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MEPS Data Assimilation System

Robert W. Schunk & Larry Gardner
For the current funding opportunity we propose to develop a master system that will enhance the user interface to the MEPS model and enable the scientific community to efficiently use the model. Furthermore, we will build and automate validation tools and improve the efficiency and robustness of the MEPS ensemble averaging scheme. Finally, we will explore the nest step toward a major advancement in MEPS b significantly improving the spatial resolution of one of the...

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).

Ploidy and Clonal Membership in Populus Tremuloides from RADseq Data

Benjamin Blonder, James A. Walton & Karen E. Mock
Ipyrad pipeline parameters files, raw sequence data, barcodes and supporting scripts for clonal and cytotype sample assignment of Populus tremuloides.

Incorporating Drones in My Classroom: Survey Data from High School Teachers 2018

Tyson Sorenson, Kelsey Hall, Olivia Horning, Joshua Dallin & Davis Francis
Survey data collected from 69 high school and middle school teachers. Survey gauges intentions of integrating drone curriculum concepts into the classroom. Dataset includes summary data, raw data and survey instrument.

Genetic Engineering in Agriculture Curricula for Grades 9-12

Tyson Sorenson, Olivia Horning, Kelsey Hall, David Francis & Joshua Dallin
This is a curriculum package that was developed for teachers to be able to integrate genetic engineering and biotechnology concepts, skills, and career applications into their classrooms. This package was developed as part of the LEARN workshop entitled "Genetic Engineering: Workshop for Teachers." This curriculum package includes five full units of instructions with lesson plans, presentation resources, and other resources for teachers. This package is intended for students in grades 9-12. Each unit is complete...

Data from: Influence of group size on the success of wolves hunting bison

Daniel R. MacNulty, Aimee Tallian, Daniel R. Stahler & Douglas W. Smith
An intriguing aspect of social foraging behaviour is that large groups are often no better at capturing prey than are small groups, a pattern that has been attributed to diminished cooperation (i.e., free riding) in large groups. Although this suggests the formation of large groups is unrelated to prey capture, little is known about cooperation in large groups that hunt hard-to-catch prey. Here, we used direct observations of Yellowstone wolves (Canis lupus) hunting their most...

Data from: Toxicity and population structure of the Rough-Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators

Michael T. J. Hague, Leleña A. Avila, Charles T. Hanifin, W. Andrew Snedden, Amber N. Stokes, , , Michael T.J. Hague & Edmund D. Brodie
Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough-Skinned Newt (Taricha granulosa)...

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: Deconstruction of a plant-arthropod community reveals influential plant traits with nonlinear effects on arthropod assemblages

Joshua G. Harrison, Casey Philbin, Zach Gompert, Glen Forister, Leonardo Hernandez, Benjamin W. Sullivan, Ian Wallace, Lyra Beltran, Craig D. Dodson, Jacob S. Francis, Amie Schlageter, Oren Shelef, Su'ad Yoon, Matthew L. Forister, Ian S. Wallace, Su'ad A. Yoon, Zachariah Gompert, Casey S. Philbin, Leonardo Hernandez-Espinoza & Glen W. Forister
1. Studies of herbivores and secondary consumer communities rarely incorporate a comprehensive characterization of primary producer trait variation, thus limiting our understanding of how plants mediate community assembly of consumers. 2. We took advantage of recent technological developments for efficient generation of phytochemical, microbial, and genomic data to characterize individual alfalfa plants (Medicago sativa; Fabaceae) growing in an old-field, semi-naturalized state for 770 traits (including 753 chemical features). Using random forest modeling, we investigated the...

