early spring, 2) Exploring winter roost selection by LABO at three spatial scales (roost, patch, and landscape), and 3) Examining the short-term effect of dormant season (October – April) prescribed fire on forest roosting bat activity in contrast with the activity in unburned stands by conducting acoustic monitoring of bat echolocation calls. During the winter of 2022/23 I tracked 9 radio-tagged LABO to 20 diurnal roosts, including 1 snag. While stand level characteristics did not appear to influence winter roost selection, bats roosted closer to forest edge than random roosts (101.8 21.08; P = 0.029). Days spent in roosts increased as temperature decreased. From November 2022 to April 2023, we deployed SM4 mini bat acoustic detectors in 20 study sites to monitor bat activity in burned and unburned stands. Stands that had undergone prescribed burning had greater bat activity than stands that were not burned, with shelterwood release sites having a more significant increase in activity than savannas or native warm-season grass fields. While our research does provide some insight into winter roosting and foraging ecology of foliage roosting bats, more research is needed to fill knowledge gaps and conserve these species.

We are experiencing biodiversity loss due to climate change and human impacts, which is not only harmful to the environment but can also alter the composition of communities and interactions among species. The late Pleistocene experienced a loss of large-bodied mammals which resulted in significant changes in community structure due to changes in body size, diet, and species associations. The impact of these changes on species interactions and community structure across the Pleistocene-Holocene transition remains poorly understood. Using a robust data set of species composition, stable isotopes, body size, and climate variables, we constructed and compared ecological networks of mammal paleocommunities on the Edwards Plateau, Texas. One site, Hall’s Cave, has a temporal resolution that allows an in-depth analysis by separating the last 22,000 years into 16 time intervals. We measured the structure of food webs using modularity, and species contributions to modularity. Additionally for Hall’s Cave, we measured an index of node overlap and segregation for each time interval. We find consistent decreases in modularity across all sites with food webs shifting from having multiple clusters in the Pleistocene to fewer clusters in the Holocene. The less complex network post extinction is largely attributed to the loss of particular species interactions. In Hall’s Cave, we find node overlap increases and modularity decreases over time. Spearman-Rank correlation analyses indicate that changes in modularity were not driven by changes in species richness or climate change. The degree of node overlap shifted across the Pleistocene-Holocene transition and was significantly different from null model expectations in the Holocene but not in the Pleistocene. These results suggest that the transition from a modular network to a network of less complexity with an overlap of interacting species may have been driven by other factors that changed the food web, such as species composition. Thus, the change in mammal food web structure of Hall’s Cave was mainly a consequence of the megafauna extinctions. Advisors: S. Kathleen Lyons and Daizaburo Shizuka

Urbanization poses a significant threat to wildlife through fragmentation, degradation, and loss of habitats. Species response to urban development is variable, from species that thrive in urban areas to those that avoid them. Eastern box turtles (Terrapene carolina carolina) can live and reproduce in urban areas; however, reports of population decline throughout the species’ range have raised concerns. The objective of this study was to compare home range size and composition, as well as the microhabitat selection of the Eastern box turtle across a developmental gradient in Clemson, SC. We tracked 14 individuals in habitats along a developmental gradient ranging from residential neighborhoods to the protected habitat of the Clemson Experimental Forest. Individuals were relocated at a frequency of once weekly during the active season (April to November) of 2022, twice weekly during the active season of 2023, and once every other week in the winter. Each time a telemetered turtle was located we recorded the coordinates and various habitat parameter (e.g., humidity, vegetation cover) at the used and two associated random locations 5-10 and 50-60 meters. We generated 95% autocorrelated kernel density estimates to represent home range size and minimum convex polygons to determine home range composition. A discrete choice framework was used to compare various habitat parameters hypothesized to influence microhabitat selection. Our results indicated turtles in small forest patches within the suburban landscape had smaller home ranges and reduced average weekly displacement compared to individuals in continuous forest areas. The increased presence of edge habitat could act as an ecological trap by encouraging behavior specific to that ecotone (e.g., nesting or thermoregulation). Our results also indicated that microhabitat selection varied across levels of development. In habitats with no development selection was influenced by vegetation cover composition (i.e., turtles selected for areas with foraging potential and woody debris). In contrast in habitats with moderate and high development, turtles selected areas with greater leaf litter depth and vegetation > 15 cm in height. Our results highlight the importance of large continuous forest patches for maintaining unrestricted home range area and movement, as well as reducing opportunities for human-caused mortality. We also call attention to the importance of a complex understory that includes deep leaf litter depth, vegetation greater than 15 cm in height, and the presence of woody debris. The results from this study help to further our understanding of how development affects the movement and behavior of the Eastern box turtle, and the results provide a means to improve backyard habitat management for this species.

