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Shrub Consumption and Immediate Changes in Shrub Community and Spatial Patterns by Reintroduced Fire in Yosemite National Park, California, USA; Supplemental Information

James Lutz, T. J. Furniss, S. J. Germain, K. M. L. Becker, Erika Blomdahl, S. A. Jeronimo, C. Alina Cansler, J. A. Freund, M. E. Swanson & A. J. Larson
Fire behavior in the Yosemite Forest Dynamics Plot during the Rim Fire as captured by the USFS Fire Behavior Assessment Team and reported in Ewell, C., D.F. Smith, M. Hilden, S. Greene, D. Coultrap, K. Robinson, N. Vaillant, A. Reiner, T. Norman. 2015. 2013 Rim Fire Stanislaus National Forest and Yosemite National Park Fire Behavior Assessment Team Summary Report. Each video was started based on a thermocouple trigger when the fire reached it.

Data from: Prediction of cooking time for soaked and unsoaked dry beans (Phaseolus vulgaris L.) using hyperspectral imaging technology

Fernando A. Mendoza, Jason A. Wiesinger, Renfu Lu, Susan Nchimbi-Msolla, Phillip N. Miklas, James D. Kelly & Karen A. Cichy
The cooking time of dry beans varies widely by genotype and is also influenced by the growing environment, storage conditions and cooking method. Thus, high throughput phenotyping methods to assess cooking time would be useful to breeders interested in developing cultivars with desired cooking time. The objective of this study was to evaluate the performance of hyperspectral imaging technology for predicting dry bean cooking time. Fourteen dry bean (Phaseolus vulgaris L.) genotypes with a wide...

Data from: Evaluating environmental DNA-based quantification of ranavirus infection in wood frog populations

Emily M. Hall, Erica J. Crespi, Caren S. Goldberg & Jesse L. Brunner
A variety of challenges arise when monitoring wildlife populations for disease. Sampling tissues can be invasive to hosts, and obtaining sufficient sample sizes can be expensive and time-consuming, particularly for rare species and when pathogen prevalence is low. Environmental DNA (eDNA)-based detection of pathogens is an alternative approach to surveillance for aquatic communities that circumvents many of these issues. Ranaviruses are emerging pathogens of ectothermic vertebrates linked to die-offs of amphibian populations. Detecting ranavirus infections...

Data from: ANDe™ : a fully integrated environmental DNA sampling system

Austen C. Thomas, Jesse Howard, Phong L. Nguyen, Tracie A. Seimon & Caren S. Goldberg
1. Species monitoring from environmental DNA (eDNA) is a powerful new technique for natural resource scientists and the number of research groups employing eDNA detection is growing rapidly. However, current eDNA sampling technologies consist mainly of do-it-yourself solutions, and the lack of purpose-built sampling equipment is limiting the efficiency and standardization of eDNA studies. 2. Here, we describe the first fully-integrated sampling system (ANDeTM) designed by a team of molecular ecologists and engineers for high-throughput...

Data from: Quantitative trait loci for cold tolerance in chickpea

Clarice J. Coyne, Deus Mugabe, Julia Piaskowski, Ping Zheng, Yu Ma, Erik Landry, Rebecca McGee, Dorrie Main, George Vandemark, Hongbin Zhang & Shahal Abbo
Fall-sown chickpea (Cicer arietinum L.) yields are often double those of spring-sown chickpea in regions with Mediterranean climates that have mild winters. However, winter kill can limit the productivity of fall-sown chickpea. Developing cold-tolerant chickpea would allow the expansion of the current geographic range where chickpea is grown and also improve productivity. The objective of this study was to identify the quantitative trait loci (QTL) associated with cold tolerance in chickpea. An interspecific recombinant inbred...

