35 Works

Data from: Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies

Ye Zheng, Ferhat Ay & Sunduz Keles
Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological signal from repetitive regions of genomes. We developed and validated mHi-C, a multi-read mapping strategy to probabilistically allocate Hi-C multi-reads. mHi-C exhibited superior performance over utilizing only uni-reads and heuristic approaches aimed at rescuing multi-reads on benchmarks. Specifically, mHi-C increased the sequencing depth by an average of 20% resulting in higher reproducibility of contact matrices and...

Measuring frequently during peak soil N2O emissions is more important than choosing the time of day to sample (Data set and statistical analysis script)

Jordi Francis Clar & Robert P Anex
Statistical analysis and data set used in the publication of the journal article: 'Measuring frequently during peak soil N2O emissions is more important than choosing the time of day to sample'. Francis Clar, J. and Anex, R. P.: Measuring frequently during peak soil N2O emissions is more important than choosing the time of day to sample.

Supplemental video 1 from: A violently tornadic supercell thunderstorm simulation spanning a quarter-trillion grid volumes: Computational challenges, I/O framework, and visualizations of tornadogenesis

Leigh Orf
This video chronicles the formation of a tornado in a simulated, supercell thunderstorm. It is Supplemental Video 1 referenced by this article: Orf, L., 2019: A violently tornadic supercell thunderstorm simulation spanning a quarter-trillion grid volumes: Computational challenges, I/O framework, and visualizations of tornadogenesis. Atmosphere: https://www.preprints.org/manuscript/201909.0029/v1

Data from: Inorganic N addition replaces N supplied to switchgrass (Panicum virgatum) by arbuscular mycorrhizal fungi

Laura Jach Smith
Arbuscular mycorrhizal fungi (AMF) provide many benefits in agroecosystems including improved soil tilth, carbon sequestration, and water and nutrient transfer to plants. AMF are known to affect plant nitrogen (N) dynamics and transfer N to plants, but there have been few studies addressing whether the amount of N transferred to plants by AMF is agronomically relevant. We used δ15N natural abundance methods and δ15N mass balance equations to estimate the amount of plant N derived...

Predaceous Toxorhynchites mosquitoes require a living gut microbiota to develop

Kerri Coon, Luca Valzania, Mark R. Brown & Michael R. Strand
Most species of mosquitoes are detritivores that feed on decaying plant and animal materials in their aquatic environment. Studies of several detritivorous mosquito species indicate they host relatively low diversity communities of microbes that are acquired from the environment while feeding. Our recent results also indicate that detritivorous species require a living gut microbiota in order to grow beyond the first instar. Less well known is that some mosquitoes, including those belonging to the genus...

Ezra Pound's \"The Music of Beowulf\"

Maxwell Gray
A digital critical edition and introduction of an unpublished essay draft (1928) of the modernist American poet Ezra Pound, held in the Pound Papers collection at the Beinecke Rare Book and Manuscript Library (Yale); built on the digital humanities platform resource Digital Mappa (version 2.0); an open-source digital humanities platform for open-access, browser-based workspaces, projects and scholarly publications.

Data from: Invasive shrubs modify rodent activity timing, revealing a behavioral rule governing diel activity

Peter W. Guiden & John L. Orrock
Animals adjust the timing of their activity to maximize benefits, such as access to resources, and minimize costs, such as exposure to predators. Despite many examples of invasive plants changing animal behavior, the potential for invasive plants to alter the timing of animal activity remains unexplored. In eastern North America, invasive shrubs might have particularly strong effects on animal activity timing during spring and fall, when many invasive shrubs retain their leaves long after native...

Data from: How extreme is extreme? Demographic approaches inform the occurrence and ecological relevance of extreme events

Christopher E. Latimer & Benjamin Zuckerberg
Projected increases in the variability of both temperature and precipitation will result in the greater likelihood and magnitude of extreme weather (e.g., cold snaps, droughts, heat waves) with potential implications for animal populations. Despite the ecological consequences of extreme weather, there are several challenges in identifying extreme events and measuring their influence on key demographic processes in free-living animals. First, there is often a mismatch between the spatial and/or temporal resolution of biological and climate...

