Hydrologic impacts of an alternative agricultural land use: a woody perennial polyculture

U.S. Department of the InteriorU.S. Geological SurveyOpe

Frontiers in alley cropping: Transformative solutions for temperate agriculture

Annual row crop systems dominate agriculture around the world and have considerable negative environmental impacts. Incremental improvements to the prevailing system have been the primary focus of efforts to reduce these negative impacts, though are likely insufficient in solving the ecological challenges of row crop agriculture. This dissertation explores alley cropping (AC) – an agroforestry practice integrating trees with crops – as a transformative land-use solution to mitigate climate change, restore ecosystem services, and improve agricultural profitability. Through an inventory of all field experiments of AC to date, I identify several major gaps in AC research. In particular, AC has held a narrow focus on systems that integrate only one timber tree species with one annual grain species. I explore broadening this focus and identify key considerations for the scalable implementation of woody polycultures and tree crops for food and fodder. To evaluate the direct benefits of such systems, I then assess the potential of diversified, food-producing AC to mitigate unintended nitrogen losses in a side-by-side field experiment with row crop agriculture. I show that transitioning to AC can rapidly tighten the nitrogen cycle even during establishment years. Finally, I evaluate the economic competitiveness of the most common temperate AC system – black walnut trees for timber with annual grain alley crops – against the widespread maize-soybean rotation. Even without monetization of environmental benefits, I demonstrate that AC can improve landowner profitability across a substantial portion of the Midwest US. By exploring the frontiers in temperate AC, this dissertation highlights a multifunctional, transformative land-use alternative for temperate agriculture

The Simons Observatory: Beam characterization for the Small Aperture Telescopes

We use time-domain simulations of Jupiter observations to test and develop a beam reconstruction pipeline for the Simons Observatory Small Aperture Telescopes. The method relies on a map maker that estimates and subtracts correlated atmospheric noise and a beam fitting code designed to compensate for the bias caused by the map maker. We test our reconstruction performance for four different frequency bands against various algorithmic parameters, atmospheric conditions and input beams. We additionally show the reconstruction quality as function of the number of available observations and investigate how different calibration strategies affect the beam uncertainty. For all of the cases considered, we find good agreement between the fitted results and the input beam model within a ~1.5% error for a multipole range l = 30 - 700.Comment: 22 pages, 21 figures, to be submitted to Ap

Hi-sAFe: a 3D agroforestry model for integrating dynamic tree–crop interactions

Agroforestry, the intentional integration of trees with crops and/or livestock, can lead to multiple economic and ecological benefits compared to trees and crops/livestock grown separately. Field experimentation has been the primary approach to understanding the tree–crop interactions inherent in agroforestry. However, the number of field experiments has been limited by slow tree maturation and difficulty in obtaining consistent funding. Models have the potential to overcome these hurdles and rapidly advance understanding of agroforestry systems. Hi-sAFe is a mechanistic, biophysical model designed to explore the interactions within agroforestry systems that mix trees with crops. The model couples the pre-existing STICS crop model to a new tree model that includes several plasticity mechanisms responsive to tree–tree and tree–crop competition for light, water, and nitrogen. Monoculture crop and tree systems can also be simulated, enabling calculation of the land equivalent ratio. The model’s 3D and spatially explicit form is key for accurately representing many competition and facilitation processes. Hi-sAFe is a novel tool for exploring agroforestry designs (e.g., tree spacing, crop type, tree row orientation), management strategies (e.g., thinning, branch pruning, root pruning, fertilization, irrigation), and responses to environmental variation (e.g., latitude, climate change, soil depth, soil structure and fertility, fluctuating water table). By improving our understanding of the complex interactions within agroforestry systems, Hi-sAFe can ultimately facilitate adoption of agroforestry as a sustainable land-use practice

The Simons Observatory: Beam characterization for the small aperture telescopes

We use time-domain simulations of Jupiter observations to test and develop a beam reconstruction pipeline for the Simons Observatory Small Aperture Telescopes. The method relies on a mapmaker that estimates and subtracts correlated atmospheric noise and a beam fitting code designed to compensate for the bias caused by the mapmaker. We test our reconstruction performance for four different frequency bands against various algorithmic parameters, atmospheric conditions, and input beams. We additionally show the reconstruction quality as a function of the number of available observations and investigate how different calibration strategies affect the beam uncertainty. For all of the cases considered, we find good agreement between the fitted results and the input beam model within an ∼1.5% error for a multipole range ℓ = 30–700 and an ∼0.5% error for a multipole range ℓ = 50–200. We conclude by using a harmonic-domain component separation algorithm to verify that the beam reconstruction errors and biases observed in our analysis do not significantly bias the Simons Observatory r-measuremen

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

Germplasm Development of Underutilized Temperate U.S. Tree Crops

In the Midwest U.S. dominated corn-soybean landscape, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. Studies of the system-level integration of such approaches have proceeded by using the currently available cultivars and breeding selections of various tree nut and fruit species. While existing varieties and breeding selections provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. and its marginal land-types is unexplored. Thus, a second tier of research includes the genetic improvement and adaptation of tree crop selections to their respective target environments throughout the Midwest U.S. Fortunately, select tree crops of interest are amendable to systematic breeding and have wild relatives that are endemic across the region. In this paper, we discuss the value of these wild relatives for broadening the adaption of cultivated tree crop selections by using the hazelnut as an example species. We present a framework using geospatial tools to define and prioritize target environments for breeding and, in turn, exploiting wild relative germplasm

Temperate agroforestry research: considering multifunctional woody polycultures and the design of long-term field trials

The many benefits of agroforestry are well-documented, from ecological functions such as biodiversity conservation and water quality improvement, to cultural functions including aesthetic value. In North American agroforestry, however, little emphasis has been placed on production capacity of the woody plants themselves, taking into account their ability to transform portions of the landscape from annual monoculture systems to diversified perennial systems capable of producing fruits, nuts, and timber products. In this paper, we introduce the concept of multifunctional woody polycultures (MWPs) and consider the design of long-term experimental trials for supporting research on agroforestry emphasizing tree crops. Critical aspects of long-term agroforestry experiments are summarized, and two existing well-documented research sites are presented as case studies. A new long-term agroforestry trial at the University of Illinois, “Agroforestry for Food,” is introduced as an experiment designed to test the performance of increasingly complex woody plant combinations in an alley cropping system with productive tree crops. This trial intends to address important themes of food security, climate change, multifunctionality, and applied solutions. The challenges of establishing, maintaining, and funding long-term agroforestry research trials are discussed

Multi-Party Agroforestry: Emergent Approaches to Trees and Tenure on Farms in the Midwest USA

Agroforestry represents a solution to land degradation by agriculture, but social barriers to wider application of agroforestry persist. More than half of all cropland in the USA is leased rather than owner-operated, and the short terms of most leases preclude agroforestry. Given insufficient research on tenure models appropriate for agroforestry in the USA, the primary objective of this study was to identify examples of farmers practicing agroforestry on land they do not own. We conducted interviews with these farmers, and, in several cases, with landowners, in order to document their tenure arrangements. In some cases, additional parties also played a role, such as farmland investors, a farmer operating an integrated enterprise, and non-profit organizations or public agencies. Our findings include eleven case studies involving diverse entities and forms of cooperation in multi-party agroforestry (MA). MA generally emerged from shared objectives and intensive planning. MA appears to be adaptable to private, investor, institutional, and public landowners, as well as beginning farmers and others seeking land access without ownership. We identify limitations and strategies for further research and development of MA