North American monarch butterfly (Danaus plexippus) populations are experiencing significant declines due to habitat loss caused by land use changes. Much of the American Midwest where milkweed, the only host plant of the monarch butterfly, was once much more abundant has been converted to a predominantly agricultural landscape. There are nineteen species of milkweed native to the northern Great Plains region occupied by South Dakota, North Dakota, and Minnesota. Some of these milkweed species may be preferable to monarch butterflies for different reasons, including morphological factors such as stem length, species-level chemical factors, and temporal factors. As monarch butterfly populations continue to decline, more information on milkweeds native to the northern Great Plains is needed to streamline efforts for monarch butterfly habitat restoration. The two objectives of this study were to 1) analyze monarch butterfly oviposition preferences on native milkweeds of the northern Great Plains and 2) conduct a survey of different pathogenic fungi isolated from native milkweed species in the northern Great Plains. To address the first objective, a common garden plot of the species of milkweed native to the Northern Great Plains was established near South Dakota State University. Using randomized block design, multiple plants of each milkweed species were planted in replicate plots, and each plant was thoroughly checked for eggs and larvae and measured for morphological factors, including stem length, width, and number of stems. Asclepias incarnata received the highest number of eggs and larvae throughout all three years of study, but monarchs laid more eggs on A. syriaca at the beginning of each season, suggesting changes in preference throughout the summer. Morphological factors were found to play no role in monarch oviposition preferences. The second objective was to survey the different species of fungus isolated from tissue samples collected from a variety of different milkweed species located in the common garden plot. Disease symptoms and high death rates were noted on various milkweed species, particularly Asclepias tuberosa, in the common garden plot throughout the 2023 season. DNA from the fungi collected from milkweed tissue samples was sequenced to determine which fungal species were the most likely culprits of the disease symptoms noted on milkweed in the common garden plot. We suspect Rhizoctonia solani to be the source of plant deaths early in the season and Fusarium acuminatum to be the source of shoot tip dieback symptoms later in the season.

Stream connectivity is crucial for fish movement and genetic diversity in fragmented landscapes. Road-crossings often act as barriers, disrupting hydrology and isolating fish populations. The Southeast Aquatic Resources Partnership (SARP) has developed rapid road-crossing assessment protocols and tools to prioritize restoration projects. However, managers lack tools for planning, directing, and initiating roadcrossing assessments. Managers also require modeling approaches to effectively identify and monitor road-crossings across dynamic stream networks. Presented here is a case study offering a roadmap for effective implementation of collaborative road-crossing assessments and prioritization of remediation projects, alongside an exploration of predictive modeling approaches to identify problematic crossings across large, dynamic stream networks. A mobile decision-support tool was created to help plan and direct assessment efforts using datasets of roads, streams, road-crossing locations, completed assessments, and species of greatest conservation need (SGCN). In 2022 and 2023, a total of 528 road-crossings were assessed, and a training workshop in August 2023 increased assessment capacity, resulting in a contribution of 91 assessments in just 1.5 days. Top remediation candidates produced through prioritization, such as Willow Creek near Watertown, South Dakota, could provide ~94 miles of quality upstream habitat. Plans to expand the tool nationwide include refining map layers and functionality to enhance agency goals and foster collaborations. Two modeling frameworks were developed and evaluated for remotely estimating road-crossing barrier severity (the degree to which fish passage is impeded): Boosted Regression Trees (BRT) using landscape-level covariates and Image Scene Classification (ISC) of aerial imagery. Results from both frameworks provided encouraging training accuracies (BRT: training correlation of 78.3%, ISC: training accuracy of ~78%) but fell short of precise predictions. However, this effort provided valuable insights into specific watersheds and landscape characteristics such as scour pool size, stream discharge, and amount of pasture at the catchment level contributing to barrier severities in eastern South Dakota. Ultimately, additional barrier assessments are needed in South Dakota to improve predictive power and accurately identify problematic road-crossing locations.