Data from: Critical disease windows shaped by stress exposure alter allocation trade-offs between development and immunity

Lucas J. Kirschman, Erica J. Crespi & Robin W. Warne
1. Ubiquitous environmental stressors are often thought to alter animal susceptibility to pathogens and contribute to disease emergence. However, duration of exposure to a stressor is likely critical, because while chronic stress is often immunosuppressive, acute stress can temporarily enhance immune function. Furthermore, host susceptibility to stress and disease often varies with ontogeny; increasing during critical developmental windows. How the duration and timing of exposure to stressors interact to shape critical windows and influence disease...

Data from: Marine subsidies change short-term foraging activity and habitat utilization of terrestrial lizards

Heather V. Kenny, Amber N. Wright, Jonah Piovia-Scott, Louie Yang, David A. Spiller, Thomas W. Schoener & Louie H. Yang
Resource pulses are brief periods of unusually high resource abundance. While population and community responses to resource pulses have been relatively well-studied, how individual consumers respond to resource pulses has received less attention. Local consumers are the first to respond to a resource pulse, and the form and timing of individual responses may influence how the effects of the pulse are transmitted throughout the community. Previous studies in Bahamian food webs have shown that detritivores...

Data from: Female ornamentation is associated with elevated aggression and testosterone in a tropical songbird

Erik D. Enbody, Jordan Boersma, Hubert Schwabl & Jordan Karubian
In males, testosterone plays a key role in ornament production and linking ornamentation with reproductive behaviors and other traits to produce an integrated phenotype. Less is known about whether females couple testosterone, ornamentation, and aggressive behaviors to achieve female-specific combinations of traits. Ornamentation in females may be the result of correlated expression with male ornamentation, or female traits could arise as the result of sex specific selection pressures. Resolving between these alternatives is necessary to...

Data from: Mechanism matters: the cause of fluctuations in boom-bust populations governs optimal habitat restoration strategy

Gina K. Himes Boor, Cheryl B. Schultz, Elizabeth E. Crone & William F. Morris
Many populations exhibit boom-bust dynamics in which abundance fluctuates dramatically over time. Past research has focused on identifying whether the cause of fluctuations is primarily exogenous, e.g., environmental stochasticity coupled with weak density dependence, or endogenous, e.g., over-compensatory density dependence. Far fewer studies have addressed whether the mechanism responsible for boom-bust dynamics matters with respect to at-risk species management. Here, we ask whether the best strategy for restoring habitat across a landscape differs under exogenously...

Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles

Ian A. Warren, J. Cristobal Vera, Annika Johns, Robert Zinna, James H. Marden, Douglas J. Emlen, Ian Dworkin & Laura C. Lavine
Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as “horns”. These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce...

Data from: Evolution of the additive genetic variance–covariance matrix under continuous directional selection on a complex behavioural phenotype

Vincent Careau, Matthew E. Wolak, Patrick A. Carter & Theodore Garland
Given the pace at which human-induced environmental changes occur, a pressing challenge is to determine the speed with which selection can drive evolutionary change. A key determinant of adaptive response to multivariate phenotypic selection is the additive genetic variance–covariance matrix (G). Yet knowledge of G in a population experiencing new or altered selection is not sufficient to predict selection response because G itself evolves in ways that are poorly understood. We experimentally evaluated changes in...

Data from: Mixed population genomics support for the central marginal hypothesis across the invasive range of the cane toad (Rhinella marina) in Australia

Daryl R. Trumbo, Brendan Epstein, Paul A. Hohenlohe, Ross A. Alford, Lin Schwarzkopf & Andrew Storfer
Understanding factors that cause species' geographic range limits is a major focus in ecology and evolution. The central marginal hypothesis (CMH) predicts that species cannot adapt to conditions beyond current geographic range edges because genetic diversity decreases from core to edge due to smaller, more isolated edge populations. We employed a population genomics framework using 24 235–33 112 SNP loci to test major predictions of the CMH in the ongoing invasion of the cane toad...

