52 Works

Data from: Meta-analysis of yield response of foliar fungicide-treated hybrid corn in the United States and Ontario, Canada

Kiersten A. Wise, Damon L. Smith, Anna Freije, Daren S. Mueller, Yuba Kandel, Tom Allen, Carl A. Bradley, Emmanuel Byamukama, Martin Chilvers, Travis Faske, Andrew Friskop, Clayton Hollier, Tamra A. Jackson-Ziems, Heather Kelly, Bob Kemerait, Paul Price, Alison Robertson & Albert Tenuta
Background: Foliar fungicide applications to corn (Zea mays) occur at one or more application timings ranging from early vegetative growth stages to mid-reproductive stages. Previous studies indicated that fungicide applications are profitable under high disease pressure when applied during the tasseling to silking growth stages. Few comprehensive studies in corn have examined the impact of fungicide applications at an early vegetative growth stage (V6) compared to late application timings (VT) for yield response and return...

Data from: Meta-analytic and economic approaches for evaluation of pesticide impact on Sclerotinia stem rot control and soybean yield in the North Central U.S.

Jaime F. Willbur, Paul Mitchell, Mamadou L. Fall, Adam M. Byrne, Scott Chapman, Crystal M. Floyd, Carl A. Bradley, Keith Ames, Martin I. Chilvers, Nathan Kleczewski, Dean Malvick, Brian Mueller, Daren Mueller, Mehdi Kabbage, Shawn P. Conley & Damon Smith
As complete host resistance in soybean has not been achieved, Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum continues to be of major economic concern for farmers. Thus, chemical control remains a prevalent disease management strategy. Pesticide evaluations were conducted in Illinois, Iowa, Michigan, Minnesota, New Jersey, and Wisconsin from 2009 to 2016, for a total of 25 site-years (n = 2057 plot-level data points). These studies were used in network meta-analyses to evaluate the...

Data from: A comparative analysis of common methods to identify waterbird hotspots

Allison L. Sussman, Beth Gardner, Evan M. Adams, Leo Salas, Kevin P. Kenow, David R. Luukkonen, Michael J. Monfils, William P. Mueller, Kathryn A. Williams, Michele Leduc-Lapierre & Elise F. Zipkin
1. Hotspot analysis is a commonly used method in ecology and conservation to identify areas of high biodiversity or conservation concern. However, delineating and mapping hotspots is subjective and various approaches can lead to different conclusions with regard to the classification of particular areas as hotspots, complicating long-term conservation planning. 2. We present a comparative analysis of recent approaches for identifying waterbird hotspots, with the goal of developing insights about the appropriate use of these...

Long-term evapotranspiration rates for rainfed corn vs. perennial bioenergy crops in a mesic landscape

Michael Abraha, Jiquan Chen, Stephen K. Hamilton & G. Philip Robertson
Hydrologic implications of the conversion of agricultural or conservation lands for annual vs. perennial bioenergy crop production are scarce. We converted three 22 year-old Conservation Reserve Program (CRP) grasslands and three 50+ year-old conventionally tilled corn-soybean rotation agricultural (AGR) lands to no-till corn, switchgrass (Panicum virgatum L.) or restored prairie. A seventh site was maintained in the preexisting CRP grassland dominated by smooth brome grass (Bromus inermis L.). We measured evapotranspiration (ET) using the eddy...

Data from: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming

Eric Meineri, Kari Klanderud, John Guittar, Deborah Goldberg & Vigdis Vandvik
Understanding the degree to which plant communities are open to seedling recruitment is key to predicting how they will be impacted by climate change. We experimentally assessed whether communities assembled under colder climates were inherently more open to recruitment than warmer-climate communities, after controlling for differences in the current climate under which the communities were growing. We then tested whether variation in openness to recruitment could be explained by community biomass or by the plant...

Benchmarking parametric and machine learning models for genomic prediction of complex traits

Christina B Azodi, Andrew McCarren, Mark Roantree, Gustavo De Los Campos, Shin-Han Shiu & Emily Bolger
The usefulness of genomic prediction in crop and livestock breeding programs has prompted efforts to develop new and improved genomic prediction algorithms, such as artificial neural networks and gradient tree boosting. However, the performance of these algorithms has not been compared in a systematic manner using a wide range of datasets and models. Using data of 18 traits across six plant species with different marker densities and training population sizes, we compared the performance of...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Sex differences in IV thrombolysis treatment for stroke: a systematic review and meta-analysis

Brent Strong, Lynda Lisabeth & Mathew Reeves
Objective: A prior meta-analysis of reports published between 2000 and 2008 found that women were 30% less likely to receive IV rt-PA treatment for stroke than men; we updated this meta-analysis to determine if this sex difference still persisted. Methods: We identified studies that reported sex-specific IV rt-PA treatment rates for acute ischemic stroke published between 2008 and 2018. Eligible studies included representative populations of ischemic stroke patients from hospital-based, registry-based, or administrative data. Random...

