Forest plantations have been long-employed to reverse land degradation and support biodiversity, and are now recognized to both take in atmospheric carbon dioxide, reducing the intensity of the greenhouse effect, and moderate local weather. It is important to consider the impact forest aging and management will have on provisioning of these services under climate change and extreme weather events, such as drought. This study encompasses a chronosequence of three Eastern White Pine stands planted in 1939, 1974 and 2002, situated in Turkey Point, Ontario, Canada. The oldest forest received two selective thinning treatments, removing 30% of trees, in 1983 and 2012. Forest water use efficiency (WUE), which represents the amount of gross ecosystem productivity (GEP) per unit of water released through evapotranspiration (E), was compared among the three sites over 2008-2013. The youngest forest’s annual WUE increased over the study period, surpassing that of the older sites by 2013. When bulk surface conductance (Gs), representing gas exchange, was compared across the sites for the same years, the youngest site had the lowest Gs, particularly during drought. Gs at the oldest forest was highest and the most variable. Statistical analysis showed that across all the sites, E was more responsive to air temperature than atmospheric demand, soil moisture, and incident radiation. This study indicated that younger plantations may be more water-conservative during drought, and that air temperature is important to consider in projections of temperate coniferous forests’ carbon and water exchange. To assess the impact of the 2012 selective thinning on tree-level and ecosystem-level water use at the oldest forest, sapflow velocity (Js), transpiration (Et) and E were compared between the two stands planted in 1939 and 1974, from 2011 to 2013. A relatively severe drought over the 2012 growing season led to a decline in Et at the unthinned site for that year, however the Et decline was more pronounced at the older, thinned site. From 2011 to 2012, Js increased at the thinned site, converse to the unthinned site – wherein Js was low as expected during drought. Hydraulic redistribution and lag time from sapflow at 1.3 m height to canopy evapotranspiration were seemingly unaffected by the thinning, indicating that low-level selective harvesting was not detrimental to the hydrological functionality of the stand, and may have been beneficial in allowing more soil moisture access per tree. As such, the stand may be better positioned to withstand recurrent dry spells resulting from precipitation variability, as predicted with climate change. / Thesis / Master of Science (MSc)

This study presents the energy, carbon (C), and water exchange dynamics of a recently afforested temperate white pine (Pinus strobus L.) forest, established on former agricultural land in 2002, in southern Ontario, Canada during the initial thirteen years (2003–2015). Our observations show that the forest became a consistent sink of C after only 5 years of its establishment (ranging from 105 g C m–2 to 216 g C m–2 between 2008 to 2015), owing to sandy soils and low residual soil organic matter from prior agricultural activities. This region frequently experiences low precipitation (P) and soil moisture (VWC) limitations and/or heat stress in late summer, causing a reduction in net ecosystem productivity (NEP). Seasonal and annual dynamics of NEP showed reduced C uptake during years with heat and/or drought events (i.e. 2007 and 2012). In 2007, the impact of a seasonal drought was much more exacerbated when combined with a heatwave, resulting in a strong C source. Similarly, the inter-annual variability of evapotranspiration (ET) gradually increased with stand age (mean 370 mm yr–1) and water use efficiency (WUE) consistently increased (mean 2.65 g C kg–1 H2O). Quantum yield, α (0.019 to 0.045) and maximum photosynthetic capacity, Amax (4.37 to 33.6 µmol m–2s–1) increased steadily as the size and density of the canopy increased with stand age. Energy fluxes were influenced by canopy development as net radiation (Rn), latent heat (LE), and sensible heat (H) flux increased, while ground heat flux (G) peaked in 2007 and then gradually declined. Our analysis showed that daily C fluxes are primarily driven by Rn and temperature (Ts, Ta) which explained 47%, 61%, 52%, and 68% of the variability in gross ecosystem productivity (GEP), ecosystem respiration (RE), NEP, and ET. This study is a significant contribution to our understanding of the energy, C, and water dynamics of young planted conifer forests and controls on their growth and C uptake. Our findings demonstrate the potential of utilizing white pine as a means to sequester atmospheric CO2 in southern Ontario and other regions of North America with similar climate and site history. / Thesis / Master of Science (MSc)