Data from: Phenological responses of 215 moth species to interannual climate variation in the Pacific Northwest from 1895 through 2013

Julie A. Maurer, Jon H. Shepard, Lars G. Crabo, Paul C. Hammond, Richard S. Zack & Merrill A. Peterson
Climate change has caused shifts in the phenology and distributions of many species but comparing responses across species is challenged by inconsistencies in the methodology and taxonomic and temporal scope of individual studies. Natural history collections offer a rich source of data for examining phenological shifts for a large number of species. We paired specimen records from Pacific Northwest insect collections to climate data to analyze the responses of 215 moth species to interannual climate...

Bird predation and landscape context shape arthropod communities on broccoli

Joseph Taylor, Olivia Smith, William Snyder, Jeb Owen, Erin Wilson-Rankin, Max Edworthy, Christina Kennedy, Chris Latimer & William Snyder
Birds increase crop yields via consumption of pests in some contexts but disrupt pest control via intraguild predation in others. Landscape complexity acts as an inconsistent mediator, sometimes increasing, decreasing, or not impacting pest control. Here, we examined how landscape context and seasonal variation mediate the impact of birds on arthropod pests and natural enemies, leaf damage, and yields of broccoli (Brassica oleracea) on highly diversified farms that spanned the USA West Coast. Our study...

Data from: Simulated winter warming negatively impacts survival of Antarctica’s only endemic insect

Jack Devlin, Laura Unfried, Melise C. Lecheta, Eleanor A. McCabe, Josiah D. Gantz, Yuta Kawarasaki, Michael A. Elnitsky, Scott Hotaling, Andrew P. Michel, Peter Convey, Scott A. L. Hayward & Nicholas M. Teets
Antarctic winters are challenging for terrestrial invertebrates, and species that live there have specialized adaptations to conserve energy and protect against cold injury in the winter. However, rapidly occurring climate change in these regions will increase the unpredictability of winter conditions, and there is currently a dearth of knowledge on how the highly adapted invertebrates of Antarctica will respond to changes in winter temperatures. We evaluated the response of larvae of the Antarctic midge, Belgica...

Plant evolution can mediate negative effects from honey bees on wild pollinators

James Milner, Tobin Northfield, Elias Bloom & David Crowder
1. Pollinators are introduced to agroecosystems to provide pollination services. Introductions of managed pollinators often promote ecosystem services, but it remains largely unknown whether they also affect evolutionary mutualisms between wild pollinators and plants. 2. Here we developed a model to assess effects of managed honey bees on mutualisms between plants and wild pollinators. Our model tracked how interactions among wild pollinators and honey bees affected pollinator and plant populations. 3. We show that when...

Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation

Lorena Torres Martínez, Stehanie Porter, Camille Wendlandt, Jessica Purcell, Gabriel S Ortiz-Barbosa, Jacob Rothschild, Mathew Lampe, Farmasin Warisha, Tram Le, Alexandra J Weisberg, Jeff Chang & Joel L Sachs
This is a compilation of the different sets of data that were gathered and analyzed to understand the evolution of plant-microbial mutualisms in a genus of native legumes in California (Acmispon) described in the paper: "Torres-Martínez L, Porter SS, Wendlandt CE, Purcell J, Ortiz-Barbosa GS, Rothschild J, Lampe M, Warisha F, Le T, Weisberg AJ, Chang JH, Sachs JL. Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation. Evolution....

Agricultural intensification heightens food safety risks posed by wild birds

Olivia Smith, Amanda Edworthy, Joseph Taylor, Matthew Jones, Aaron Tormanen, Christina M. Kennedy, Zhen Fu, Christopher Latimer, Kevin Cornell, Lucas Michelotti, Chika Sato, Tobin Northfield, William Snyder & Jeb Owen
1. Agricultural intensification and simplification are key drivers of recent declines in wild bird populations, heightening the need to better balance conservation with food production. This is hindered, however, by perceptions that birds threaten food safety. While birds are known reservoirs of foodborne pathogens, there remains uncertainty about the links between landscape context, farming practices, and actual crop contamination by birds. 2. Here, we examine relationships between landscape context, farming practices, and pathogen contamination by...