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

Tom Theeuwen, Pádraic Flood, Korbinian Schneeberger, Paul Keizer, Willem Kruijer, Edouard Severing, Evangelos Kouklas, Jos Hageman, Raúl Wijfjes, Vanessa Calvo-Baltanas, Frank Becker, Sabine Schnabel, Leo Willems, Wilco Ligterink, Jeroen Van Arkel, Roland Mumm, José Gualberto, Linda Savage, David Kramer, Joost Keurentjes, Fred Van Eeuwijk, Maarten Koornneef, Jeremy Harbinson, Mark Aarts & Erik Wijnker
Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions....

Maintaining historic disturbance regimes increases species’ resilience to catastrophic hurricanes

Erica H Henry, Martha O Burford Reiskind, Aerin Land & Nick M Haddad
As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system’s resilience to these events remains unknown. Following Hurricane Irma’s landfall in our habitat restoration study sites, we found that rare ecosystems with active, human-imposed management suffered less damage in a hurricane’s path than unmanaged systems. At the...

Fusarium virguliforme transcriptional plasticity is revealed by host colonization of corn vs. soybean

Amy Baetsen-Young, Jennifer Wai, Robert VanDuren & Brad Day
We exploited the broad host range of Fusarium virguliforme to identify differential fungal responses leading to either an endophytic or a pathogenic lifestyle during colonization of corn (Zea mays) and soybean (Glycine max), respectively. To provide a foundation to survey the transcriptomic landscape, we produced an improved de novo genome assembly and annotation of F. virguliforme using PacBio sequencing. Next, we conducted a high-resolution time course of F. virguliforme colonization and infection of both soybean,...

Data from: Transcriptional profiling of the murine airway response to acute ozone exposure

Adelaide Tovar, Gregory J. Smith, Joseph M. Thomas, Wesley L. Crouse, Jack R. Harkema & Samir N. P. Kelada
Ambient ozone (O3) exposure has serious consequences on respiratory health, including airway inflammation and injury. Decades of research have yielded thorough descriptions of these outcomes; however, less is known about the molecular processes that drive them. The aim of this study was to further describe the cellular and molecular responses to O3 exposure in murine airways, with a particular focus on transcriptional responses in two critical compartments: conducting airways (CA) and airway macrophages (AM). After...

Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical-temperate congener pair

Carina Baskett, Lucy Schroeder, Marjorie Weber & Douglas Schemske
The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination...

Data from: Impacts of climate variability and adaptation strategies on crop yields and soil organic carbon in the US Midwest

Lin Liu & Bruno Basso
Climate change is likely to increase the frequency of drought and more extreme precipitation events. The objectives of this study were i) to assess the impact of extended drought followed by heavy precipitation events on yield and soil organic carbon (SOC) under historical and future climate, and ii) to evaluate the effectiveness of climate adaptation strategies (no-tillage and new cultivars) in mitigating impacts of increased frequencies of extreme events and warming. We used the validated...

Rapid and predictable evolution of admixed populations between two Drosophila species pairs

Daniel Matute, Aaron Comeault, Eric Earley, Antonio Serrato-Capuchina, David Peede, Anaïs Monroy-Eklund, Wen Huang, Corbin Jones, Trudy Mackay & Jerry Coyne
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea. Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for...

Data from: Habitat type influences Danaus plexippus (Lepidoptera: Nymphalidae) oviposition and egg survival on Asclepias syriaca (Gentianales: Apocynaceae)

Andrew T. Myers, Christie A. Bahlai & Douglas A. Landis
As agricultural practices intensify, species once common in agricultural landscapes are declining in abundance. One such species is the monarch butterfly (Danaus plexippus L.), whose eastern North American population has decreased approximately 80% during the past 20 years. One hypothesis explaining the monarch’s decline is reduced breeding habitat via loss of common milkweed (Asclepias syriaca L.) from agricultural landscapes in the north central United States due to adoption of herbicide tolerant row crops. Current efforts...

Data from: Linking dynamical complexities from activation signals to transcription responses

Genghong Lin, Feng Jiao, Qiwen Sun, Moxun Tang, Jianshe Yu & Zhan Zhou
The transcription of inducible genes involves signaling pathways that induce DNA binding of the downstream transcription factors to form functional promoter states. How the transcription dynamics is linked to the temporal variations of activation signals is far to be fully understood. In this work, we develop a mathematical model with multiple promoter states to address this question. Each promoter state has its own activation and inactivation rates, and is selected randomly with a probability that...

