This Microsoft Excel document provides complete results for AgriGo gene ontology analyses of differentially methylated genes in the form of three tables, as follows: Table 1. AgriGO GO Slim Results for Biological Process, Molecular Function and Cellular Compartment for Sham, AdjDBC and TumDBC Tissues Table 2. AgriGO GO Slim Results for Biological Process, Molecular Function and Cellular Compartment for Sham, AdjBaP and TumBaP Tissues Table 3. AgriGO GO Slim Results for Biological Process, Molecular Function...

The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing...

Ploidy levels sometimes vary among individuals or populations, particularly in plants. When such variation exists, accurate determination of cytotype can inform studies of ecology or trait variation and is required for population genetic analyses. Here we propose and evaluate a statistical approach for distinguishing low-level ploidy variants (e.g., diploids, triploids and tetraploids) based on genotyping-by-sequencing data. The method infers cytotypes based on observed heterozygosity and the ratio of DNA sequences containing different alleles at thousands...

Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to...

1.Trait-based models of ecological communities typically assume intraspecific variation in functional traits is not important, though such variation can change species trait rankings along gradients in resources and environmental conditions, and thus influence community structure and function. 2. We examined the degree of intraspecific relative to interspecific variation, and reaction norms of 11 functional traits for 57 forest understory plant species, including: intrinsic water-use efficiency (iWUE), Δ15N, 5 leaf traits, 2 stem traits and 2...

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For...

The designation of landscape-scale national monuments has generated intense debate as to whether their regional economic effects are positive or negative. National monuments can restrict land uses, thus favoring economic development based on the low-wage tourism industry relative to higher-wage extractive industries. Utah’s Grand Staircase-Escalante National Monument has been managed for landscape-scale conservation whilst protecting existing valid uses. We assess post-designation trends in the ranching, mining, and tourism industries, after which pre- and post-designation paths...

Understanding the processes that generate novel adaptive phenotypes is central to evolutionary biology. We used comparative analyses to reveal the history of tetrodotoxin (TTX) resistance in TTX-bearing salamanders. Resistance to TTX is a critical component of the ability to use TTX defensively but the origin of the TTX-bearing phenotype is unclear. Skeletal muscle of TTX-bearing salamanders (modern newts, family: Salamandridae) is unaffected by TTX at doses far in excess of those that block action potentials...

Materials were created for school-based agricultural educators (7th-12 grade) to use for students in Utah. This curriculum covers multiple days of instruction but 3-5 (50-minute sessions) days is what it is intended for. Includes a unit plan for the instructor, presentation slides (PPT and PFD), worksheets, and other materials. This curriculum focuses on careers in urban agriculture.

Forty-two teachers who attended the Urban Agriculture Workshop were surveyed after the workshop to assess the value of various aspects of the workshop and to measure pre-post gains in knowledge, ability, and importance. Also to measure attitudes, subjective norms, perceived behavioral controls, and behavioral intention. Demographics were also collected. Data show the results. Survey Instrument is attached. Scaling varies (see instrument).

The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion,...

Many organisms migrate between distinct habitats, exploiting variable resources while profoundly affecting ecosystem services, disease spread, and human welfare. However, the very characteristics that make migration captivating and significant also make it difficult to study, and we lack a comprehensive understanding of which species migrate and why. Here we show that, among mammals, migration is concentrated within Cetacea and Artiodactyla but also diffusely spread throughout the class (found in 12 of 27 orders). We synthesize...

We present a scientific replication of a benthic algae nuisance threshold study originally conducted in Montana, but we do so using a different sampling methodology in a different state. Respondents are asked to rate eight photographs that depict varying algae conditions. Our initial results show that Utah resident preferences for benthic algae levels are quite similar to those of Montana residents, thus replicating the Montana study. For the full Utah sample, though, Cronbachís ? indicated...

