<p dir="ltr">For several decades, the ecological dominance of white oak (<i>Quercus alba</i>) has been declining throughout the species’ native range in eastern North America with failure to recruit new individuals into the overstory. White oak’s decline is concerning as the species is of great cultural, ecological, and economic value. Planting artificial regeneration is one approach to bolstering flagging natural white oak regeneration insufficient in vigor or quantity to supplant mature canopy white oak. Shelterwood harvests and artificial regeneration alone or in combination are frequently suggested to be an effective means of securing sufficient white oak regeneration in central hardwood understories. Because there is a much more comprehensive body of work examining northern red oak (<i>Quercus rubra</i>) than white oak artificial regeneration, managerial prescriptions for artificial regeneration of white oak are commonly generalized from northern red oak prescriptions. If the two species are silvically different, however, they should be managed differently to achieve maximum effectiveness of regenerative prescriptions.</p><p><br></p><p dir="ltr">I conducted both a silvicultural field trial and a more controlled shade and competition study to examine artificial white oak regeneration responses to light and competition gradients. In the silvicultural field trial, I tested the impacts of varied lengths of competition control, geographical seed source, and canopy cover on growth and survival of artificial white oak regeneration within an expanding shelterwood system. After three growing seasons, my results indicated that seedlings grow and survive at the greatest rates in areas of up to approximately 50% canopy closure, or conditions found in harvest gaps.</p><p dir="ltr">In a shade and competition study, I compared artificial northern red oak and white oak growth, morphology, and physiology responses to three light levels (10% or low, 30% or medium, and full sun or high) under the presence or absence of an invasive competitor (Amur honeysuckle (<i>Lonicera maackii</i>)). After two years, my results indicated that medium light levels resulted in the greatest height and diameter growth as well as the greatest nonstructural carbohydrate amounts in both root and shoot organs of both species. Interestingly, my physiology results indicated that northern red oak seedlings displayed lower light compensation points and greater quantum yields than white oak seedlings. These traits potentially indicate greater shade tolerance of northern red oak than white oak. Further, white oak foliar nitrogen in shaded treatments, quantum yield, and light compensation points were impacted more severely by competition than equivalent northern red oak measures, indicating that white oak seedlings may not be as well equipped to handle invasive competition pressures. These results indicate that these two upland oak species are fundamentally different, and these differences should be considered when writing management prescriptions.</p>

<p dir="ltr">Coastal ecosystems are critically important habitats for the services they provide on a global and local scale. Maritime forests are found within the southern Atlantic coast, and they serve as a boundary between the ocean and land. These forests stabilize coastlines, recharge groundwater, and provide a protective buffer against storm damage. Southern live oak (<i>Quercus virginiana</i>) was historically the dominant canopy species in maritime forests; however, previous land conversions to loblolly pine (<i>Pinus taeda</i>) plantations have shifted the abundance of loblolly pine to become the dominant canopy tree in maritime forests. Loblolly pines are fast growing, and they regenerate vigorously but they are not well adapted to coastal stressor. In recent decades, outbreaks of southern pine beetle (<i>Dendroctonus frontalis</i>) have provided restoration practitioners an opportunity to clear tracts of pine dominated maritime forest to restore live oak to the canopy. This research project is comprised of two experiments studying the performance of planted <i>Q. virginiana</i> seedlings on maritime forest restoration sites in coastal Georgia. The first experiment evaluated planting density (1-meter, 2-meters, 3-meters), mulch (with or without), and fertilizer (with or without). Overall seedling survival was 99% after four years. The application of fertilizer had an initial positive effect on seedling diameter after the first growing season. The application of mulch increased seedling height in the second to fourth growing seasons, diameter in third and fourth, and crown width in the fourth growing season. Planting density had no consistent effect over the first four years, and no biological significance was observed for foliar nutrient content. The second experiment examined eight different groupings of intra- and interspecific competition between <i>Q. virginiana</i> and <i>P. taeda</i> including: oak or pine alone; oak surrounded by oak, pine, or oak/pine; pine surrounded by pine, oak, or pine/oak at 0.5-m spacing between all seedlings. Two years after outplanting, survival did not vary by treatment. Oak centered competition plots were positively impacted by border tree height and diameter in year one and border height positively affected the center tree height in year two. Pine centered competition plots were positively impacted by border tree height in year one and year two. Oak centered competition plots with a mix of oak and pine on the border had significantly lower osmotic potential than other pine centric treatments after two years. Overall, oak centered treatments had lower osmotic potential than pine centered treatments. Ectomycorrhizal (EMF) species composition changed, and relative abundance increased from the initial planting to two years later but there was no variation between treatments and most EMF species were generalists. These results highlight the importance of mulch and fertilizer to reduce transplant shock and how competing seedlings can train seedlings to allocate photosynthate to shoot growth to help promote aboveground growth.</p>

