66 Works

Data from: Clinical and laboratory predictors of influenza infection among individuals with influenza-like illness presenting to an urban Thai hospital over a five-year period

Kathryn B. Anderson, Sriluck Simasthien, Veerachai Watanaveeradej, Alden L. Weg, Damon W. Ellison, Detchvijitr Suwanpakdee, Chonticha Klungthong, Thipwipha Phonpakobsin, Phirangkul Kerdpanich, Danabhand Phiboonbanakit, Robert V. Gibbons, Stefan Fernandez, Louis R. Macareo, In-Kyu Yoon & Richard G. Jarman
Early diagnosis of influenza infection maximizes the effectiveness of antiviral medicines. Here, we assess the ability for clinical characteristics and rapid influenza tests to predict PCR-confirmed influenza infection in a sentinel, cross-sectional study for influenza-like illness (ILI) in Thailand. Participants meeting criteria for acute ILI (fever > 38°C and cough or sore throat) were recruited from inpatient and outpatient departments in Bangkok, Thailand, from 2009-2014. The primary endpoint for the study was the occurrence of...

Data from: Attracting Common Carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management

Ratna Ghosal, Jessica J. Eichmiller, Bruce A. Witthuhn & Peter W. Sorensen
Measurement of environmental DNA (eDNA) is becoming a common technique to survey for rare and invasive fish due to its sensitivity and specificity. However, its utility is limited by an incomplete understanding of factors governing its sources and fates. Failure to detect eDNA is especially difficult to interpret so surveillance techniques often collect large numbers of samples across broad regions. If, however, fish could be reliably attracted to a single location where their eDNA could...

Data from: Herbivory and eutrophication mediate grassland plant nutrient responses across a global climatic gradient

T. Michael Anderson, Daniel M. Griffith, James B. Grace, Eric M. Lind, Peter B. Adler, Lori A. Biederman, Dana M. Blumenthal, Pedro Daleo, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Andrew S. MacDougall, Rebecca L. McCulley, Suzanne M. Prober, Anita C. Risch, Mahesh Sankaran, Martin Schütz, Eric W. Seabloom, Carly J. Stevens, Lauren L. Sullivan, Peter D. Wragg & Elizabeth T. Borer
Plant stoichiometry, the relative concentration of elements, is a key regulator of ecosystem functioning and is also being altered by human activities. In this paper we sought to understand the global drivers of plant stoichiometry and compare the relative contribution of climatic vs. anthropogenic effects. We addressed this goal by measuring plant elemental (C, N, P and K) responses to eutrophication and vertebrate herbivore exclusion at eighteen sites on six continents. Across sites, climate and...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: Nickel exposure has complex transgenerational effects in a butterfly

Megan E. Kobiela & Emilie C. Snell-Rood
Heavy metal pollution is a major problem in urban and industrial environments, and has a myriad of negative effects on animals. Quantifying the amount of population-level variation that exists for heavy metal tolerance and how plastic responses to heavy metals play out across generations are essential for understanding how animals respond to pollution. As an initial step towards studying transgenerational effects and population-level variation in concert, we brought cabbage white butterflies (Pieris rapae) from two...

Data from: Digitizing extant bat diversity: an open-access repository of 3D μCT-scanned skulls for research and education

Jeff J. Shi, Erin P. Westeen & Daniel L. Rabosky
Biological specimens are primary records of organismal ecology and history. As such, museum collections are invaluable repositories for testing ecological and evolutionary hypotheses across the tree of life. Digitizing and broadly sharing the phenotypic data from these collections serves to expand the traditional reach of museums, enabling widespread data sharing, collaboration, and education at an unprecedented scale. In recent years, μCT-scanning has been adopted as one way for efficiently digitizing museum specimens. Here, we describe...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Data from: Evaluating active learning methods for annotating semantic predications

Jake Vasilakes, Rubina Rizvi, Genevieve B. Melton, Serguei Pakhomov & Rui Zhang
Objectives: This study evaluated and compared a variety of active learning strategies, including a novel strategy we proposed, as applied to the task of filtering incorrect SemRep semantic predications. Materials and Methods: We evaluated three types of active learning strategies – uncertainty, representative, and combined– on two datasets of semantic predications from SemMedDB covering the domains of substance interactions and clinical medicine, respectively. We also designed a novel combined strategy with dynamic β without hand-tuned...