Temperate forests are an important global carbon sink. However, various environmental disturbances can impact carbon sequestration capabilities of these forests. In 2021, a record-breaking defoliation, caused by the spongy moth (Lymantria dispar L., formerly knows as the gypsy moth) occurred in eastern North America. In this study, we assess the impact of this spongy moth defoliation on carbon uptake in a mature oak-dominated temperate forest in the Great Lakes region in Canada, using eddy covariance flux data from 2012 to 2022. The forest is more than 90 years old and known as CA-TPD site in the AmeriFlux and global FLUXNET networks. Study results showed that prior to spongy moth defoliation the forest was a carbon sink with mean annual gross ecosystem productivity (GEP) of 1,367 ± 104, ecosystem respiration (RE) of 1,201 ± 145 and, net ecosystem productivity (NEP) of 197 ± 74 g C m−2 yr−1 over the 2012–2020 period. However, due the defoliation in the early growing season in 2021, GEP declined to 959 g C m-2 yr-1 and RE increased to 1,345 g C m-2 yr-1 causing the forest to became a large source of carbon with annual NEP of -351 g C m-2 yr−1. This large decline in annual NEP was a result of both reduced GEP (30%) and elevated RE (12%). However, in 2022, forest carbon fluxes recovered to pre-infestation levels, with a GEP value of 1,671 g C m-2 yr-1, an RE value of 1,287 g C m-2 yr-1, and an NEP value of 298 g C m-2 yr-1, indicating that the forest was once again a large carbon sink. This research demonstrates that major transient natural disturbances such as the 2021 spongy moth defoliation can have a significant impact on forest carbon dynamics in a future warmer climate. The extent to which North American temperate forests will remain a major carbon sink will depend on the severity and intensity of these disturbance events and rate of recovery of forests following the disturbance. / Thesis / Master of Science (MSc) / Temperate deciduous forests play an important role in carbon sequestration from the atmosphere. However, the impact of climate change, extreme weather, and disturbance events can alter the extent to which these forests sequester carbon, in some cases shifting their role from being a carbon sink to becoming a carbon source to the atmosphere. In 2021, a spongy moth infestation severely defoliated a mature oak-dominated temperate forest north of Lake Erie, Ontario, Canada, turning the forest from a carbon sink to a carbon source. Our analysis indicates that meteorological conditions during the early spring might have influenced the severity of this infestation. Specifically, the prevalence of dry and warm weather conditions enabled the moth to survive and thrive longer. This study shows the significant influence of natural disturbances on forest carbon dynamics as temperatures continue to rise due to climate change. The future role forests play in carbon sequestration will be determined by the severity of disturbance events and the effectiveness of forests to recover in the aftermath of these events.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24662号 / 農博第2545号 / 新制||農||1098(附属図書館) / 学位論文||R5||N5443(農学部図書室) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 小杉 緑子, 教授 北山 兼弘, 教授 北島 薫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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The overall theme of this thesis focuses on the joint modeling of longitudinal covariates and a censored survival outcome, where a survival outcome is modeled using a conditional quantile regression. In traditional joint modeling approaches, a survival outcome is usually parametrically modeled as a Cox regression. Censored quantile regressions can model a survival outcome without pre-specifying a parametric likelihood function or assuming a proportional hazard ratio. Existing censored quantile methods are mostly limited to fixed cross-sectional covariates, while in many longitudinal studies, researchers wish to investigate the associations between longitudinal covariates and a survival outcome. The first part considers the problem of joint modeling with a survival outcome under a mixture of censoring: left censoring, interval censoring or right censoring. We pose a linear mixed effect model for a longitudinal covariate and a conditional quantile regression for a censored survival outcome, assuming that a longitudinal covariate and a survival outcome are conditional independent on individual level random effects. We propose a Gibbs sampling approach as an extension of a censored quantile based data augmentation algorithm, to allow for a longitudinal covariate process. We also propose an iterative algorithm that alternately updates individual level random effects and model parameters, where a censored survival outcome is treated in the way of re-weighting. Both of our methods are illustrated by the application to the LEGACY Girls cohort Study to understand the influence of individual genetic profiles on the pubertal development (i.e., the onset of breast development) while adjusting for BMI growth trajectories. The second part considers the problem of joint modelling with a random right censoring survival outcome. We pose a linear mixed effect model for a longitudinal covariate and a conditional quantile regression for a censored survival outcome, assuming that a longitudinal covariate and a survival outcome are conditional independent on individual level random effects. We propose a Gibbs sampling approach as an extension of a censored quantile based data augmentation algorithm, to allow for a longitudinal covariate process. Theoretical properties for the resulting parameter estimates are established. We also propose an iterative algorithm that alternately updates individual level random effects and model parameters, where a censored survival outcome is treated in the way of re-weighting. Both of our methods are illustrated by the application to Mayo Clinic Primary Biliary Cholangitis Data to assess the effect of drug D-penicilamine on risk of liver transplantation or death, while controlling for age at registration and serBilir marker.