Metapopulations are shaped by the dispersal between populations in a landscape. Disturbance events can disrupt this connectivity resulting in local population extinction. For my dissertation, I used a combination of empirical and theoretical techniques to examine dispersal in response to disturbance and assessed it’s population-level consequences. My research used capture-mark-recapture sampling techniques to evaluate stream salamander movement in response to (1) a supraseasonal drought and (2) mountaintop-removal-mining (MTR) and valley-filling (VF) and (3) agent-based simulation modeling to evaluate population extinction risk in response to varying dispersal and mortality rates. First, I evaluated the effects of a supraseasonal drought, a severe drought that occurs outside of predictable seasonal dry periods for an extended period of time, on the movement frequency distribution, survival, and growth rates of adult Desmognathus fuscus. I found that salamanders were more likely to move immediately after the supraseasonal drought compared to before or during the drought. Salamanders who moved experienced slightly higher growth rates post-drought. Although movement frequency was low during the drought, survival was higher for individuals who moved in comparison to individuals who remained in their original capture location. My results suggest that adult salamanders were potentially displaying an adaptive movement strategy to resist drought conditions by moving away from affected (i.e., dry) areas within the study stream during the drought and moving towards replenished resources in other areas after the drought ended. Next, I evaluated movement pathways (e.g. within-stream, overland), movement frequency distribution curves, individual body condition, and dispersal rates for two common stream salamander species (D. fuscus and D. monticola) within a reclaimed MTR and VF landscape and compared these populations with populations from an undisturbed, reference landscape. I found that stream salamanders utilized within-stream dispersal pathways in the reference and MTR and VF landscape. However, overland movement was only detected in the reference landscape, not in the MTR and VF landscape. Body condition was a potential driver for individuals engaging in dispersal and was overall lower for individuals in the MTR and VF landscape compared to the reference landscape. My results indicated that overland connectivity between salamander populations in the MTR and VF landscape was disrupted compared to the undisturbed landscape and resulted in population isolation, which, if left unchanged, could result in local population extirpation. Finally, I constructed two agent-based models with different metapopulation structures and investigated how differences in extinction risk was affected by differences in dispersal and mortality probabilities between populations and between areas. I found that differences in dispersal and mortality did influence population extinction risk. My models demonstrated that increased dispersal into a population decreased it’s extinction risk but only when population differences in mortality was low. In addition, when mortality was higher for an area, populations located on the fringe of the metapopulation network had a higher extinction risk compared to the populations that bordered other populations. My results indicated that maintaining connectivity between populations lowers population extinction risk, especially in areas of lower habitat quality resulting from a disturbance event. This research demonstrates that long-distance movement allows populations to resist the negative effects of environmental and anthropogenic disturbance. Therefore, maintaining and, when applicable, restoring both aquatic and terrestrial habitat is likely vital for stream salamander population persistence.