- .fastq files (Raw data from 79 individuals) - zipped - *.vcf file (variant call files) - *.gl (genotype likelihoods file) - k8admixProps.csv (admixture proportions) - k8gprob_mngt.txt (mean genotypes estimated by entropy) - All scripts for analysis can be found at Github repository. https://github.com/schimar/hts_tools

On October 30, 2007 NASA launched rocket 36.218 carrying the mission: “Investigation of Mid Latitude Ionospheric Irregularities Associated with Terrestrial Weather Systems” also known as the STORMS Mission. The rocket was launched from Wallops Island, Virginia (37.95◦ N, 284.53◦ E, 67.5◦ dip angle) at twelve minutes past local midnight. It flew along an azimuth of 114◦ and reached apogee near 394 km. The rocket payload had a suite of instruments from Utah State University/Space Dynamic...

Large biases associated with climate projections are problematic when it comes to their regional application in the assessment of water resources and ecosystems. We produced a set of regional climate projections that have the systematic biases reduced. The dataset first utilized a statistical regression technique and a global reanalysis dataset to correct biases in the globally-simulated variables that are subsequently used to drive the regional model. The bias-corrected global simulation data led to a more...

Natural convection is a phenomenon in which a flow of the fluid surrounding a body is induced by a change in density due to the temperature difference between the body and the fluid. This flow can be highly non-linear and turbulent, generating eddies. The complex interaction between the convective, viscous and buoyant forces requires the use of modern turbulent simulation tools for simulation. The accuracy of these tools, due to non-linearity, is difficult to assess....

We measured fluxes of methane, a suite of non-methane hydrocarbons (C2-C11), light alcohols, and carbon dioxide from oil and gas produced water storage and disposal ponds in Utah (Uinta Basin) and Wyoming (Upper Green River Basin) United States during 2013-2016. In this paper, we discuss the characteristics of produced water composition and air-water fluxes, with a focus on flux chamber measurements. In companion papers, we will (1) report on inverse modeling methods used to estimate...

Premise of the study: Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one...

Trophic interactions are a fundamental topic in ecology, but we know little about how competition between apex predators affects predation, the mechanism driving top-down forcing in ecosystems. We used long-term datasets from Scandinavia (Europe) and Yellowstone National Park (North America) to evaluate how grey wolf (Canis lupus) kill rate was affected by a sympatric apex predator, the brown bear (Ursus arctos). We used kill interval (i.e. the number of days between consecutive ungulate kills) as...

1.Trade-offs between the reproductive and immune systems are predicted when resources are limited, but are difficult to measure. 2.We used 15N labeled amino acids to directly compare protein allocation by lizards to eggs and healing wounds. 3.We showed that these two demands compete for the same resource, and that the ratio of protein allocation between them was related to body size, reproductive stage, and plasma corticosterone levels. 4.On average, rates of leucine deposition into eggs...

How polymorphisms are maintained within populations over long periods of time remains debated, because genetic drift and various forms of selection are expected to reduce variation. Here, we study the genetic architecture and maintenance of phenotypic morphs that confer crypsis in Timema cristinae stick insects, combining phenotypic information and genotyping-by-sequencing data from 1360 samples across 21 populations. We find two highly divergent chromosomal variants that span megabases of sequence and are associated with color polymorphism....

Despite growing concerns regarding increasing frequency of extreme climate events and declining population sizes, the influence of environmental stochasticity on the relationship between population carrying capacity and time-to-extinction has received little empirical attention. While time-to-extinction increases exponentially with carrying capacity in constant environments, theoretical models suggest increasing environmental stochasticity causes asymptotic scaling, thus making minimum viable carrying capacity vastly uncertain in variable environments. Using empirical estimates of environmental stochasticity in fish metapopulations, we showed that...

The buckwheat Eriogonum corymbosum is widely distributed throughout the southwestern United States, forming a complex of eight varieties. Eriogonum corymbosum var. nilesii is a primarily yellow-flowered taxon reported only from Clark County, Nevada. A previous genetic study by our research group found that variety nilesii is genetically distinct from other E. corymbosum varieties, based on a limited number of populations. Here, we assess genetic variation in 14 newly sampled yellow-flowered populations from southern Nevada, southern...

The Borich calculator analyzed the data from the EcoChallenge (Explore) workshop to determine professional development needs of educators for future workshop planning. The calculator takes into account IMPORTANCE and PERCEIVED COMPETENCE of each item and calculates Mean Weighted Discrepancy Scores (MWDS). Those are then ranked and the data shows those results. The survey instrument is attached. The workshop was student-centered but allowed for educational professionals to engage with the materials (Exploring careers in AFNR).