Data from: Monitoring vultures in the 21st century: the need for standardized protocols

Paula L. Perrig, Sergio A. Lambertucci, Emiliano Donadio, Julian Padro & Jonathan N. Pauli
This article calls on scientists, managers and organizations focused on vulture conservation to promote and use standardized monitoring programs based on sampling of molted feathers.

Fluorescent biomarkers demonstrate prospects for spreadable vaccines to control disease transmission in wild bats

Kevin Bakker, Tonie Rocke, Rachel Abbott, Carlos Tello, Jorge Carrera, William Valderrama, Carlos Shiva, Nestor Falcon, Jorge Osorio & Daniel Streicker
Vaccines that autonomously transfer among individuals have been proposed as a strategy to control infectious diseases within wildlife populations. However, understanding rates of spread and epidemiological efficacy in real world systems remain elusive. Here, we investigated whether topical vaccines that transfer among bats through social contacts can control vampire bat rabies, a medically and economically important zoonosis in Latin America. Field experiments in 3 Peruvian bat colonies which used fluorescent biomarkers as a proxy for...

Data from: A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error

Jesus A. Ballesteros & Prashant P. Sharma
Horseshoe crabs (Xiphosura) are traditionally regarded as sister to the clade of terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent phylogenomic analyses, but the non-monophyly of Arachnida has consistently been disregarded as artifactual. We reevaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic dataset to date, expanding outgroup sampling and including data from whole genome sequencing projects. In spite of uncertainty in theplacement of some arachnid clades, all analyses show...

Estimating correlations among demographic parameters in population models

Thomas Riecke, Alan Leach, James Sedinger, Benjamin Sedinger & Perry Williams
Estimating correlations among demographic parameters is critical to understanding population dynamics and life-history evolution, where correlations among parameters can inform our understanding of life-history trade-offs, result in effective applied conservation actions, and shed light on evolutionary ecology. The most common approaches rely on the multivariate normal distribution, and its conjugate inverse Wishart prior distribtion. However, the inverse Wishart prior for the covariance matrix of multivariate normal distributions has a strong influence on posterior distributions. As...

Ordered phylogenomic subsampling enables diagnosis of systematic errors in the placement of the enigmatic arachnid order Palpigradi

Jesús Ballesteros, Carlos Santibáñez López, Ľubomír Kováč, Efrat Gavish-Regev & Prashant Sharma
The miniaturized arachnid order Palpigradi has ambiguous phylogenetic affinities, due to its odd combination of plesiomorphic and derived morphological traits. This lineage has never been sampled in phylogenomic datasets because of its small body size and fragility of most species, a sampling gap of immediate concern to recent disputes over arachnid monophyly. To redress this gap, we sampled a population of the cave-inhabiting species Eukoenenia spelaea from Slovakia and inferred its placement in the phylogeny...

Data from: Forest structure and snow depth alter the movement patterns and subsequent expenditures of a forest carnivore, the Pacific marten

Marie Martin, Katie Moriarty & Jonathan Pauli
Energetic balance is central to the survival and persistence of free-ranging animals. Quantifying expenditures and identifying factors that drive energetics informs our understanding of species’ ecology and their responses to shifting environmental conditions. Approaches used to estimate energetic expenditures of free-ranging species, such as doubly-labelled water (DLW), are precise but difficult to implement. Global positioning system (GPS) collars and accelerometers have emerged as alternatives for estimating expenditures, but these techniques have few applications in terrestrial...

Data from: Linking plant genes to insect communities: identifying the genetic bases of plant traits and community composition

Hilary L. Barker, Jennifer F. Riehl, Carolina Bernhardsson, Kennedy Rubert-Nason, Liza Holeski, Pär K. Ingvarsson & Richard L. Lindroth
Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen, endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To...

Data from: Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

Ricardo Kriebel, Bryan T. Drew, Chloe P. Drummond, Jesús Guadalupe González Gallegos, Ferhat Celep, Mohamed M. Mahdjoub, Jeffrey P. Rose, Chun-Lei Xiang, Guo-Xiong Hu, Jay B. Walker, Emily M. Lemmon, Alan R. Lemmon & Kenneth J. Sytsma
Premise of the Study: A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega‐genus Salvia. Methods: A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of...