Human manipulation of river systems has long been a known contributor to the loss of freshwater biodiversity. By accounting for environmental causes of hydrologic variation among rivers, we can better understand how ecoregion mediates flow regimes and forecast species that may be at risk. Presumably, natural variation associated with ecoregion boundaries exerts strong influence on flow regimes, and may mediate relationships between other features (e.g., land use, dam operations) and hydrology. However, such between-ecoregion variation is poorly investigated, particularly at fine spatial and temporal scales. I characterized 10 hydrologic metrics, representing the five key dimensions of the flow regime (magnitude, frequency, duration, timing, and rate-of-change) using 30+ years of daily streamflow data collected at 375 real-time monitoring gages in streams spanning mountain (MT), Piedmont (PD), and coastal plain (CP) ecoregions of the southeastern U.S. Random forest and redundancy analysis models were used to rank the relative importance of stream-size, land-cover, climatic, physiographic, and impoundment conditions in upstream watersheds for predicting downstream flow characteristics, and to assess the transferability of these relationships across ecoregions. Stream size was the “master variable” that consistently influenced flow conditions across all ecoregions and dimensions, whereas the influences of other factors varied considerably among ecoregions. For example, watershed urbanization and topography tended to be the most important predictors of flow conditions in PD streams, whereas carbonitic geology and annual climate conditions tended to be the most important predictors in MT streams, with wetland land cover, climate, and topography tended to be most strongly associated with flow conditions in CP streams. Anthropogenic influences like land use and dams had stronger influences on flow duration, predictability, and rate-of-change than on magnitude or frequency. Notably, duration, predictability, and rate-of-change profoundly influence riverine biota but are not addressed by common streamflow regulations like minimum- or mean-flow management standards. Contrary to predictions, PD streams were not hydrologically intermediate to MT and CP streams. Rather, they exhibited the most-variable base-flow magnitudes, most-frequent yet shortest-lasting high-flow events, and flashiest hydrographs of any ecoregion. My results suggest that attempts to model and manage flow should account for all five flow dimensions, given their presumably strong influence on fish ecology and evolution, but should also account for substantial differences in landscape-flow-ecology relationships among ecoregions.

To better understand wood turtle (Glyptemys insculpta) population trends, two standardized population survey protocols were recently developed for use by state monitoring programs. The protocols were independently developed, tested, and deployed for population monitoring in the eastern and upper midwestern United States. It was unknown if the sampling designs result in similar detection success or if data from the two protocols are compatible for broad-scale analyses. Additionally, neither monitoring protocol includes a sampling design that allows for the separation of detection (p) into availability (pa), and detection given availability (pd). Wood turtles typically remain near streams year-round, but they spend a large portion of their time moving throughout the riparian and upland habitat during the active months, which includes moving in and out of the survey area. If pa is non-random and pd or pa are influenced by demographic factors such as sex or age class, then abundance estimates derived from standardize protocol data may be biased. In Chapter 1, I first discuss the ecology of wood turtles, including distribution and habitat associations. I then provide information on wood turtle population survey techniques, focusing on the two standardized protocols referred to as the Eastern Protocol and Midwestern Protocol. I also discuss abundance modeling and the factors that can impact modeling accuracy. Lastly, I state the goals of this thesis research and provide a summary of the chapters. In Chapter 2, we used survey results from a modified wood turtle sampling design that included a double observer approach within surveys. This allowed us to separately estimate pd and pa,to determine if pa is random or Markovian and what covariates influence pd or pa. We modified the wood turtle survey protocol used in the upper Midwest to include a double-pass design, allowing us to estimate pa and pd using a robust design capture-recapture model. Our results indicated that pa was non-random and that pd increased with turtle carapace length. Our study suggests that model assumptions for current wood turtle population models may be violated, likely resulting in an overestimation of abundance. The results of Chapter 2 improve our understanding of potential biases associated with the Midwestern protocol, and thus the modifications needed to obtain accurate population estimates. In Chapter 3, we compared p and expected count estimates between constrained and unconstrained survey designs for aquatic-focused and terrestrial-focused surveys at wood turtle monitoring sites from across the distribution of the species within the United States. We estimated adult wood turtle p and expected count for aquatic-focused and terrestrial-focused surveys using N-mixture models and generalized linear mixed models, respectively. Our study supports that constrained and unconstrained surveys can be used interchangeably for population monitoring if survey type is accounted for in the population models. However, our findings indicated that, within sampling periods at monitoring sites, restricting all survey replicates to only aquatic or only terrestrial surveys is optimal for use in population abundance and trend models. This information can be used to guide the creation of a range-wide protocol that maximizes flexibility in survey design while maintaining data congruency across space.