<p>Comprehensive sensitivity and uncertainty analysis has been performed for light-water reactor and heavy-water reactor lattices using three techniques; adjoint-based sensitivity analysis, Monte Carlo sampling, and direct numerical perturbation. The adjoint analysis was performed using a widely accepted, commercially available code, whereas the Monte Carlo sampling and direct numerical perturbation were performed using new codes that were developed as part of this work. Uncertainties associated with fundamental nuclear data accompany evaluated nuclear data libraries in the form of covariance matrices. As nuclear data are important parameters in reactor physics calculations, any associated uncertainty causes a loss of confidence in the calculation results. The quantification of output uncertainties is necessary to adequately establish safety margins of nuclear facilities. In this work, the propagation of uncertainties associated with both physics parameters (e.g. microscopic cross-sections) and lattice model parameters (e.g. material temperature) have been investigated, and the uncertainty of all relevant lattice calculation outputs, including the neutron multiplication constant and few-group, homogenized cross-sections have been quantified. Sensitivity and uncertainty effects arising from the resonance self-shielding of microscopic cross-sections were addressed using a novel set of resonance integral corrections that are derived from perturbations in their infinite-dilution counterparts. It was found that the covariance of the U238 radiative capture cross-section was the dominant contributor to the uncertainties of lattice properties. Also, the uncertainty associated with the prediction of isotope concentrations during burnup is significant, even when uncertainties of fission yields and decay rates were neglected. Such burnup related uncertainties result solely due to the uncertainty of fission and radiative capture rates that arises from physics parameter covariance. The quantified uncertainties of lattice calculation outputs that are described in this work are suitable for use as input uncertainties to subsequent reactor physics calculations, including reactor core analysis employing neutron diffusion theory.</p> / Doctor of Philosophy (PhD)

<p>Simulation plays a key role in nuclear reactor safety analysis and being able to assess the accuracy of results obtained by simulation increases their credibility. This thesis examines the propogation of nuclear data uncertainties through lattice level physics calcualtions. These input uncertainties are in the form of covariance matrices, which dictate the variance and covariance of specified nuclear data to one another. These covariances are available within certain nuclear data libraries, however they are generally only available at infinite dilution for a fixed temperature. The overall goal of this research is to examine the importance of various applications of covariance and their associated nuclear data libraries, and most importantanly to examine the effects of dilution and self-shielding on the results. One source of nuclear data and covariances are the TENDL libraries which are based on a reference ENDF data library and are in continuous energy. Each TENDL library was created by randomly perturbing the reference nuclear data at its most fundamental level according to its covariance. These perturbed nuclear data libraries in TENDL format were obtained and NJOY was used to produce cross sections in 69 groups for which the covariance was calculated at multiple temperatures and dilutions. Temperature was found to have little effect but covarances evaluated at various dilutions did differ significantly. Comparisons of the covariances calculated from TENDL with those in SCALE and ENDF/B-VII also revealed significant differences. The multigroup covariance library produced at this stage was then used in subsequent analyses, along with multigroup covariance libraries available elsewhere, in order to see the differences that arise from covariance library sources. Monte Carlo analysis of a PWR pin cell was performed using the newly created covariance library, a specified reference set of nuclear data, and the lattice physics transport solver DRAGON. The Monte Carlo analysis was then repeated by systematically changing the input covariance matrix (for example using an alternative matrix like that included with the TSUNAMI package) or alternate input reference nuclear data. The uncertainty in k-infinite and the homogenized two group cross sections was assessed for each set of covariance data. It was found that the source of covariance data as well as dilution had a significant effect on the predicted uncertainty in the homogenized cell properties, but the dilution did not significanty affect the predicted uncertainty in k-infinite.</p> / Master of Applied Science (MASc)