Datasets for Mixed support for gene flow as a constraint to local adaptation and contributor to the limited geographic range of an endemic salamander

Steven Micheletti
Understanding mechanisms that underlie species range limits is at the core of evolutionary ecology. Asymmetric gene flow between larger core populations and smaller edge populations can swamp local adaptation at the range edge and inhibit further range expansion. However, empirical tests of this theory are exceedingly rare. We tested the hypothesis that asymmetric gene flow can constrain local adaptation and thereby species’ range limits in an endemic US salamander (Ambystoma barbouri) by determining if gene...

Selfing rate variation within species is unrelated to life-history traits or geographic range position

Jeremiah Busch & Carly Prior
Premise: In plants, populations and species vary widely along the continuum from outcrossing to selfing. Life-history traits and ecological circumstances influence among-species variation in selfing rates but their general role in explaining intraspecific variation is unknown. Using a database of plant species, we test whether life-history traits, geographic range position, or abundance predict selfing rate variation among populations. Methods: We identified species where selfing rates were estimated in at least three populations at known locations....

Coevolution, diversification, and alternative states in two-trophic communities

Tobin Northfield, Jörgen Ripa, Lucas Nell & Anthony Ives
Single-trait eco-evolutionary models of arms races between consumers and their resource species often show inhibition rather than promotion of community diversification. In contrast, modeling arms races involving multiple traits, we found that arms races can promote diversification when trade-off costs among traits make simultaneous investment in multiple traits either more beneficial or more costly. Coevolution between resource and consumer species generates an adaptive landscape for each, with the configuration giving predictable suites of consumer and...

Data from: Reproductive character displacement shapes a spatially structured petal color polymorphism in Leavenworthia stylosa

Nicholas A. Norton, M. Thilina R. Fernando, Christopher R. Herlihy & Jeremiah W. Busch
Character displacement is a potentially important process driving trait evolution and species diversification. Floral traits may experience character displacement in response to pollinator-mediated competition (ecological character displacement) or the risk of forming hybrids with reduced fitness (reproductive character displacement). We test these and alternative hypotheses to explain a yellow-white petal color polymorphism in Leavenworthia stylosa, where yellow morphs are spatially associated with a white-petaled congener (L. exigua) that produces hybrids with complete pollen sterility. A...

Data from: Agricultural practices for food safety threaten pest control services for fresh produce

Daniel S. Karp, Rebekah Moses, Sasha Gennet, Matthew S. Jones, Shimat Joseph, Leithen K. M'Gonigle, Lauren C. Ponisio, William E. Snyder & Claire Kremen
Over the past decade, several foodborne disease outbreaks provoked widespread reforms to the fresh produce industry. Subsequent concerns about wildlife vectors and contaminated manures created pressure on growers to discontinue use of manure-based composts and remove nearby semi-natural vegetation. Despite widespread adoption, impacts of these practices on ecosystem services such as pest control have not been assessed. We used a landscape-scale field experiment to quantify associations between compost applications, semi-natural vegetation, pest control services and...

Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis

Jon M. Mallatt, Catherine Waggoner Craig & Matthew J. Yoder
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The...

Data from: Seasonal variation in behavioral thermoregulation and predator avoidance in a small mammal

Charlotte R. Milling, Janet L. Rachlow, Timothy R. Johnson, Jennifer S. Forbey & Lisa A. Shipley
Understanding behavioral responses of animals to the thermal environment is of increasing importance under changing climate regimes. Thermoregulatory behaviors, such as exploitation of thermal refugia or temporal partitioning of activity, can buffer organisms against hot and cold thermal extremes but may conflict with other life history needs. Our objective was to evaluate strategies for behavioral thermoregulation by a small-bodied endotherm to test hypotheses about tradeoffs between thermal and security needs across seasons. We quantified the...

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