Data from: Warming alters food web-driven changes in the CO2 flux of experimental pond ecosystems

Trisha B. Atwood, Edd Hammill, Pavel Kratina, Hamish S. Greig, Jonathan B. Shurin & John S. Richardson
Evidence shows the important role biota play in the carbon cycle, and strategic management of plant and animal populations could enhance CO2 uptake in aquatic ecosystems. However, it is currently unknown how management-driven changes to community structure may interact with climate warming and other anthropogenic perturbations to alter CO2 fluxes. Here we showed that under ambient water temperatures, predators (three-spined stickleback) and nutrient enrichment synergistically increased primary producer biomass, resulting in increased CO2 uptake by...

Data from: Limited alpine climatic warming and modeled phenology advancement for three alpine species in the Northeast United States

Kenneth D. Kimball, Michael L. Davis, Douglas M. Weihrauch, Georgia L. D. Murray & Kenneth Rancourt
Premise of the study: Most alpine plants in the Northeast United States are perennial and flower early in the growing season, extending their limited growing season. Concurrently, they risk the loss of reproductive efforts to late frosts. Quantifying long-term trends in northeastern alpine flower phenology and late-spring/early-summer frost risk is limited by a dearth of phenology and climate data, except for Mount Washington, New Hampshire (1916 m a.s.l.). Methods: Logistic phenology models for three northeastern...

Data from: Stick insect genomes reveal natural selection's role in parallel speciation

Victor Soria-Carrasco, Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Thomas L. Parchman, J. Spencer Johnston, C. Alex Buerkle, Jeffrey L. Feder, Jens Bast, Tanja Schwander, Scott P. Egan, Bernard J. Crespi & Patrik Nosil
Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess...

Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections

Brittany J. Teller, James H. Marden & Katriona Shea
1. Despite the fact that seeds are unlikely to be identical—even among siblings within a maternal individual—dispersal models typically use one mean trait value to represent the ability of an entire species to disperse. Previous work has shown that the environmental conditions under which individuals leave the maternal site strongly affect how far seeds will travel. However, less is known about how trait variation within individuals contributes to dispersal or how such variation might interact...

Data from: The evolution of life cycle complexity in aphids: ecological optimization, or historical constraint?

Nate B. Hardy, Daniel A. Peterson & Carol D. Von Dohlen
For decades, biologists have debated why many parasites have obligate multi-host life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, i.e., change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (non-aphidines) – groups that differ in...

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: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches

Martin P. Schilling, Paul G. Wolf, Aaron M. Duffy, Hardeep S. Rai, Carol A. Rowe, Bryce A. Richardson & Karen E. Mock
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...

Cytotype and genotype predict mortality and recruitment in Colorado quaking aspen (Populus tremuloides)

Benjamin Blonder, Courtenay Ray, James Walton, Marco Castaneda, K. Dana Chadwick, Michael Clyne, Pierre Gaüzere, Lars Iversen, Madison Lusk, G. Richard Strimbeck, Savannah Troy & Karen Mock
Species responses to climate change depend on environment, genetics, and interactions among these factors. Intraspecific cytotype (ploidy level) variation is a common type of genetic variation in many species. However, the importance of intraspecific cytotype variation in determining demography across environments is poorly known. We studied the tree species quaking aspen (Populus tremuloides), which occurs in diploid and triploid cytotypes. This widespread species is experiencing contractions in its western range, which could potentially be linked...

Data from: Relative bee abundance varies by collection method and flowering richness: implications for understanding patterns in bee community data

Philip Hahn, Marirose Kuhlman, Skylar Burrows, Dan Mummey & Philip Ramsey
Pollination by wild bees is a vital ecosystem process in natural and managed systems. Recent declines in wild bee populations have led to increases in conservation actions and monitoring of bee communities. Pan traps are a commonly used sampling method for monitoring bee populations due to their efficiency and low cost. However, potential biases inherent in different sampling techniques may result in misleading characterizations of bee communities across space and time. In this paper, we...

