40 Works

Data from: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

Michael G. Branstetter, Bryan N. Danforth, James P. Pitts, Brant C. Faircloth, Philip S. Ward, Matthew L. Buffington, Michael W. Gates, Robert R. Kula & Seán G. Brady
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...

Data from: Intraspecific variability and reaction norms of forest understory plant species traits

Julia I. Burton, Steven S. Perakis, Sean C. McKenzie, Caitlin E. Lawrence & Klaus J. Puettmann
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...

Data from: Evolutionary history of a complex adaptation: tetrodotoxin resistance in salamanders

Charles T. Hanifin & William F. Gilly
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...

Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. De Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert & Patrik Nosil
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...

Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Torrey W. Rodgers, Charles C. Y. Xu, Jacalyn Giacalone, Karen M. Kapheim, Kristin Saltonstall, Marta Vargas, Douglas W. Yu, Panu Somervuo, W. Owen McMillan & Patrick A. Jansen
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...

Data from: Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

Zachariah Gompert & Karen E. Mock
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...

DNA methylation in lung tissues of mouse offspring exposed in utero to polycyclic aromatic hydrocarbons: Appendix E. Results of gene ontology analysis for differentially methylated genes

Trevor Fish & Abby Benninghoff
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...

Grand Staircase Escalante Economic Effects Data

Paul M. Jakus & Sherzod B. Akhundjanov
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...

Curriculum: Careers in Urban Agriculture (grades 7-12)

Tyson Sorensen, Kelsey Hall, David Francis & Joshua Dallin
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.

Survey Data from Utah Urban Agricultural Workshop

Tyson Sorensen, Kelsey Hall, David Francis & Joshua Dallin
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).

Data from: Wolf in sheep's clothing: model misspecification undermines tests of the neutral theory for life histories

Matthieu Authier, Lise M. Aubry & Emmanuelle Cam
Understanding the processes behind change in reproductive state along life-history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life-history trajectories is due to state dependence and is hence neutral:...

Data from: Convergent adaptation to dangerous prey proceeds through the same first-step mutation in the garter snake Thamnophis sirtalis

Michael Thomas Jonathan Hague, Chris R. Feldman, , , Michael T.J. Hague & Edmund D. Brodie
Convergent phenotypes often result from similar underlying genetics, but recent work suggests convergence may also occur in the historical order of substitutions en route to an adaptive outcome. We characterized convergence in the mutational steps to two independent outcomes of tetrodotoxin (TTX) resistance in separate geographic lineages of the common garter snake (Thamnophis sirtalis) that coevolved with toxic newts. Resistance is largely conferred by amino acid changes in the skeletal muscle sodium channel (NaV1.4) that...

Data from: Predator foraging response to a resurgent dangerous prey

Aimee Tallian, Douglas W. Smith, Daniel R. Stahler, Matthew C. Metz, Rick L. Wallen, Chris Geremia, Joel Ruprecht, C. Travis Wyman & Daniel R. MacNulty
Prey switching occurs when a generalist predator kills disproportionately more of an abundant prey species and correspondingly spares a rarer species. Although this behaviour is a classic stabilizing mechanism in food web models, little is known about its operation in free-living systems which often include dangerous prey species that resist predation. We used long-term (1995–2015) data from a large mammal system in northern Yellowstone National Park, USA, to understand how prey preference of a wild,...

Data from: Biodiverse cities: the nursery industry, homeowners, and neighborhood differences drive urban tree composition

Meghan Avolio, Diane Pataki, Tara Trammell, Joanna Endter-Wada, Meghan L. Avolio, Diane E. Pataki & Tara L. E. Trammell
In arid and semi-arid regions, where few if any trees are native, city trees are largely human-planted. Societal factors such as resident preferences for tree traits, nursery offerings, and neighborhood characteristics are potentially key drivers of urban tree community composition and diversity, however they remain critically understudied. We investigated patterns of urban tree structure in residential neighborhoods of the Salt Lake Valley, Utah, combining biological variables, such as neighborhood and plant nursery tree species and...

Data from: Spatial-temporal dynamics of Neotropical velvet ant (Hymenoptera: Mutillidae) communities along a forest-savanna gradient

Júlio Miguel Alvarenga, Cecília Rodrigues Vieira, Leandro Braga Godinho, Pedro Henrique Campelo, James Purser Pitts & Guarino Rinaldi Colli
Understanding how and why biological communities are organized over space and time is a major challenge and can aid biodiversity conservation in times of global changes. Herein, spatial-temporal variation in the structure of velvet ant communities was examined along a forest-savanna gradient in the Brazilian Cerrado to assess the roles of environmental filters and interspecific interactions upon community assembly. Velvet ants were sampled using 25 arrays of Y-shaped pitfall traps with drift fences for one...