Data from: Metrics matter: the effect of parasite richness, intensity and prevalence on the evolution of host migration

Allison K. Shaw, Julie Sherman, F Barker, Marlene Zuk & F. Keith Barker
Parasites have long been thought to influence the evolution of migration, but precisely determining the conditions under which this occurs by quantifying costs of infection remains a challenge. Here we developed a model that demonstrates how the metric used to describe infection (richness/diversity, prevalence, or intensity) shapes the prediction of whether migration will evolve. The model shows that predictions based on minimizing richness yield opposite results compared to those based on minimizing prevalence, with migration...

Data from: Within-individual variation in sexual displays: signal or noise?

Jessie C. Tanner & Mark A. Bee
Animal sexual displays are typically repeated over time and consist of components that are also repeated within a display, creating potential for within-individual variation in signal production. Across taxa, patterns of variation in and female preferences for temporal properties of signals are well documented, but data describing how within-individual variation functions in communication are scarce. Is within-individual variation itself a signal of male quality, or noise that obscures another signal encoded by a temporal pattern?...

Data from: Genome-wide association analyses in the model rhizobium Ensifer meliloti

Brendan Epstein, Reda A.L. Abou-Shanab, Abdelaal Shameldsin, Margaret R. Taylor, Joseph Guhlin, Liana T. Burghardt, Matthew Nelson, Michael J. Sadowsky, Peter Tiffin & Reda A. I. Abou-Shanab
Genome-wide association studies (GWAS) can identify genetic variants responsible for naturally occurring and quantitative phenotypic variation and therefore provide a powerful complement to approaches that rely on de novo mutations for characterizing gene function. Although bacteria should be amenable to GWAS, few GWAS have been conducted on bacteria, and the extent to which non-independence among genomic variants (e.g. linkage disequilibrium, LD) and the genetic architecture of phenotypic traits will affect GWAS performance is unclear. We...

Data from: Linking beaver dam affected flow dynamics to upstream passage of Arctic grayling

Kyle A. Cutting, Jake M. Ferguson, Michelle L. Anderson, Kristen Cook, Stacy C. Davis & Rebekah Levine
Beaver reintroductions and beaver dam structures are an increasingly utilized ecological tool for rehabilitating degraded streams, yet beaver dams can potentially impact upstream fish migrations. We collected two years of data on Arctic grayling movement through a series of beaver dams in a low gradient mountain stream, utilizing radio-telemetry techniques, to determine how hydrology, dam characteristics, and fish attributes impeded passage and movement rates of spawning grayling. We compared fish movement between a “normal” flow...

Data from: Mycorrhizal interactions do not influence plant-herbivore interactions in populations of Clarkia xantiana ssp. xantiana spanning from center to margin of the geographic range

Lana G. Bolin, John W. Benning & David A. Moeller
Multispecies interactions can be important to the expression of phenotypes and in determining patterns of individual fitness in nature. Many plants engage in symbiosis with arbuscular mycorrhizal fungi (AMF), but the extent to which AMF modulate other species interactions remains poorly understood. We examined multispecies interactions among plants, AMF, and insect herbivores under drought stress using a greenhouse experiment and herbivore choice assays. The experiment included six populations of Clarkia xantiana (Onagraceae), which span a...

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: Moose movement rates are altered by wolf presence in two ecosystems

Mark A. Ditmer, John R. Fieberg, Ron A. Moen, Steven K. Windels, Seth P. Stapleton & Tara R. Harris
Predators directly impact prey populations through lethal encounters, but understanding non-lethal, indirect effects is also critical because foraging animals often face tradeoffs between predator avoidance and energy intake. Quantifying these indirect effects can be difficult even when it is possible to monitor individuals that regularly interact. Our goal was to understand how movement and resource selection o a predator (wolves; Canis lupus) influences the movement behavior of a prey species (moose; Alces alces). We tested...

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph Frederic Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximillian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & Stephen A. Smith
Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available...

Data from: Adaptation, chance, and history in experimental evolutionary reversals to unicellularity

María Rebolleda-Gómez & Michael Travisano
Evolution is often deemed irreversible. The evolution of complex traits that require many mutations makes their reversal unlikely. Even in simpler traits, reversals might become less likely as neutral or beneficial mutations, with deleterious effects in the ancestral context, become fixed in the novel background. This is especially true in changes that involve large re-organizations of the organism and its interactions with the environment. The evolution of multicellularity involves the reorganization of previously autonomous cells...