<p dir="ltr">Managing a forest presents many challenges for tree farmers, especially when relying on traditional manual methods. Previous research highlights the wide range of tasks involved in forest management, from planting and nurturing trees to harvesting and selling timber. These conventional approaches often result in inefficiencies and unexpected difficulties at various stages. However, advances in technology, specifically through the use of LiDAR-based reconstruction and differential geometry, have made it feasible to accurately measure tree sizes and identify species with a single capture.</p><p dir="ltr">To help tree farmers overcome these challenges, this thesis proposes the development of a cross-platform solution named WoodWiz. WoodWiz comprises two synergistic components: a mobile application for real-time, on-site tree measurements, and a web-based platform for comprehensive forest management. The measurement feature in mobile app streamlines the data collection process, reducing time and labor, while MyForest offers a detailed view of the forest's status, facilitating efficient management and planning. Additionally, WoodWiz includes a Library feature, providing a repository of forestry resources and best practices, and a community platform to foster collaboration and knowledge sharing among forestry professionals. This integrated system simplifies the wide range of tasks involved in forest management—from planting and nurturing to harvesting and selling timber—thereby reducing inefficiencies and addressing the unexpected difficulties typically associated with traditional methods.</p><p dir="ltr">The development of WoodWiz involved extensive research, design, and evaluation, culminating in a robust tool that not only streamlines forest management tasks but also provides tree farmers with actionable insights for decision-making. By automating critical measurements and facilitating data access, WoodWiz improves the accuracy of forest inventory and health assessments, leading to more informed and strategic management practices. The potential impacts of this solution on the forestry industry include increased productivity, improved sustainability of forest resources, and enhanced profitability for tree farmers. This thesis details the iterative process of WoodWiz's development, highlights its key features, and evaluates its effectiveness in transforming forest management practices.</p>

<p>Forest management involves numerous stochastic elements. To sustainably manage forest resources, it is crucial to acknowledge these sources as uncertainty or risk, and incorporate them in adaptive decision-making. Here, I developed several stochastic programming models in the form of passive or active adaptive management for natural mixed-species hardwood forests in Indiana. I demonstrated how to use these tools to deal with time-invariant and time-variant natural disturbances in optimal planning of harvests.</p> <p> Markov decision process (MDP) models were first constructed based upon stochastic simulations of an empirical forest growth model for the forest type of interest. Then, they were optimized to seek the optimal or near-optimal harvesting decisions while considering risk and uncertainty in natural disturbances. In particular, a classic expected-criterion infinite-horizon MDP model was first used as a passive adaptive management tool to determine the optimal action for a specific forest state when the probabilities of forest transition remained constant over time. Next, a two-stage non-stationary MDP model combined with a rolling-horizon heuristic was developed, which allowed information update and then adjustments of decisions accordingly. It was used to determine active adaptive harvesting decisions for a three-decade planning horizon during which natural disturbance probabilities may be altered by climate change.</p> <p> The empirical results can be used to make some useful quantitative management recommendations, and shed light on the impacts of decision-making on the forests and timber yield when some stochastic elements in forest management changed. In general, the increase in the likelihood of damages by natural disturbance to forests would cause more aggressive decisions if timber production was the management objective. When windthrow did not pose a threat to mixed hardwood forests, the average optimal yield of sawtimber was estimated to be 1,376 ft³/ac/acre, while the residual basal area was 88 ft²/ac. Assuming a 10 percent per decade probability of windthrow that would reduce the stand basal area considerably, the optimal sawtimber yield per decade would decline by 17%, but the residual basal area would be lowered only by 5%. Assuming that the frequency of windthrow increased in the magnitude of 5% every decade under climate change, the average sawtimber yield would be reduced by 31%, with an average residual basal area slightly around 76 ft²/ac. For validation purpose, I compared the total sawtimber yield in three decades obtained from the heuristic approach to that of a three-decade MDP model making <i>ex post</i> decisions. The heuristic approach was proved to provide a satisfactory result which was only about 18% lower than the actual optimum.</p> These findings highlight the need for landowners, both private and public, to monitor forests frequently and use flexible planning approaches in order to anticipate for climate change impacts. They also suggest that climate change may considerably lower sawtimber yield, causing a concerning decline in the timber supply in Indiana. Future improvements of the approaches used here are recommended, including addressing the changing stumpage market condition and developing a more flexible rolling-horizon heuristic approach.

