110 Works

Development of a Low-Cost, Open Source Miniature Rotary Cell Culture System to Simulate Microgravity within an Irradiated Environment

Elizabeth Vargas & JR Dennison
A major challenge for astronauts in long-duration space travel is combatting the hazardous spaceflight environment caused by microgravity and increased levels of ionizing radiation. Microgravity damages cellular DNA by increasing the production of harmful reactive oxygen species, while ionizing radiation damages DNA by creating double-stranded DNA (dsDNA) breaks. Cellular damage due to microgravity and radiation has been investigated using ground-based models, but most models consider microgravity and ionizing radiation alone, or asynchronously. Synchronous modeling better...

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.

Data from: Density-dependent space use affects interpretation of camera trap detection rates

Kate Broadley, Cole Burton, Stan Boutin, Tal Avgar & Stan Boutin
Camera-traps (CTs) are an increasingly popular tool for wildlife survey and monitoring. Estimating relative abundance in unmarked species is often done using detection rate as an index of relative abundance, which assumes a positive linear relationship with true abundance. This assumption may be violated if movement behavior varies with density, but the degree to which movement is density-dependent across taxa is unclear. The potential confounding of population-level relative abundance indices by movement depends on how...

Data from: Corridors or risk? movement along, and use of, linear features vary predictably among large mammal predator and prey species

Melanie Dickie, Michael Cody & Tal Avgar
1. Space-use behaviour reflects trade-offs in meeting ecological needs and can have consequences for individual survival and population demographics. The mechanisms underlying space-use can be understood by simultaneously evaluating habitat selection and movement patterns, and fine-resolution locational data are increasing our ability to do so. 2. We use high-resolution location data and an integrated step-selection analysis to evaluate caribou, moose, bear, and wolf habitat selection and movement behavior in response to anthropogenic habitat modification, though...

Data from: Increased soil temperature and decreased precipitation during early life stages constrain grass seedling recruitment in cold desert restoration

Jeremy J. James, Roger Sheley, Elizabeth Leger, Peter B. Adler, Stuart Hardegree, Elise Gornish & Matt Rinella
1. Seed-based restoration is one of the most difficult challenges for dryland restoration. Identifying environmental conditions that drive variation in seed and seedling mortality across similar restoration efforts could increase understanding of when and where restoration outcomes are likely to be favorable and identify new tools and strategies to improve outcomes. 2. We asked how variation in a suite of environmental predictors influenced germination, emergence, seedling establishment, and juvenile survival of four commonly sown perennial...

Data from: Diel predator activity drives a dynamic landscape of fear

Michel T. Kohl, Daniel R. Stahler, Matthew C. Metz, James D. Forester, Matthew J. Kauffman, Nathan Varley, Patrick J. White, Douglas W. Smith, Daniel R. MacNulty & P. J. White
A ‘landscape of fear’ (LOF) is a map that describes continuous spatial variation in an animal’s perception of predation risk. The relief on this map reflects, for example, places that an animal avoids to minimize risk. Although the LOF concept is a potential unifying theme in ecology that is often invoked to explain the ecological and conservation significance of fear, little is known about the daily dynamics of a LOF. Despite theory and data to...

Data from: Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle

Zachariah Gompert & Frank J. Messina
Trade-offs have often been invoked to explain the evolution of ecological specialization. Phytophagous insects have been especially well studied, but there has been little evidence that resource-based trade-offs contribute to the evolution of host specialization in this group. Here, we combine experimental evolution and partial genome resequencing of replicate seed beetle selection lines to test the trade-off hypothesis and measure the repeatability of evolution. Bayesian estimates of selection coefficients suggest that rapid adaptation to a...

Data from: Bayesian inference of selection in a heterogeneous environment from genetic time-series data

Zachariah Gompert
Evolutionary geneticists have sought to characterize the causes and molecular targets of selection in natural populations for many years. Although this research program has been somewhat successful, most statistical methods employed were designed to detect consistent, weak to moderate selection. In contrast, phenotypic studies in nature show that selection varies in time and that individual bouts of selection can be strong. Measurements of the genomic consequences of such fluctuating selection could help test and refine...

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: Large niche differences emerge at the recruitment stage to stabilize grassland coexistence

Chengjin Chu & Peter B. Adler
Niche differences and average fitness differences jointly determine coexistence. However, little empirical information about the magnitude of these two mechanisms is available. Using multispecies population models fit to long-term demographic data for common, co-occurring species in five grassland and shrubland plant communities in western North America, we estimated the strength of stabilizing niche differences and average fitness differences. In all five communities, both pairwise and full community comparisons showed evidence for strong stabilizing mechanisms and...