<p>Understanding the response of forest carbon uptake and growth to interannual climate variability and forest management practices is important, given the large quantity of carbon stored in forests, and their significant role in the global carbon cycle. Since 2004, biometric and micrometeorological measurements were taken in an age-sequence (10-, 38- and 73-years-old as of 2012) of white pine (<em>Pinus strobes</em> L.) plantation forests in southern Ontario, Canada, providing an 8 year record of carbon sequestration, growth and climate. The 73-year old conifer site was thinned in early 2012, where 25% of trees were removed to improve light and water dynamics of this stand, providing an opportunity to study the impacts of thinning on its carbon cycle. Additionally, in 2012, similar biometric and micrometeorological measurements were initiated in a naturally-regenerated, managed 80-year-old deciduous (Carolinian) forest, located in close proximity to the pine stands. Similar to the conifer sites, the deciduous site is also a managed forest. The objectives of this study were to determine differences in carbon pools and carbon sequestration capacity: (a) across an age-sequence of afforested, managed conifer stands; (b) between similarly-aged managed coniferous and deciduous stands; and (c) in a mature conifer plantation before and after a thinning event. Results show that carbon assimilated in the stem of mature white pine trees follows a linear growth trend, while that of young white pines shows an exponential increase in carbon assimilation over the course of this study. Overall, carbon sequestration increased with stand age across the age-sequence, except when disturbed by an event such as thinning. Thinning substantially reduced the live aboveground carbon pool (by 14%), while increasing woody debris (by 122%) due to logging residue left on-site. Comparison between the mature coniferous and deciduous stands, showed that total aboveground carbon storage within the pine stand (144 t C/ha) was generally higher than in the oak-dominated deciduous stand (83 t C/ha), despite both growing in similar soil and climate. While monthly tree growth exhibited a positive correlation with mean monthly temperature across all sites, tree growth negatively correlated with precipitation at the 10-year old white pine and 80-year old deciduous sites and no apparent correlation existed at the 73- and 38-year old sites. At the three coniferous stands, total annual net primary productivity (NPP) exhibited no correlation with mean growing season temperature or precipitation. This suggested that tree growth in young coniferous stands could be as sensitive as that of mature deciduous stands to precipitation. However, overall NPP seemed to be less sensitive to climatic variables across these stands, irrespective of their age and NPP may be driven more by stand physiology. Finally, eddy covariance and biometric estimations of NPP and NEP were compared, and results showed that although some growth trends do compare between the two techniques, magnitude discrepancies do exist and should be studied further. Results from this study will be informative to forest managers, forest conservationists and those interested in forest carbon sequestration.</p> / Master of Science (MSc)

<p>Modern advances in biometeorological monitoring technology have improved the capacity for measuring ecosystem exchanges of mass, energy and scalars (such as CO₂). Translating these measurements into robust and accurate scientific information (and ultimately, understanding) requires careful assessment of operations throughout the biometeorological data life cycle. In response, this research analyzed and optimized aspects of data collection, management and filtering for an ecosystem exchange measurement program over an age-sequence of temperate white pine forests.</p> <p>A comprehensive data workflow and management system (DWMS) was developed and implemented to support the entire data life cycle for all past, present and future measurement operations in our research group, and meet the needs of a collaborative, student-led data management environment. Best practices for biometeorological data management were introduced and used as standards to assess system performance.</p> <p>Roving eddy covariance (rEC) systems were examined as a means of producing reliable time-integrated carbon exchange estimates at multiple sites, by rotating an EC system in a resource-mindful approach. When used with an optimal gap-filling model and rEC rotation schedule (2 sites with 15-day rotations), the results suggested its viability, as annual NEE estimate uncertainties ranged between 35 and 63% of the annual NEE flux magnitude at our study sites – even though approximately 70% of half-hours were filled.</p> <p>Lastly, a data-driven approach was used to investigate the effects of different friction velocity and footprint filtering methods on time-integrated carbon exchange estimates at our fetch-limited forests. Though predicted flux source areas varied considerably between footprint models, our objective analyses identified the model (Kljun et al., 2004) and within-fetch requirement (80%) that optimized reliability and representativeness of carbon exchange estimates. Applying this footprint model decreased annual NEE by 31 to 129% (59 to 207 g C m^-2 y^-1) relative to no footprint application, and highlighted the importance of objective analyses of EC flux filtering methods.</p> / Doctor of Philosophy (PhD)