Data from: Integrating tracking and resight data enables unbiased inferences about migratory connectivity and winter range survival from archival tags

Clark Rushing, Aimee Van Tatenhove, Andrew Sharp, Viviana Ruiz-Gutierrez, Mary Freeman, Paul Sykes, Aaron Given & Scott Sillett
Archival geolocators have transformed the study of small, migratory organisms but analysis of data from these devices requires bias correction because tags are only recovered from individuals that survive and are re-captured at their tagging location. Data and code provided in this repository can be used to replicate the simulation and Painted Bunting case study results presented by Rushing et al. (2021) showing that integrating geolocator recovery data and mark–resight data enables unbiased estimates of...

Water availability dictates how plant traits predict demographic rates

Alice Stears, Peter Adler, Dana Blumenthal, Julie Kray, Kevin Mueller, Troy Ocheltree, Kevin Wilcox & Daniel Laughlin
A major goal in ecology is to make generalizable predictions of organism responses to environmental variation based on their traits. However, straightforward relationships between traits and fitness are rare and likely vary with environmental context. Characterizing how traits mediate demographic responses to the environment may enhance predictions of organism responses to global change. We synthesized 15 years of demographic data and species-level traits in a shortgrass steppe to determine whether the effects of leaf and...

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee

Meaghan Pimsler, Kennan Oyen, James Herndon, Jason Jackson, James Strange, Michael Dillon & Jeff Lozier
Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared Bombus vosnesenskii workers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species’ range to correlate...

Data for behavioral state-dependent habitat selection analysis of translocated female greater sage-grouse, North Dakota 2018-2020

Simona Picardi, Peter Coates, Jesse Kolar, Shawn O'Neil, Steven Mathews & David Dahlgren
This dataset is associated with the article, "Behavioral state-dependent habitat selection and implications for animal translocations" (Picardi et al., 2021, Journal of Applied Ecology). Post-release monitoring of translocated animals can be used to inform future translocation protocols. In particular, quantifying habitat selection of translocated individuals may help identify features that characterize suitable settlement habitat and inform the choice of future release sites; however, because translocated animals undergo post-release behavioral modification, the underlying behavioral state needs...

Modeling management strategies for chronic disease in wildlife: predictions for the control of respiratory disease in bighorn sheep

Kezia Manlove, Emily Almberg, E. Frances Cassirer, Jennifer Ramsey, Keri Carson, Justin Gude & Raina Plowright
1. Controlling persistent infectious disease in wildlife populations is an on-going challenge for wildlife managers and conservationists worldwide. 2. Here, we develop a dynamic pathogen transmission model capturing key features of M. ovipneumoniae infection, a major cause of population declines in North American bighorn sheep (Ovis canadensis). We explore the effects of model assumptions and parameter values on disease dynamics, including density versus frequency dependent transmission, the inclusion of a carrier class versus a longer...

Tipping the balance: the role of seed density, abiotic filters, and priority effects in seed-based wetland restoration

Emily Tarsa, Bailey Holdaway & Karin Kettenring
Sowing native seeds is a common approach to reintroduce native plants to degraded systems. However, this method is often overlooked in wetland restoration despite the immense global loss of diverse native wetland vegetation. Developing guiding principles for seed-based wetland restoration is critical to maximize native plant recovery, particularly in previously invaded wetlands. Doing so requires a comprehensive understanding of how restoration manipulations, and their interactions, influence wetland plant community assembly. With a focus on the...

The effect of plant invasion on soil microbial carbon-use efficiency in semiarid grasslands of the Rocky Mountain West

Megan Nasto, Morgan McLeod, Lorinda Bullington, Ylva Lekberg & John Stark
1. Grassland ecosystems invaded by exotic plant species often exhibit substantially higher aboveground productivity and soil nitrogen (N) than the native communities they replace. These shifts are likely associated with altered microbial carbon (C) and N cycling, but we know surprisingly little about how these processes change with plant invasion. 2. Targeting four invasive plant species common in the Rocky Mountain West, we collected soils from invaded and adjacent uninvaded grassland field plots, as well...

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  • Utah State University
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  • University of Washington