<p>Due to overpopulation and resource-poor habitat structure, deer threaten the<a> future of oak and other browse-sensitive species in hardwood forests. </a>Appropriate tools must be used to ensure desirable, diverse, and ecologically stable regeneration of future forests and the sustainability of native plant communities. We performed two experiments and a review to examine the effectiveness of available methods for managing browse of hardwood seedlings and to discover how these interact with each other and other silvicultural methods. First, we examined how fencing interacts with controlled-release fertilization, seed source (genetically select and non-select), and site type (afforested and reforested sites) to enhance the regeneration of planted northern red oak (<i>Quercus rubra </i>L.), white oak (<i>Quercus alba</i>), black cherry (<i>Prunus serotina</i>), and black walnut (<i>Juglans nigra</i>) at five sites in Indiana. Fencing proved to be the greatest determinant of seedling growth, survival, and quality. Fertilizer enhanced the early growth of white oak and black cherry, though for black cherry this occurred only inside fences. Select seed sources grew better and showed greater quality; however, the survival of select seedlings was limited by deer browse in absence of fences. Trees at afforested sites had lower survival if left non-fenced. Secondly, we also investigated how fencing and invasive shrub removal affected natural regeneration, species richness, and ground-layer plant cover under closed-canopy forests. Honeysuckle (<i>Lonicera maackii</i>) removal had a variable effect depending on species and site. Positive effects were most common for shade-intolerant species, while negative effects occurred for a few shade-tolerant species at some sites. Deer fencing had a positive effect on cherry and hackberry seedling density, and a negative effect on elm seedling density. Honeysuckle and deer fencing interacted antagonistically in some instances. Fencing without honeysuckle removal resulted in lower elm abundance and herbaceous-layer cover. In the densest invasions, leaving honeysuckle intact resulted in a complete lack of recruitment into the sapling layer. Our experiment suggests that invasive shrub removal and fencing be done together. Finally, we synthesized the existing literature on browse management options for hardwood regeneration to evaluate their relative effectiveness. Fences, tree shelters, repellents, facilitation by neighboring plants, deer population control, timber harvest, and slash all had positive effects on height growth of regenerating seedlings under deer browse pressure. Fences were more effective at reducing browse than repellents, while fertilizers increased browse and had no effects on growth. </p>

<p dir="ltr">The Temperate Plains ecoregion of Indiana has experienced significant agricultural development since the 19th century, which has left streams vulnerable to impacts such as sedimentation and nutrient accumulation. This thesis describes first the accuracy of the USDA Cropland Data Layer (CDL) in land cover change, and second, the relationships between agricultural and forested land covers and stream biological integrity. I first employed the CDL to review land cover change, particularly relating to agriculture and forest, for the area of interest between 2010 and 2020. I determined that the CDL improved in accuracy for the area of interest in the chosen timeframe for non-agricultural and non-forest land cover. I concluded that the CDL was best used as a supplement to primary-source land cover measures. Next, I calculated the fish Index of Biotic Integrity (IBI) scores for 20 sampled agricultural and forested streams in North-Central Indiana. I also assessed the stream habitats at all sites using the Qualitative Habitat Evaluation Index (QHEI) and percent cultivated crops in drainage basin areas for all streams. Forested streams had significantly higher QHEI scores than agricultural streams (median = 62 and 40.4, respectively). No other relationships were statistically different, including IBI and land cover category, which may have been due to the small sample size (n = 20). I concluded that future studies may build on these findings by controlling for agricultural drainage types or using precise measures of forested land cover.</p>