Despite making up less than two percent of the overall landscape in the arid and semi-arid western US, riparian areas are a crucial resource for agriculture, livestock, and wildlife. However, many have impaired function and reduced riparian cover. Low-Cost, Low-Tech Tools (LCLTT) are a subset of Process-Based Restoration (PBR) used for riparian restoration that were chosen for their cost-effectiveness and minimal technical requirements. LCLTT has been tested in mountainous areas of the western US but only recently implemented in the Northern Great Plains (NGP). Given their novelty as an approach toward restoration for the region, professional restoration and landowner communities are skeptical about LCLTT. The objective of this research was to address these concerns by determining the short-term impacts of LCLTT on vegetation communities and soil moisture (SM) in riparian areas located in livestock production systems. Forage production, SM, and the proportions of vegetation functional groups and ground cover were compared between stream reaches treated with LCLTT and untreated control reaches. The findings of this research show that in both the riparian corridor and historic floodplain, the LCLTT treatment reduced bare ground (-16% and -13%, P=0.04 and P=0.003, respectively) and increased upland vegetation (21% and 31%, P=0.002 and P < 0.0001, respectively), with increased surface water in the riparian corridor (13%, P=0.005) and increased graminoid vegetation (18%, P=0.0007) in the historic floodplain. Throughout the study, the upper 15cm of the soil profile had more moisture (0.08 m3/m3, P=0.04) in treatment reaches with an extended release of moisture during the summer. A seasonal analysis of SM showed no significant differences between treatment and control reaches during spring, but higher water content was observed in treatment reaches in the 0-15 cm range in summer (0.12 m3/m3, P=0.001), and both the 0-15 and 15-30 cm ranges in fall (both 0.13 m3/m3, P=0.0002). No changes to forage production were observed. Research regarding PBR from other locations showed similar changes to stream processes and plant communities in the early stages of restoration. While this research demonstrated short-term impacts in the initial year post-restoration, previous, longer-term research in other regions has observed that changes from PBR increase and compound with time. The results of this and similar research indicate that LCLTT could be a timeand cost-effective tool for landowners and managers to restore prairie streams and riparian areas in a livestock production setting in the NGP.

Floating marine structures, like the brown macroalgae Sargassum, provide essential habitat and support several life history stages for many marine organisms; habitat fragmentation and persistence of these floating habitats are poorly understood. Extending landscape ecology principles to the seascape realm requires new methodologies to understand dynamics of patch mosaics and functional utility of the moving seascape system. I examine Sargassum in a seascape ecology context, exploring 1) structural descriptions of the Sargassum patch seascape and whether 2) historical Sargassum patch distribution is represented by delineated proposed and finalized Sargassum-as-a-critical-habitat designations under the US Endangered Species Act (ESA). I utilize historical Sargassum data at two spatial scales: a coarse scale (1.6km) and a medium scale (328m) to determine whether habitat fragmentation processes are occurring at either spatial scale across seven marine regions in the Northern Atlantic Ocean. In the Gulf of Mexico specifically, the size of Sargassum patches is increasing, while the Caribbean Sea Sargassum patch density has increased by an order of magnitude during the study period suggesting habitat gain. In the Northern Brazil Shelf and the Sargasso Sea, there is evidence of habitat fragmentation occurring due to rapid changes in patch density, proportion of seascape, and distance between patches. In addition, all regions within the study area exhibit cyclic patterns, which suggests Sargassum habitat characteristics may occur alternating between high and low years, which can impact critical habitat strategies for Sargassum. Lastly, Sargassum patches were found to exhibit a notable increase in occurrence within the ESA's proposed green turtle critical habitat designation of Sargassum when compared with the ESA's loggerhead critical habitat Sargassum designation Sargassum. These data provide valuable insight into Sargassum as an important and highly dynamic seascape that may provide critical habitat for dispersal-stage juvenile sea turtles during their oceanic ‘lost years.'

