Nonparametric conditional density estimation in a deep learning framework for short-term forecasting

Environmental and Ecological Statistics - Short-term forecasting is an important tool in understanding environmental processes. In this paper, we incorporate machine learning algorithms into a...     

Estimating the Number of Tree Species in a Forest Community using Survey Data

Using some large samples as actual populations we study a series of promising estimators for number of species in a population. We recommend a nonparametric estimator, CM2f = cs + fc1/(2c2) where cs is the number of species observed, c1 and c2 are the numbers of species occurring once and twice respectively on the sample plots, and f is the finite population correction for sampling, from such data as collected by Forest Inventory and Analysis (FIA) of the US Forest Service. For FIA samples, there are estimated to be 0, 4, 3, 1 and 6 rare tree species not sampled in Minnesota, Missouri, Pennsylvania, New, York, and Ohio respectively.     

Do evergreen and deciduous trees have different effects on net N mineralization in soil?

Evergreen and deciduous plants are widely expected to have different impacts on soil nitrogen (N) availability because of differences in leaf litter chemistry and ensuing effects on net N mineralization (N(min)). We evaluated this hypothesis by compiling published data on net N(min) rates beneath co-occurring stands of evergreen and deciduous trees. The compiled data included 35 sets of co-occurring stands in temperate and boreal forests. Evergreen and deciduous stands did not have consistently divergent effects on net N(min) rates; net N(min) beneath deciduous trees was higher when comparing natural stands (19 contrasts), but equivalent to evergreens in plantations (16 contrasts). We also compared net N(min) rates beneath pairs of co-occurring genera. Most pairs of genera did not differ consistently, i.e., tree species from one genus had higher net N(min) at some sites and lower net N(min) at other sites. Moreover, several common deciduous genera (Acer, Betula, Populus) and deciduous Quercus spp. did not typically have higher net N(min) rates than common evergreen genera (Pinus, Picea). There are several reasons why tree effects on net N(min) are poorly predicted by leaf habit and phylogeny. For example, the amount of N mineralized from decomposing leaves might be less than the amount of N mineralized from organic matter pools that are less affected by leaf litter traits, such as dead roots and soil organic matter. Also, effects of plant traits and plant groups on net N(min) probably depend on site-specific factors such as stand age and soil type.     

Spatial variability of atrazine and metolachlor dissipation on dryland no-tillage crop fields in Colorado

An area of interest in precision farming is variable-rate application of herbicides to optimize herbicide use efficiency and minimize negative off-site and non-target effects. Site-specific weed management based on field scale management zones derived from soil characteristics known to affect soil-applied herbicide efficacy could alleviate challenges posed by post-emergence precision weed management. Two commonly used soil-applied herbicides in dryland corn (Zea mays L.) production are atrazine and metolachlor. Accelerated dissipation of atrazine has been discovered recently in irrigated corn fields in eastern Colorado. The objectives of this study were (i) to compare the rates of dissipation of atrazine and metolachlor across different soil zones from three dryland no-tillage fields under laboratory incubation conditions and (ii) to determine if rapid dissipation of atrazine and/or metolachlor occurred in dryland soils. Herbicide dissipation was evaluated at time points between 0 and 35 d after soil treatment using a toluene extraction procedure with GC/MS analysis. Differential rates of atrazine and metolachlor dissipation occurred between two soil zones on two of three fields evaluated. Accelerated atrazine dissipation occurred in soil from all fields of this study, with half-lives ranging from 1.8 to 3.2 d in the laboratory. The rapid atrazine dissipation rates were likely attributed to the history of atrazine use on all fields investigated in this study. Metolachlor dissipation was not considered accelerated and exhibited half-lives ranging from 9.0 to 10.7 d in the laboratory.     

Fundamental trade-offs generating the worldwide leaf economics spectrum

Recent work has identified a worldwide "economic" spectrum of correlated leaf traits that affects global patterns of nutrient cycling and primary productivity and that is used to calibrate vegetation-climate models. The correlation patterns are displayed by species from the arctic to the tropics and are largely independent of growth form or phylogeny. This generality suggests that unidentified fundamental constraints control the return of photosynthates on investments of nutrients and dry mass in leaves. Using novel graph theoretic methods and structural equation modeling, we show that the relationships among these variables can best be explained by assuming (1) a necessary trade-off between allocation to structural tissues versus liquid phase processes and (2) an evolutionary tradeoff between leaf photosynthetic rates, construction costs, and leaf longevity.     

Changes in hardwood forest understory plant communities in response to European earthworm invasions

European earthworms are colonizing earthworm-free northern hardwood forests across North America. Leading edges of earthworm invasion provide an opportunity to investigate the response of understory plant communities to earthworm invasion and whether the species composition of the earthworm community influences that response. Four sugar maple-dominated forest sites with active earthworm invasions were identified in the Chippewa National Forest in north central Minnesota, USA. In each site, we established a 30 x 150 m sample grid that spanned a visible leading edge of earthworm invasion and sampled earthworm populations and understory vegetation over four years. Across leading edges of earthworm invasion, increasing total earthworm biomass was associated with decreasing diversity and abundance of herbaceous plants in two of four study sites, and the abundance and density of tree seedlings decreased in three of four study sites. Sample points with the most diverse earthworm species assemblage, independent of biomass, had the lowest plant diversity. Changes in understory plant community composition were most affected by increasing biomass of the earthworm species Lumbricus rubellus. Where L. rubellus was absent there was a diverse community of native herbaceous plants, but where L. rubellus biomass reached its maximum, the herbaceous-plant community was dominated by Carex pensylvanica and Arisaema triphyllum and, in some cases, was completely absent. Evidence from these forest sites suggests that earthworm invasion can lead to dramatic changes in the understory community and that the nature of these changes is influenced by the species composition of the invading earthworm community.     