Current Population Surveys: Uniform October Files, 1968-1990

Robert Hauser
This data collection consists of a "uniform" set of Current Population Surveys (CPS) October files. The October files contain the core questions included in every CPS as well as a supplemental series of questions on school enrollment. This extract makes data on school retention and enrollment accessible across all publicly available years. Records contain information for each individual between the ages of 3 and 34 years and for the head of household and the spouse...

Current Population Surveys: Uniform March Files, 1964-1988

Robert D. Mare & Christopher Winship
The principal investigators for this data collection created a "uniform" series of Current Population Surveys: Annual Demographic Files (March) that have a rectangular file structure and use one set of documentation. These Current Population Survey (CPS) files are annual surveys of the population of the United States conducted by the United States Census Bureau and are often referred to as the March CPS Demographic Supplements. The files contain records for families selected in the samples...

Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel

Joseph L. Gage, Brieanne Vaillancourt, John P. Hamilton, Norma C. Manrique-Carpintero, Timothy J. Gustafson, Kerrie Barry, Anna Lipzen, William F. Tracy, Mark A. Mikel, Shawn M. Kaeppler, C. Robin Buell & Natalia De Leon
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence/absence variations (PAVs). In this study, we present the draft de novo genome assembly of PHJ89, an Oh43-type inbred line. Using three separate reference genome assemblies (B73, PH207, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate...

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: Differing climatic mechanisms control transient and accumulated vegetation novelty in Europe and eastern North America

Kevin Burke, John Williams, Simon Brewer, Walter Finsinger, Thomas Giesecke, David Lorenz & Alejandro Ordonez
Understanding the mechanisms that produce novel ecosystems is of joint interest to conservation biologists and paleoecologists. Here, we define and differentiate transient from accumulated novelty and evaluate four climatic mechanisms proposed to cause species to reshuffle into novel assemblages: high climatic novelty, high spatial rates of change (displacement), high variance among displacement rates for individual climate variables, and divergence among displacement vector bearings. We use climate simulations to quantify climate novelty, displacement, and divergence across...

Climate induced stress and mortality in vervet monkeys

Christopher Young, Tyler Bonnell, Leslie Brown, Marcus Dostie, André Ganswindt, Stefan Kienzle, Richard McFarland, Peter Henzi & Louise Barrett
As the effects of global climate change become more apparent, animal species will become increasingly affected by extreme climate and its effect on the environment. There is a pressing need to understand animal physiological and behavioural responses to climatic stressors. We used the reactive scope model as a framework to investigate the influence of drought conditions on vervet monkey (Chlorocebus pygerythrus) behaviour, physiological stress and survival across 2.5-years in South Africa. Data were collected on...

Data from: Linking the foraging behavior of three bee species to pollen dispersal and gene flow

Johanne Brunet, Yang Zhao & Murray K. Clayton
Foraging behaviors that impact gene flow can guide the design of pollinator strategies to mitigate gene flow. Reduced gene flow is expected to minimize the impact of genetically engineered (GE) crops on feral and natural populations and to facilitate the coexistence of different agricultural markets. The goal of this study is to link foraging behavior to gene flow and identify behaviors that can help predict gene flow for different bee species. To reach this goal,...

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: The mechanisms affecting seedling establishment in restored savanna understories are seasonally dependent

Quinn M. Sorenson & Ellen I. Damschen
1. Globally, agricultural land is increasingly being abandoned with over 200 million hectares recovering from agricultural use. Regeneration of plant communities sharply differ in their structure and composition after agricultural impacts, yet the mechanisms underpinning these dramatic changes are poorly understood. It is critical to determine the relative importance of abiotic and biotic factors that limit plant establishment and success during the recovery process. In particular, belowground competition for resources in soils impacted by former...

Registration Year

  • 2019

Resource Types

  • Dataset
  • Audiovisual
  • Interactive Resource


  • University of Wisconsin-Madison
  • University of Wisconsin–Madison
  • Michigan State University
  • University of Georgia
  • University of Minnesota
  • University of Kentucky
  • University of Illinois at Urbana Champaign
  • Iowa State University
  • Joint Genome Institute
  • University of Washington