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
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: Resilience of seed production to a severe El Niño‐induced drought across functional groups and dispersal types

Michael J. O'Brien, Daniel Peréz-Aviles & Jennifer S. Powers
More frequent and severe El Niño Southern Oscillations (ENSO) are causing episodic periods of decreased rainfall. Although the effects of these ENSO-induced droughts on tree growth and mortality have been well studied, the impacts on other demographic rates such as reproduction are less well known. We use a four-year seed rain dataset encompassing the most severe ENSO-induced drought in more than 30 years to assess the resilience (i.e. resistance and recovery) of the seed composition...

Data from: Systematic analysis of complex genetic interactions

Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Elizabeth N. Koch, Carles Pons, Andrius Jonas Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo … & Chad L. Myers
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended...

Data from: Edaphic factors, successional status, and functional traits drive habitat associations of trees in naturally regenerating tropical dry forests

Leland K. Werden, Justin M. Becknell & Jennifer S. Powers
1. Many studies have examined individual environmental drivers of tropical tree species distributions, but edaphic and successional gradients have not been considered simultaneously. Furthermore, determining how functional traits influence species distributions along these gradients may help to elucidate mechanisms behind community assembly. 2. To assess the influence of environmental filtering on tropical dry forest (TDF) tree species distributions we used forest inventory data from sites with large edaphic and successional gradients in NW Costa Rica....

Data from: The role of diversification in the continental scale community assembly of the American oaks (Quercus)

Jeannine Cavender-Bares, Shan Kothari, José Eduardo Meireles, Matthew A. Kaproth, Paul S. Manos & Andrew L. Hipp
Premise of the study: Evolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effects that influence regional species pools and the composition of communities. We consider the consequences of the diversification process in shaping trait evolution and assembly of oak-dominated communities throughout the continental U.S. Methods: Within the US oaks, we tested for phylogenetic and functional trait patterns...

Data from: Cracking the case: seed traits and phylogeny predict time to germination in prairie restoration species

Rebecca S. Barak, Taran M. Lichtenberger, Alyssa Wellman-Houde, Andrea T. Kramer & Daniel J. Larkin
1. Traits are important for understanding how plant communities assemble and function, providing a common currency for studying ecological processes across species, locations, and habitat types. However, most studies relating species traits to community assembly rely upon vegetative traits of mature plants. Seed traits, which are understudied relative to whole-plant traits, are key to understanding assembly of plant communities. This is particularly true in restored communities, which are typically started from seed, making germination a...

Data from: Little plant, big city: a test of adaptation to urban environments in common ragweed (Ambrosia artemisiifolia)

Amanda J. Gorton, David A. Moeller & Peter Tiffin
A full understanding of how cities shape adaptation requires characterizing genetically-based phenotypic and fitness differences between urban and rural populations under field conditions. We used a reciprocal transplant experiment with the native plant common ragweed, (Ambrosia artemisiifolia), and found that urban and rural populations have diverged in flowering time, a trait that strongly affects fitness. Although urban populations flowered earlier than rural populations, plants growing in urban field sites flowered later than plants in rural...

Data from: Species-specific spatiotemporal patterns of leopard, lion and tiger attacks on humans

Craig Packer, Shweta Shivakumar, Vidya Athreya, Meggan E. Craft, Harshawardhen Dhanwatey, Poonam Dhanwatey, Bhim Gurung, Anup Joshi, Hadas Kushnir, John D.C. Linnell, Nicholas M. Fountain-Jones & John D. C. Linnell
1. Large carnivores of the genus Panthera can pose serious threats to public safety. Although the annual number of attacks on humans is rare compared to livestock depredation, such incidents undermine popular support for wildlife conservation and require immediate responses to protect human life. 2. We used a space-time scan method to perform a novel spatiotemporal analysis of 908 attacks on humans by lions, leopards and tigers to estimate the risks of further attacks in...

Registration Year

  • 2018

Resource Types

  • Dataset
  • Text


  • University of Minnesota
  • Utah State University
  • Duke University
  • Iowa State University
  • University of Washington
  • Stanford University
  • University of Michigan-Ann Arbor
  • The Ohio State University
  • University of California, Berkeley
  • German Center for Integrative Biodiversity Research