Seeing the forest for the heterogeneous trees: stand-scale resource distributions emerge from tree-scale structure

Forest ecosystem processes depend on local interactions that are modified by the spatial pattern of trees and resources. Effects of resource supplies on processes such as regeneration are increasingly well understood, yet we have few tools to compare resource heterogeneity among forests that differ in structural complexity. We used a neighborhood approach to examine understory light and nutrient availability in a well-replicated and large-scale variable-retention harvesting experiment in a red pine forest in Minnesota, USA. The experiment included an unharvested control and three harvesting treatments with similar tree abundance but different patterns of retention (evenly dispersed as well as aggregated retention achieved by cutting 0.1- or 0.3-ha gaps). We measured light and soil nutrients across all treatments and mapped trees around each sample point to develop an index of neighborhood effects (NI). Field data and simulation modeling were used to test hypotheses that the mean and heterogeneity of resource availability would increase with patchiness because of greater variation in competitive environments. Our treatments dramatically altered the types and abundances of competitive neighborhoods (NI) in each stand and resulted in significantly nonlinear relationships of light, nitrogen and phosphorus availability to NI. Hence, the distribution of neighborhoods in each treatment had a significant impact on resource availability and heterogeneity. In dense control stands, neighborhood variation had little impact on resource availability, whereas in more open stands (retention treatments), it had large effects on light and modest effects on soil nutrients. Our results demonstrate that tree spatial pattern can affect resource availability and heterogeneity in explainable and predictable ways, and that neighborhood models provide a useful tool for scaling heterogeneity from the individual tree to the stand. These insights are needed to anticipate the outcomes of silvicultural manipulations and should become more holistically integrated into both basic ecological and management science.     

Soil microbes drive the classic plant diversity-productivity pattern

Ecosystem productivity commonly increases asymptotically with plant species diversity, and determining the mechanisms responsible for this well-known pattern is essential to predict potential changes in ecosystem productivity with ongoing species loss. Previous studies attributed the asymptotic diversity-productivity pattern to plant competition and differential resource use (e.g., niche complementarity). Using an analytical model and a series of experiments, we demonstrate theoretically and empirically that host-specific soil microbes can be major determinants of the diversity-productivity relationship in grasslands. In the presence of soil microbes, plant disease decreased with increasing diversity, and productivity increased nearly 500%, primarily because of the strong effect of density-dependent disease on productivity at low diversity. Correspondingly, disease was higher in plants grown in conspecific-trained soils than heterospecific-trained soils (demonstrating host-specificity), and productivity increased and host-specific disease decreased with increasing community diversity, suggesting that disease was the primary cause of reduced productivity in species-poor treatments. In sterilized, microbe-free soils, the increase in productivity with increasing plant species number was markedly lower than the increase measured in the presence of soil microbes, suggesting that niche complementarity was a weaker determinant of the diversity-productivity relationship. Our results demonstrate that soil microbes play an integral role as determinants of the diversity-productivity relationship.     

Impact of a proposed revision of the IESTI equation on the acute risk assessment conducted when setting maximum residue levels (MRLs) in the European Union (EU): A case study

ABSTRACT

Proposals to update the methodology for the international estimated short-term intake (IESTI) equations were made during an international workshop held in Geneva in 2015. Changes to several parameters of the current four IESTI equations (cases 1, 2a, 2b, and 3) were proposed. In this study, the overall impact of these proposed changes on estimates of short-term exposure was studied using the large portion data available in the European Food Safety Authority PRIMo model and the residue data submitted in the framework of the European Maximum Residue Levels (MRL) review under Article 12 of Regulation (EC) No 396/2005. Evaluation of consumer exposure using the current and proposed equations resulted in substantial differences in the exposure estimates; however, there were no significant changes regarding the number of accepted MRLs. For the different IESTI cases, the median ratio of the new versus the current equation is 1.1 for case 1, 1.4 for case 2a, 0.75 for case 2b, and 1 for case 3. The impact, expressed as a shift in the IESTI distribution profile, indicated that the 95th percentile IESTI shifted from 50% of the acute reference dose (ARfD) with the current equations to 65% of the ARfD with the proposed equations. This IESTI increase resulted in the loss of 1.2% of the MRLs (37 out of 3110) tested within this study. At the same time, the proposed equations would have allowed 0.4% of the MRLs (14 out of 3110) that were rejected with the current equations to be accepted. The commodity groups that were most impacted by these modifications are solanacea (e.g., potato, eggplant), lettuces, pulses (dry), leafy brassica (e.g., kale, Chinese cabbage), and pome fruits. The active substances that were most affected were fluazifop-p-butyl, deltamethrin, and lambda-cyhalothrin.