65 Works

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Integrating abundance and diet data to improve inferences of food web dynamics

Jake M. Ferguson, , Brianna H. Witteveen, John B. Hopkins & Briana H. Witteveen
1. Both population abundances and chemical tracers are useful tools for studying consumer-resource interactions. Food web models parameterized with abundances are often used to understand how interactions structure communities and to inform management decisions of complex ecological systems. Unfortunately, collecting abundance data to parameterize these models is often expensive and time-consuming. Another approach is to use chemical tracers to estimate the proportional diets of consumers by relating the tracers in their tissues to those found...

Data from: Root responses to elevated CO2, warming, and irrigation in a semi-arid grassland: integrating biomass, length, and life span in a 5‐year field experiment

Kevin E. Mueller, Daniel R. LeCain, M. Luke McCormack, Elise Pendall, Mary Carlson & Dana M. Blumenthal
1.Plant roots mediate the impacts of environmental change on ecosystems, yet knowledge of root responses to environmental change is limited because few experiments evaluate multiple environmental factors and their interactions. Inferences about root functions are also limited because root length dynamics are rarely measured. 2.Using a five‐year experiment in a mixed‐grass prairie, we report the responses of root biomass, length, and lifespan to elevated carbon dioxide (CO2), warming, elevated CO2 and warming combined, and irrigation....

Data from: Genomewide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Nathan Taitano, Vivian Bernau, Lev Jardón-Barbolla, Brian Leckie, Michael Mazourek, Kristin Mercer, Leah McHale, Andrew Michel, David Baumler, Michael Kantar, Esther Van Der Knapp & Esther Van Der Knaap
Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping-by-sequencing (GBS), yielding 32,623 filtered...

Data from: The evolution of marine larval dispersal kernels in spatially structured habitats: analytical models, individual-based simulations, and comparisons with empirical estimates

Allison K. Shaw, Cassidy C. D'Aloia & Peter M. Buston
Understanding the causes of larval dispersal is a major goal of marine ecology, yet most research focuses on proximate causes. Here, we ask how ultimate, evolutionary causes affect dispersal. Building on Hamilton and May's 1977 classic paper (``Dispersal in stable habitats"), we develop analytic and simulation models for the evolution of dispersal kernels in spatially structured habitats. First, we investigate dispersal in a world without edges and find that most offspring disperse as far as...

Data from: High specialization and limited structural change in plant‐herbivore networks along a successional chronosequence in tropical montane forest

Conor M. Redmond, John Auga, Bradley Gewa, Simon T. Segar, Scott E. Miller, Kenneth Molem, George D. Weiblen, Phillip T. Butterill, Gibson Maiyah, Amelia S.C. Hood, Martin Volf, Leonardo R. Jorge, Yves Basset, Vojtech Novotny, Philip T. Butterill & Amelia S. C. Hood
Secondary succession is well‐understood, to the point of being predictable for plant communities, but the successional changes in plant‐herbivore interactions remains poorly explored. This is particularly true for tropical forests, despite the increasing importance of early successional stages in tropical landscapes. Deriving expectations from successional theory, we examine properties of plant‐herbivore interaction networks while accounting for host phylogenetic structure along a succession chronosequence in montane rainforest in Papua New Guinea. We present one of the...

Data from: Is it the song or the singers? Acoustic and social experiences shape adult reproductive tactics and condition

Susan L. Balenger, Elizabeth Bastiaans & Marlene Zuk
When sexual signals are perceived during growth and development they can provide information regarding the social conditions likely to be encountered as an adult. Perception of cues related to the presence and density of future mates and potential competitors can result in altered adult phenotypes. Previous studies have shown that adult male Teleogryllus oceanicus field crickets from a Kauai, Hawaii population reared alone and without hearing conspecific song are more phonotactic than those reared with...

Data from: Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Paul D. Blischak, Maribeth Latvis, Diego F. Morales-Briones, Jens C. Johnson, Verónica S. Di Stilio, Andrea D. Wolfe & David C. Tank
Premise of the Study: Targeted enrichment strategies for phylogenomic inference are a time‐ and cost‐efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results: We present Fluidigm2PURC, an open source Python utility for processing paired‐end Illumina data from double‐barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling...

Registration Year

  • 2018
    65

Resource Types

  • Dataset
    65

Affiliations

  • University of Minnesota
    65
  • Utah State University
    4
  • Duke University
    4
  • Iowa State University
    4
  • University of Washington
    3
  • Stanford University
    3
  • University of Michigan-Ann Arbor
    3
  • The Ohio State University
    3
  • University of California, Berkeley
    3
  • German Center for Integrative Biodiversity Research
    3