66 Works

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: 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: 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: 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: 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: 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: 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: 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: Tropical dry forest trees and lianas differ in leaf economic spectrum traits but have overlapping water-use strategies

Leland K. Werden, Bonnie G. Waring, Christina M. Smith-Martin & Jennifer S. Powers
Tree species in tropical dry forests employ a wide range of strategies to cope with seasonal drought, including regulation of hydraulic function. However, it is uncertain if co-occurring lianas also possess a diversity of strategies. For a taxonomically diverse group of 14 tree and 7 liana species, we measured morphological and hydraulic functional traits during an unusual drought and under non-drought conditions to determine (i) if trees have different water-use strategies than lianas and (ii)...

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: 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: 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: Diversification rates of the “Old Endemic” murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity

Dakota Michael Rowsey, Lawrence R. Heaney & Sharon A. Jansa
Diversity-dependent cladogenesis occurs when a colonizing lineage exhibits increasing interspecific competition as it ecologically diversifies. Repeated colonization of a region by closely related taxa may cause similar effects as species within each lineage compete with one another. This may be particularly relevant for secondary colonists, which could experience limited diversification due to competition with earlier, incumbent colonists over evolutionary time. We tested the hypothesis that an incumbent lineage may diminish the diversification of secondary colonists...

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: Plant community response to switchgrass (Panicum virgatum) population source in establishing prairies

Shelby A. Flint, Nicholas R. Jordan & Ruth G. Shaw
Ecological restoration and revegetation efforts entail the translocation of native plant populations. Risks associated with these efforts include failure of translocated populations to establish or, conversely, such strong establishment that they excessively dominate the recipient community. The role that selective breeding plays in mediating these risks is unclear but of increasing importance as efforts to restore and establish multifunctional grasslands also increase. In a three-year, spatially replicated study, we seeded experimental prairie communities with either...

Data from: Mating consequences of contrasting hermaphroditic plant sexual systems

Caitlin E. Tomaszewski, Mason W. Kulbaba & Lawrence D. Harder
For hermaphroditic angiosperms with multiple flowers the sex roles can be exclusively combined in bisexual flowers (monocliny), strictly separated among different flowers (monoecy), or arrayed in mixtures of bisexual flowers with female flowers (gynomonoecy) or male flowers (andromonoecy). The hypothesized benefits favoring the evolution of these contrasting hermaphroditic sexual systems are typically examined individually, usually by assessing success through only one sex role. We tested predictions of most hypotheses experimentally with an andromonoecious species, Anticlea...

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: 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...

Data from: The insect-focused classification of fruit syndromes in tropical rainforests: an inter-continental comparison

Chris Dahl, Richard Ctvrtecka, Sofia Gripenberg, Owen T. Lewis, Simon T. Segar, Petr Klimes, Katerina Sam, Dominic Rinan, Jonah Filip, Roll Lilip, Pitoon Kongnoo, Montarika Panmeng, Sutipun Putnaul, Manat Reungaew, Marleny Rivera, Hector Barrios, Stuart J. Davies, Sarayudh Bunyavejchewin, Joseph S. Wright, George D. Weiblen, Vojtech Novotny & Yves Basset.
We propose a new classification of rainforest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit-feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand) and Wanang (Papua New Guinea). The three plots differed...

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...

Presentation Panel on Preservation Best Practices

Lisa Johnston, Francis Pierce-McManomon & Kieron Niven
How do existing practices for digital preservation apply to digital 3D data? What are current digital curation practices and how do they translate to 3D data? What guidance exists or is being developed to provide steps for forward migration and format longevity of 3D data? What is raw 3D data and how do we record digital provenance? How can we work around proprietary file formats? http://www.dpconline.org/handbook/technical-solutions-and-tools/file-formats-and-standards

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: 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...

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