<p dir="ltr">Reflectance spectroscopy has been increasingly used in forestry due to its ability to rapidly, efficiently, and non-destructively detect tree stress, enabling timely and cost-effective forest management decisions. This dissertation synthesizes three studies and five experiments to understand and improve our ability to use spectral data to estimate a variety of foliar physiochemical traits and identify spectral responses in multi-stress environments, thus, advancing our understanding and application of hyperspectral data in forest management.</p><p dir="ltr">The first study seeks to refine the hyperspectral approach to monitoring tree stress by selecting optimal wavelength ranges to enhance the estimation of foliar traits, such as CO₂ assimilation rate, specific leaf area, leaf water content, and concentrations of foliar nitrogen, sugars, and gallic acid. The study revealed that model performance varied significantly across the different wavelength ranges tested and consistently, including longer wavelength regions improved trait estimation for all traits modeled. This research also established a framework for discovering novel or previously unknown absorption features associated with functional traits, thereby laying the groundwork for expanded spectral applications. This advancement enables the estimation of diverse foliar traits and facilitates detailed stress detection in trees.</p><p dir="ltr">The second study focuses on assessing the effectiveness of hyperspectral data in estimating foliar functional trait responses to various biotic and abiotic stressors and to differentiate those stressors in black walnut (<i>Juglans nigra </i>L.) and red oak (<i>Quercus rubra</i> L.) seedlings. We demonstrated that spectral data can reliably estimate a wide range of foliar traits, highlighting its potential as a surrogate for reference data in understanding plant responses to stress. This research revealed that spectral leaf predictions can effectively provide stress-specific insights into tree physiochemical responses to biotic and abiotic stressors.</p><p dir="ltr">The third study explores the application of hyperspectral reflectance to identify drought-induced foliar responses in black walnut seedlings during their initial field establishment. Chemometric models developed from greenhouse experiments were applied to spectral data collected in the field to assess their transferability and accuracy in predicting various leaf traits under drought stress. Using only spectral data, we demonstrated that seedlings show distinct spectral responses to past and ongoing drought stress, with varying degrees depending on seed provenances. This research aims to provide practical insights for utilizing spectral analysis in real-world conditions and understanding the challenges of using spectral tools in the field.</p><p dir="ltr">Collectively, this dissertation demonstrates the robust potential of hyperspectral reflectance technology in advancing the monitoring of tree health. By optimizing spectral range selection, reliably estimating tree foliar traits under stress conditions, differentiating various stressors in controlled environments, and effectively detecting current and past drought stress in field conditions, this research offers valuable insights for improving forest health monitoring and management strategies in response to environmental challenges.</p>

<p>Here, we seek to address the importance of biodiversity in plant ecosystems. We examined the productivity-diversity relationship through the lens of the modern coexistence theory, using a combination of both experimentation and mathematical simulation. We did this by tracking and comparing the productivity of mixed and monoculture plots, analyzing the growth responses of individual trees at forest plots (Chapter 1), confirming the productivity-diversity relationship in a greenhouse experiment using local herbaceous plants (Chapter 2), and finally simulating the productivity response of monoculture vs polyculture plantations to specialist enemy attack (Chapter 3).</p><p>It is no surprise that biodiversity has been decreasing at an exponential rate on the global scale because of effects such as habitat fragmentation, invasive species, spreading pathogens, and anthropogenic influences. Ecologists often found that plants in more species rich locations often exhibited higher productivity and stability in the face of stress. One such phenomenon is known as the productivity diversity relationship that implies biodiversity is key to sustaining ecosystems. Notably, while efforts are being put forth to address ecosystem destruction, much of the current tree planting strategy in the USA is based on timber profit rather than forest productivity and species coexistence with tree biology often being a secondary consideration. These thought processes are in opposition with historical experiments that indicate polyculture communities create more biomass making them significantly more productive than monocultures. However, we also acknowledge that it is not simply biodiversity that must be taken into consideration for a productive ecosystem but also species interaction through coexistence indicate whether or not a community will persevere. These interactions can be addressed using the modern coexistence theory which depends on these complementarity and fitness similarities for species to coexist through time. Here, we seek to address the importance of biodiversity in plant ecosystems. We examined the productivity-diversity relationship through the lens of the modern coexistence theory, using a combination of both experimentation and mathematical simulation. We did this by tracking and comparing the productivity of mixed and monoculture plots, analyzing the growth responses of individual trees at forest plots (Chapter 1), confirming the productivity-diversity relationship in a greenhouse experiment using local herbaceous plants (Chapter 2), and finally simulating the productivity response of monoculture vs polyculture plantations to specialist enemy attack (Chapter 3). Our research across the combination of approaches used found that species with overlapping niches and very different finesses will exclude one another due to high competition. Further, the productivity diversity correlation is necessary for ecosystem growth, but it is not sufficient for species coexistence. However, species can maintain this positive relationship despite a lack of coexistence if they maintain niche complementarity. Lastly, using a theoretic game model we were able to identify the impacts of a specialist pest on polyculture and monoculture forest. These results showed that a polyculture forest was more productive than that of a monoculture forest regardless of the presence of a specialist enemy. The results of the multiple threads of evidence found from these combined experiments indicate that while the productivity diversity correlation is important to ecosystems it is likely due to the impacts of niche complementarity that determine whether or not species will be productive within an ecosystem.</p>