Experimental Validation Data for CFD of Steady and Transient Mixed Convection on a Vertical Flat Plate

Blake W. Lance
Simulations are becoming increasingly popular in science and engineering. One type of simulation is Computation Fluid Dynamics (CFD) that is used when closed forms solutions are impractical. The field of Verification & Validation emerged from the need to assess simulation accuracy as they often contain approximations and calibrations. Validation involves the comparison of experimental data with simulation outputs and is the focus of this work. Errors in simulation predictions may be assessed in this way....

Grazing Exclosure Experiment on the Henry Mountains of Southern Utah

Johan du Toit & Dustin Ranglack
The data contained herein are the results of a grazing exclosure experiment on the Henry Mountains of S. Utah [38°5’ N, 100°50’W] to determine the relative impacts of bison, cattle, and lagomorphs on forage availability. Exclosures were erected in October 2011 and the standing crop of grass inside both exclosure types (full and partial), as well as an open reference plot was clipped in October 2012. Additionally, the local ranching community was surveyed to measure...

USU Rayleigh-scatter lidar 2014-2015 Nightly Temperatures

Leda Sox, Vincent B. Wickwar & Tao Yuan
Temperatures from a collocated Rayleigh-scatter lidar (RSL) and sodium resonance lidar were compared night-by-night, at different altitude levels, and hour-by-hour. Three zipped files are provided. USU RSL 2014-2015 [O] Corrected Temperatures.zip contains 36 files, one per night and hour, in RSLHourlyTemperaturesYYYYMMDDhour#.txt filename format. USU RSL 2014-2015 Hourly Temperatures.zip contains 36 files, one per night and hour, in RSLHourlyTemperaturesYYYYMMDDhour#.txt filename format. USU RSL 2014-2015 Nightly Temperatures.zip contains 19 files, one per night, in RSLTemperaturesYYYYMMDD.txt filename format.

Data for allometric equations of Chrysolepis sempervirens, Cornus sericea, Corylus cornuta ssp. californica, and Leucothoe davisiae.

James A. Lutz, J. A. Freund, A. J. Larson, M. E. Swanson, T. J. Furniss, K. M. L. Becker, E. M. Blomdahl, C. A. Cansier, S. J. Germain & S. M. A. Jeronimo
This data set includes measurements of 40 stems of Chrysolepis sempervirens (Kellogg) Hjelmq. (bush chinquapin), 41 stems of Cornus sericea L. (redosier dogwood), 50 stems of Corylus cornuta Marsh. ssp. californica (A. DC.) E. Murray, and 40 stems of Leucothoe davisiae Torrey (Sierra laurel), as reported in Lutz et al. (2014, 2017). Nomenclature follows Flora of North America (1993+).

MetaCom: Automated Data Processing and Analysis of Metagenomic Community Sequences

Cody A. Tramp & Charles D. Miller
Advances in next generation sequencing technology have allowed metagenomic researchers to study the composition of bacterial communities through analysis of the vast numbers of sequence reads that these technologies generate. It is not feasible to analyze and interpret this large amount of data manually and individual research groups must create automated scripts and programs to analyze this data. Here, we present MetaCom, a program that offers a common set of analysis and organizational tools that...

Data from: Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches

Paul G. Wolf, Martin P. Schilling, Aaron M. Duffy, Hardeep S. Rai, Carol A. Rowe, Karen E. Mock & Bryce A. Richardson
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in...

Data from: The scaling of population persistence with carrying capacity does not asymptote in populations of a fish experiencing extreme climate variability

Richard S.A. White, Brendan A. Wintle, Peter A. McHugh, Douglas J. Booker, Angus R. McIntosh & Richard S. A. White
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...

Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

Dorothea Lindtke, Kay Lucek, Victor Soria-Carrasco, Romain Villoutreix, Timothy E. Farkas, Rüdiger Riesch, Stuart R. Dennis, Zach Gompert & Patrik Nosil
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....

Data from: Competition between apex predators? Brown bears decrease wolf kill rate on two continents

Aimee Tallian, Andres Ordiz, Matthew C. Metz, Cyril Milleret, Camilla Wikenros, Douglas W. Smith, Daniel R. Stahler, Jonas Kindberg, Daniel R. MacNulty, Petter Wabakken, Jon E. Swenson & Håkan Sand
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...

Data from: Stable isotope tracers reveal a trade-off between reproduction and immunity in a reptile with competing needs

Andrew M. Durso & Susannah S. French
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...

Registration Year

  • 2017

Resource Types

  • Dataset
  • Text


  • Utah State University
  • University of Montana
  • Oregon State University
  • Swiss Federal Institute of Aquatic Science and Technology
  • University of California, Berkeley
  • University of Nevada Reno
  • McGill University
  • University of Connecticut
  • University of Utah
  • Notre Dame University