Data from: Early mechanistic events induced by low molecular weight polycyclic aromatic hydrocarbons in mouse lung epithelial cells: a role for eicosanoid signaling

Katelyn J. Siegrist, Deedee Romo, Brad L. Upham, Michael Armstrong, Kevin Quinn, Lauren Vanderlinden, Ross S. Osgood, Kalpana Velmurugan, Marc Elie, Jonathan Manke, Dominik Reinhold, Nichole Reisedorph, Laura Saba & Alison K. Bauer
Low molecular weight polycyclic aromatic hydrocarbons (LMW PAHs; <206.3 g/mol) are under regulated environmental contaminants (e.g., secondhand smoke) that lead to gap junction dysregulation, p38 MAPK activation, and increased mRNA production of inflammatory mediators, such as cytokines and cyclooxygenase (COX2), in lung epithelial cells. However, the early mechanisms involving lipid signaling through the arachidonic acid pathway and subsequent eicosanoid production leading to these downstream events are not known. Common human exposures are to mixtures of...

Data from: Mapping of Dynamic Transcriptome Changes Associated with Silica-Triggered Autoimmune Pathogenesis in the Lupus-Prone NZBWF1 Mouse.

James Pesta & Abby Benninghoff
The dataset contains six files of tabular data with an accompanying README file. Supplementary file 1: Customized probe annotation file for the Nanostring nCounter Mouse PanCancer Immune Profiling Panel (catalog # 115000142). This file is provided as supporting material for a journal article. Codes for columns are in file. Supplementary file 2: Microsoft Excel document with output from nSolver for differential expression analyses for pairwise comparisons noted by each named sheet. This data set is...

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Alyssa Burkhardt, Kevin Childs, Jie Wang, Marina Ramon & Frank Martin
Background: Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts. Results: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry...

Recent evolutionary history predicts population but not ecosystem level patterns

Sarah Fitzpatrick, Madison Miller & John Kronenberger
In the face of rapid anthropogenic environmental change, it is increasingly important to understand how ecological and evolutionary interactions affect the persistence of natural populations. Augmented gene flow has emerged as a potentially effective management strategy to counteract negative consequences of genetic drift and inbreeding depression in small and isolated populations. However, questions remain about the long-term impacts of augmented gene flow and whether changes in individual and population fitness are reflected in ecosystem structure,...

Data from: Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection

Kyle J. Card, Thomas LaBar, Jasper B. Gomez & Richard E. Lenski
Populations often encounter changed environments that remove selection for the maintenance of particular phenotypic traits. The resulting genetic decay of those traits under relaxed selection reduces an organism’s fitness in its prior environment. However, whether and how such decay alters the subsequent evolvability of a population upon restoration of selection for a previously diminished trait is not well understood. We addressed this question using Escherichia coli strains from the long-term evolution experiment (LTEE) that independently...

Data from: Genes, geology, and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

Laura E. Grieneisen, Marie J. E. Charpentier, Susan C. Alberts, Ran Blekhman, Gideon Bradburd, Jenny Tung & Elizabeth A. Archie
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviors, environments, genetics, and geographic distance. However, which factors are most important remains unknown. Here we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota)...

Data from: Regulation of reproductive processes with Dynamic Energy Budgets

Erik B. Muller, Konstadia Lika, Roger M. Nisbet, Irvin R. Schultz, Jerome Casas, Andre Gergs, Cheryl A. Murphy, Diane Nacci & Karen H. Watanabe
1. Linking organismal level processes to underlying suborganismal mechanisms at the molecular, cellular and organ level constitutes a major challenge for predictive ecological risk assessments. This challenge can be addressed with the simple bioenergetic models in the family of Dynamic Energy Budget (DEB), which consist of a small number of state equations quantifying universal processes, such as feeding, maintenance, development, reproduction and growth. 2. Motivated by the need for process-based models to evaluate the impact...

Data from: Deterministic tropical tree community turnover: evidence from patterns of functional beta diversity along an elevational gradient

Nathan G. Swenson, Pedro Anglada-Cordero & John A. Barone
Explaining the mechanisms that produce the enormous diversity within and between tropical tree communities is a pressing challenge for plant community ecologists. Mechanistic hypotheses range from niche-based deterministic to dispersal-based stochastic models. Strong tests of these hypotheses require detailed information regarding the functional strategies of species. A few tropical studies to date have examined trait dispersion within individual forest plots using species trait means in order to ask whether coexisting species tend to be more...

Registration Year

  • 2019
    52

Resource Types

  • Dataset
    52

Affiliations

  • Michigan State University
    52
  • United States Department of Agriculture
    3
  • University of Wisconsin-Madison
    3
  • The University of Texas at Austin
    2
  • University of Michigan–Ann Arbor
    2
  • Duke University
    2
  • Michigan Department of Natural Resources
    2
  • University of North Carolina at Chapel Hill
    2
  • University of Minnesota
    2
  • Purdue University
    2