Epibionts on seagrass leaves contribute substantially to productivity and trophic interactions in seagrass ecosystems. Differences in epibiont assemblages and factors that contribute to epibiont diversity have been little studied on the seagrass Halodule wrightii in the northern Gulf of Mexico (nGoM). We used a metabarcoding approach to describe epibiont assemblages on H. wrightii leaves in four bays across the nGoM and to test whether epibiont assemblages differed spatially at local levels (within bays) or regional levels (from west to east). Furthermore, we tested if epibiont diversity was related to environmental conditions and/or seagrass productivity. Epibiont assemblages differed significantly between bays and between sites within bays. The diversity of non-diatom algal and animal epibionts was positively correlated with salinity and seagrass production. Our results show that each seagrass bed supported a relatively distinct assemblage of epibionts, which appear to be structured by both regional and local conditions.

Much of the landscape of the United States has been altered by humans, leading to the eradication of most populations of large mammalian predators. Consequently, many species of mammalian mesopredators (medium-sized mammalian predators) have come to dominate the landscape. Species such as the gray fox (Urocyon cinereoargenteus) may appear to be on the rise and doing well due to their widespread range, but at a local scale may need monitoring and less is known in areas of its range. Others such as the plains spotted skunk have a wide range across the plains but are on the decline even with the lack of dominant apex predators. Unpacking the trends of these mesopredators in a changing environment can be complicated, but necessary. In my first chapter I look at the plains spotted skunk (Spilogale interrupta) as it is in decline range-wide. We developed a presence-only species distribution model using only occurrence records from Great Plains and adjacent prairie ecoregions. We found most scales of response to be at the 100m scale, except for water cover which occurred at the 6km scale. Water cover was the strongest predictor of spotted skunk occurrence. We found non-linear relationships between spotted skunk presence and anthropomorphic variables such as open space and development where skunks were positively associated with these landcovers at lower levels but would become negatively associated when both landcovers became more prevalent. When we projected our results across the region, our predictive map showed strong predicted habitat suitability in areas with heterogenous landscapes and abundant riparian areas. This may indicate that the plains spotted skunk may be a habitat generalist and distribution may be driven more by fine scale resources such as prey density or shelter rather than landcover alone. For my second chapter, I examined a more common, charismatic, furbearer species: the gray fox (Urocyon cinereoargenteus). To address a gap in our understanding of the gray fox we initiated a large-scale camera trapping effort to understand how this species responds to forest types and forest configuration across multiple spatial scales. Specifically, we sought to explore how the gray fox responds to the configuration of forest patches, and density of forest edge habitat. We found across spatial scales, gray foxes were negatively associated with evergreen forest cover and positively associated with deciduous forest cover. The negative association with evergreen forest is likely due to the type of evergreen forest in this area which is mainly pine plantations. We also found the top models selected at all scales included some form of landscape configuration metric such as edge or patch density. We also note that even though the patterns did not change between scales the configuration metrics may depend on the scale of investigation. When investigated at a small scale, deciduous forest patch density best explained gray fox occupancy whereas at a medium scale, evergreen forest edge and deciduous forest edge density best explained gray fox occupancy and finally at large scales we saw evergreen forest edge density as the best model.