<p dir="ltr">To examine how forest management affects terrestrial salamanders, this dissertation: (1) examines the effects of timber harvesting strategies on salamanders; (2) examines the effects of prescribed fire for oak regeneration on salamander populations; and (3) explores the influence of artificial cover object (ACO) wood type, size and shape, and placement on salamander monitoring results. These projects were conducted at the Hardwood Ecosystem Experiment (HEE) and Martell Experimental Forest in Indiana. Long-term salamander monitoring data from the HEE were used to examine the effects of clearcuts, shelterwoods, and patch cuts on salamander captures collected up to eleven years post-harvest and were analyzed with a before-after-control-impact (BACI) design. Clearcuts and patch cuts had negative effects on salamanders 4-6 years post-harvest, which coincided with a drought; however, preparatory and establishment shelterwood harvests showed no effects on salamander captures, suggesting that retaining canopy cover may protect salamanders from compound disturbances such as drought. Also at the HEE, capture-recapture techniques were used to examine salamander population estimates before and after fire. Only two of three fires affected salamander populations. In the short term, prescribed fire effects on salamanders may be weak and intermittent and microclimate may have a greater effect on populations, although the longer-term effects of fire remain unknown. At Martell Experimental Forest, salamander numbers were compared beneath ACOs of different wood types, sizes and shapes, and grid arrays of different spacings. Pine ACOs were preferred over ash, while several small ACOs yielded equal salamander numbers to one large ACO of equal total area. High ACO density may increase capture probability but reduce the area sampled by each ACO, while lower density ACO grids may cover a larger area with the same sampling effort and produce more comparable results, but with less precision; choice of ACO experimental design will therefore require careful consideration of management goals. This dissertation also suggests strategies to support salamander populations as guidelines for managers to consider in management planning.</p>

<p dir="ltr">Non-native biological invasions are one of the leading concerns for global biodiversity. The establishment of invasive species reduces local biodiversity, shifts species composition, changes successional trajectories, and alters ecosystem functions. This thesis examines two aspects of invasive plants: (1) the distribution and the most important climatic and anthropogenic drivers of invasive trees across the eastern United States, and (2) an evaluation of invasive plant removal and herbaceous recovery from a government cost-share program that provides financial support for invasive plant management by private landowners.</p><p><br></p><p dir="ltr">Our first study focused on identifying the distribution of invasive trees, and the factors associated with their distribution. This is essential to predicting spread and planning subsequent management. Using USDA Forest Inventory Analysis (FIA) data and random forest modeling, we examined the distribution, and variables associated with the distribution, of invasive tree species. Invasive trees were found in 10,511 out of 299,387 FIA plots. Invasive species basal area and density (trees per ha; TPH) were highest within the central and southern Appalachian Mountains, Michigan, the Northeast, and the southern Coastal Plain of the United States. A random forest model of invasive species basal area (R²= 0.47, RMSE = 0.47) and density (R²=0.46, RMSE=0.50) vs. environmental variables found that both invasive basal area and density were most strongly associated with human footprint, followed by various climatic variables. An equivalent model of native tree basal (R²=0.53, RMSE=9.25) and TPH (R²=0.47, RMSE=8.64) found that native tree basal area and density were most strongly associated with aridity followed by various climatic variables. As human footprint increased, invasive tree basal area and density increased. These results suggest that the distribution of invasive trees is reliant on human alterations to forests.</p><p><br></p><p dir="ltr">Our second study focused on Environmental Quality Incentives Program (EQIP), a federal cost-share program that has provided $25 billion of financial assistance to farmers and non-industrial private forest owners. Few studies have examined whether this program facilitates the recovery of the herbaceous layer while decreasing the dominance of invasive plant species. We surveyed the herbaceous layer of EQIP-treated and untreated (reference) forests across three physiographic regions of Indiana. Using non-metric multidimensional scaling (NMDS) ordination and linear mixed effects models, we evaluated the species composition, richness, diversity, evenness, floristic quality index, and herbaceous-layer cover of EQIP and reference sites. We also used linear mixed models to evaluate how EQIP site treatment affected the diversity of native plant species. Sites treated with EQIP contracts typically had significantly higher native species richness, Shannon’s diversity, and floristic quality than reference sites. There were significant separations in species composition between EQIP treated and reference forests state-wide and in the southern non-glaciated region of Indiana, although composition overlapped between EQIP and reference forests. Our study suggests that EQIP-funded treatments promote increased species richness and diversity. However, the persistent overlap in species composition we observed may signify biotic homogenization due to a long-shared history of anthropogenic disturbances between EQIP and reference sites. Therefore, active restoration of the herbaceous layer might be needed to allow a full recovery after invasive removal.</p>