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: 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: 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 & M. L. Davis
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: 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...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: Weak interspecific interactions in a sagebrush steppe? Conflicting evidence from observations and experiments

Peter B. Adler, Andrew Kleinhesselink, Giles Hooker, J. Bret Taylor, Brittany Teller, Stephen P. Ellner & Joshua B. Taylor
Stable coexistence requires intraspecific limitations to be stronger than interspecific limitations. The greater the difference between intra- and interspecific limitations, the more stable the coexistence, and the weaker the competitive release any species should experience following removal of competitors. We conducted a removal experiment to test whether a previously estimated model, showing surprisingly weak interspecific competition for four dominant species in a sagebrush steppe, accurately predicts competitive release. Our treatments were 1) removal of all...

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 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, Craig D. Dodson, 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: Global macroevolution and macroecology of passerine song

William David Pearse, Ignacio Morales-Castilla, Logan S. James, Maxwell Farrell, Frédéric Boivin, T. Jonathan Davies & William D. Pearse
Studying the macroevolution of the songs of Passeriformes (perching birds) has proved challenging. The complexity of the task stems not just from the macroevolutionary and macroecological challenge of modelling so many species, but also from the difficulty in collecting and quantifying birdsong itself. Using machine learning techniques, we extracted songs from a large citizen science dataset, and then analysed the evolution, and biotic and abiotic predictors of variation in birdsong across 578 passerine species. Contrary...

Data from: Evolution of larval competitiveness and associated life history traits in response to host shifts in a seed beetle

Charles W. Fox, Frank J. Messina, F. J. Messina & C. W. Fox
Resource competition is frequently strong among parasites that feed within small discrete resource patches, such as seeds or fruits. The properties of a host can influence the behavioral, morphological, and life history traits of associated parasites, including traits that mediate competition within the host. For seed parasites, host size may be an especially important determinant of competitive ability. Using the seed beetle, Callosobruchus maculatus, we performed replicated, reciprocal host shifts to examine the role of...

Data from: The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks

Kay Lucek, Zach Gompert & Patrik Nosil
Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host-plant associated ecotype formation in Timema cristinae stick insects. Using mate-pair...

Data from: Evolution of mammalian migrations for refuge, breeding, and food

Gitanjali E. Gnanadesikan, William D. Pearse & Allison K. Shaw
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...

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: Tree circumference dynamics in four forests characterized using automated dendrometer bands

Valentine Herrmann, Sean M. McMahon, Matteo Detto, James A. Lutz, Stuart J. Davies, Chia-Hao Chang-Yang & Kristina J. Anderson-Teixeira
Stem diameter is one of the most commonly measured attributes of trees, forming the foundation of forest censuses and monitoring. Changes in tree stem circumference include both irreversible woody stem growth and reversible circumference changes related to water status, yet these fine-scale dynamics are rarely leveraged to understand forest ecophysiology and typically ignored in plot- or stand-scale estimates of tree growth and forest productivity. Here, we deployed automated dendrometer bands on 12–40 trees at four...

Data from: Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars

Andrea E. Glassmire, Christopher S. Jeffrey, Matthew L. Forister, Thomas L. Parchman, Chris C. Nice, Joshua P. Jahner, Joseph S. Wilson, Thomas R. Walla, Lora A. Richards, Angela M. Smilanich, Michael D. Leonard, Colin R. Morrison, Wilmer Simbaña, Luis A. Salagaje, Craig D. Dodson, Jim S. Miller, Eric J. Tepe, Santiago Villamarin-Cortez & Lee A. Dyer
Chemically mediated plant–herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry...

Data from: Genome-wide association reveals the locus responsible for four-horned ruminant

James W. Kijas, Tracy Hadfield, Marina Naval Sanchez & Noelle Cockett
Phenotypic variability in horn characteristics, such as their size, number and shape, offers the opportunity to elucidate the molecular basis of horn development. The objective of this study was to map the genetic determinant controlling the production of four horns in two breeds, Jacob sheep and Navajo-Churro, and examine whether an eyelid abnormality occurring in the same populations is related. Genome-wide association mapping was performed using 125 animals from the two breeds that contain two-...

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  • Utah State University
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  • Princeton University