Forests play a pivotal role in sustaining global biodiversity and mitigating the global climate, as they serve as the primary refuge for terrestrial biodiversity and effectively capture and store atmospheric carbon dioxide. However, changing climate and land use are altering the geographic distribution, physical structure, and productivity of forested ecosystems that can have profound impacts on biodiversity conservation, forest productivity, and global climate. This dissertation contributes to our understanding of multifaceted interactions between the physical and biological structural complexity and ecosystem functions in forested landscapes across the United states by using openly available data from two national networks: the National Ecological Observatory Network (NEON) and Ameriflux. The first chapter provides a critical review and synthesis of historical and contemporary approaches for quantifying biodiversity, assessing their relevance and constraints, and emphasizing the necessity for new methods to monitor biodiversity on a landscape scale. Alongside a comprehensive review and synthesis of existing literature, this chapter introduces an innovative method for computing a multi-trophic diversity (MDI) index that offers a comprehensive assessment of diversity across multiple trophic levels, encompassing plants, beetles, and birds. This index holds promise for streamlining biodiversity monitoring on a landscape scale by employing remotely sensed data and has broad applications in forest management. The second chapter introduces a new method to calculate a combined terrain and canopy structural complexity metric using widely-available LiDAR data, enabling the prediction of MDI– a combined diversity metric that integrates diversity across trophic levels; developed in chapter one. Specifically, this chapter investigates how structural complexity of terrain and forest canopy influence the diversity of primary producers (plants), herbivores (beetles), and omnivores (birds). This chapter underscores the importance of considering both structural complexity and forest type in addition to climate and geographical factors when making land management decisions to promote biodiversity and ecosystem health. The third chapter explores the links between complexity (biological and structural) and ecosystem functions, specifically focusing on key ecosystem processes like net ecosystem exchange (NEE), ecosystem respiration (Reco), and gross primary productivity (GPP). The findings of this chapter highlight the importance of including complexity (structural and biological) in predicting ecosystems functions including carbon sequestration potential of a landscape.

Freshwater ecosystems are facing a crisis with extinction rates of aquatic species exceeding those of their terrestrial counterparts by up to fivefold. This decline is predominantly attributed to evolving land use patterns within watersheds, leading to chemical and physical transformations in freshwater habitats. Northwest Arkansas (NWA) represents one of the fastest-growing regions in the United States, undergoing substantial shifts in land use. Consequently, the status of aquatic life in this region remains uncertain. Addressing this concern, the latest Arkansas Wildlife Action Plan emphasizes the necessity of distribution and population data to guide conservation efforts for Species of Greatest Conservation Need (SGCN). Among these species are three Allocapnia stonefly species—A. jeanae, A. ozarkana, and A. warreni—historically found in NWA during their winter emergence periods. In this study, I conducted an analysis combining fine-scale, site-specific surveys, and species-specific assessments to provide insights into the presence and richness of Allocapnia along three major river systems in NWA: the White River, Clear Creek, and West Fork White River. To inform my analyses, I utilized historical stonefly surveys conducted 50 and 30 years ago. I conducted Allocapnia surveys at 22 sites during winter emergence periods in 2020-2021 and 2021-2022, with an average of 10 visits per site. Specimens were collected from emergent structures and identified in the laboratory. To gain an understanding of the relationships between independent variables (including land use, latitude, draining area, and Strahler stream order) and the presence of each Allocapnia species, I employed orthogonal partial least square regression. Additionally, univariate threshold analyses were conducted to pinpoint critical points in land use values that resulted in significant declines in Allocapnia richness. My findings reveal that Allocapnia were predominantly found in forested streams, with no occurrences recorded at highly urbanized sampling sites. Notably, A. rickeri and A. mohri displayed high prevalence and abundance in large, high-order sections within the West Fork White River basin, suggesting a greater resilience to land use changes compared to other Allocapnia species. Allocapnia jeanae demonstrated successful dispersion within the NWA landscape over the past five decades, albeit primarily restricted to tributaries, with limited occurrences within the mainstem of sampled rivers. Allocapnia ozarkana, although persisting, were collected in low numbers. Allocapnia warreni was not detected in Clear Creek and has not been recorded in this area for over half a century, indicating a likely extirpation. Land use thresholds were identified at 64.3% (±25.17) for forest, 26.19% (±5.18) for agriculture, 8.56% (±0.74) for urban, and 1.51% (±0.16) for impervious surface cover. These thresholds highlight the critical importance of concentrating conservation efforts on the protection of forested headwaters to ensure the preservation of vital habitats for aquatic shredding macroinvertebrates, such as Allocapnia. Additional actions in agricultural and urban areas should include the maintenance of riparian zones and stormwater management In the face of an evolving landscape, understanding the effects of land use on aquatic life remains imperative to safeguard our natural resources and ensure the sustainability of our ecosystems.