Estimating Continuous Treatment Effects in Panel Data using Machine Learning with a Climate Application

This paper introduces and proves asymptotic normality for a new semi-parametric estimator of continuous treatment effects in panel data. Specifically, we estimate the average derivative. Our estimator uses the panel structure of data to account for unobservable time-invariant heterogeneity and machine learning (ML) methods to preserve statistical power while modeling high-dimensional relationships. We construct our estimator using tools from double de-biased machine learning (DML) literature. Monte Carlo simulations in a nonlinear panel setting show that our method estimates the average derivative with low bias and variance relative to other approaches. Lastly, we use our estimator to measure the impact of extreme heat on United States (U.S.) corn production, after flexibly controlling for precipitation and other weather features. Our approach yields extreme heat effect estimates that are 50% larger than estimates using linear regression. This difference in estimates corresponds to an additional $3.17 billion in annual damages by 2050 under median climate scenarios. We also estimate a dose-response curve, which shows that damages from extreme heat decline somewhat in counties with more extreme heat exposure

A community survey of symbiotic mine site fungi along a gradient of recovery on mine sites in the Carolinas

Abstracts from the April 12-14, 2019 MASC Conferenc

Do Hiccups Echo? Late Holocene Interaction and Ceramic Production in Southern Papua New Guinea

The last five decades of research into Papua New Guinean archaeology have revealed a variety of rapid late Holocene cultural changes. The Ceramic Hiccup (c. 1200 – 800 years b.p.) is a little understood period of change along the south Papuan coast. It presents itself at the terminus of the Early Papuan Pottery (EPP) tradition as a rapid change in ceramic styles, lithic exchange, and settlement patterns. Previous interpretations have invoked causal factors such as migration, environment, and conflict. This article investigates this period of change by examining exchange and mobility patterns during EPP, through the Ceramic Hiccup, and into the ensuing traditions. Physico-chemical analysis (scanning electron microscopy, SEM) of 39 potsherds was conducted to understand changes in ceramic production during this period at two key sites, Taurama (AGN and AJA) and Eriama 1 (ACV), in the Port Moresby region of the south coast of Papua New Guinea. Although our interpretations are provisional due to a small sample size, it is argued here that, following the highly interactive period of EPP, a migration of ceramic manufacturing groups from the west supplants the local tradition (EPP) during the Ceramic Hiccup. There is a decline in interaction between ceramic communities toward the latter stages of EPP, with increased isolation and standardization of ceramics. This decline of interaction in the region is associated with a decline in chemical variability in ceramic components. The Ceramic Hiccup is representative of introduced ceramics, increased interaction and mobility

Evolution of symbiosis genes in an invasive ectomycorrhizal fungus

Abstracts from the April 12-14, 2019 MASC Conferenc

Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon

Increasing levels of atmospheric carbon dioxide (CO(2)) and rates of nitrogen (N)-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO(2) (eCO(2)) and N-fertilization in spatially separated field samples, in the forest floor, 0–2, 2–5, and 5–10 cm depth intervals in a loblolly pine Free-Air Carbon Dioxide Enrichment (FACE) experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0–2 cm and forest floor intervals. Composition shifted in forest floor, 0–2 and 2–5 cm intervals in response to N-fertilization, but the shift was most distinct in the 0–2 cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e., phosphorus, organic matter, calcium, pH) was also observed. In the 0–2 cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae, and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO(2) relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes

Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.

Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth

Phylogeny and evolution of medical species of candida and related taxa: a multigenic analysis

Hemiascomycetes are species of yeasts within the order Saccharomycetales. The order encompasses disparate genera with a variety of life styles, including opportunistic human pathogens (e.g., Candida albicans), plant pathogens (e.g., Eremothecium gossypii), and cosmopolitan yeasts associated with water and decaying vegetation. To analyze the phylogeny of medically important species of yeasts, we selected 38 human pathogenic and related strains in the order Saccharomycetales. The DNA sequences of six nuclear genes were analyzed by maximum likelihood and Bayesian phylogenetic methods. The maximum likelihood analysis of the combined data for all six genes resolved three major lineages with significant support according to Bayesian posterior probability. One clade was mostly comprised of pathogenic species of Candida. Another major group contained members of the family Metschnikowiaceae as a monophyletic group, three species of Debaryomyces, and strains of Candida guilliermondii. The third clade consisted exclusively of species of the family Saccharomycetaceae. Analysis of the evolution of key characters indicated that both codon reassignment and coenzyme Q9 likely had single origins with multiple losses. Tests of correlated character evolution revealed that these two traits evolved independently

Maximizing ecological and evolutionary insight in bisulfite sequencing data sets

Genome-scale bisulfite sequencing approaches have opened the door to ecological and evolutionary studies of DNA methylation in many organisms. These approaches can be powerful. However, they introduce new methodological and statistical considerations, some of which are particularly relevant to non-model systems. Here, we highlight how these considerations influence a study’s power to link methylation variation with a predictor variable of interest. Relative to current practice, we argue that sample sizes will need to increase to provide robust insights. We also provide recommendations for overcoming common challenges and an R Shiny app to aid in study design

Exploration of climate influences on the abundance of galls on red willow (Salix /aevigata) across two riparian communities in Southern California

In Southern California, the red willow (Sa/ix laevigata Bebb) hosts a variety of gall-inducing parasitic insects. However, little is known about the ecology of these parasites, particularly the characterization of their microclimate preferences. This study explores the relationship between microclimate and gall frequencies in S. laevigata in the Ballona Wetlands and Temescal Canyon, and gall count correlated with biotic and abiotic factors such as soil pH, soil moisture and willow density. Significantly more galls per leaf were found at Temescal Canyon than Ballona Wetlands. Although the number of galls per leaf correlated negatively with soil pH, soil moisture content and canopy openness, only site and gall location were found to significantly predict the number of galls. These results suggest that additional or interacting microclimate factors may influence gall frequencies between Temescal Canyon and the Ballona Wetlands

Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci

<p>Abstract</p> <p>Background</p> <p>The soil fungus <it>Rhizoctonia solani </it>anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of <it>R. solani </it>AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of <it>R. solani </it>AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of <it>R. solani </it>AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of <it>R. solani </it>AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89).</p> <p>Results</p> <p>Populations of <it>R. solani </it>AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of <it>R. solani </it>AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of <it>R. solani </it>AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Φ_{<it>ST </it>}= 0.257, significant at P < 0.05) but not for locus pP42F (Φ_{<it>ST </it>}= 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of <it>R. solani </it>AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of <it>R. solani </it>AG-3.</p> <p>Conclusion</p> <p>The two sisters populations of the basidiomycete fungus <it>R. solani </it>AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.</p