44 Works

Downscaling-based segmentation for unresolved images of highly heterogeneous granular porous samples

Svyatoslav Korneev, Xiaofan Yang, John Zachara, Timothy Scheibe & Ilenia Battiato
We propose a simple and efficient algorithm of downscaling followed by segmentation to reconstruct the unresolved pore space from X-ray computed tomography (XCT) images of natural geological porous media columns. Contrary to widely employed single and multilevel threshold-based segmentation, the proposed method is based on a continuous map between pixel intensity and local pixel porosity that does not rely on the definition of arbitrary thresholds. The approach is used to generate a high-resolution binary image...

Data from: Soil fungi underlie a phylogenetic pattern in plant growth responses to nitrogen enrichment

Rachel C. Wooliver, John K. Senior, Brad M. Potts, Michael E. Van Nuland, Joseph K. Bailey & Jennifer A. Schweitzer
1. Under increasing anthropogenic nitrogen (N) deposition, some plant species will thrive while others will not. Previous work has shown that plant phylogeny can predict these responses, and that interactions with mycorrhizal fungi are a mechanism that drives variation in plant responses to N enrichment. Yet, much of this work has ignored the roles of other root-associated fungi and whole soil fungal communities in driving these responses. 2. We tested whether soil fungi mediate responses...

Data from: Species coexistence through simultaneous fluctuation-dependent mechanisms

Andrew D. Letten, Manpreet K. Dhami, Po-Ju Ke & Tadashi Fukami
Understanding the origins and maintenance of biodiversity remains one of biology's grand challenges. From theory and observational evidence we know that variability in environmental conditions through time is likely critical to the coexistence of competing species. Nevertheless, strong experimental tests of fluctuation-driven coexistence are rare, and have typically focused on just one of two potential mechanisms, the temporal storage effect, to the neglect of the theoretically equally plausible mechanism known as relatively nonlinearity of competition....

Data from: Priority effects are weakened by a short, but not long, history of sympatric evolution

Peter C. Zee & Tadashi Fukami
Priority effects, or the effects of species arrival history on local species abundances, have been documented in a range of taxa. However, factors determining the extent to which priority effects affect community assembly remain unclear. Using laboratory populations of the bacterium Pseudomonas fluorescens, we examined whether shared evolutionary history affected the strength of priority effects. We hypothesized that sympatric evolution of populations belonging to the same guild would lead to niche differentiation, resulting in phenotypic...

Data from: Invasive rat eradication strongly impacts plant recruitment on a tropical atoll

Coral A. Wolf, Hillary S. Young, Kelly M. Zilliacus, Alex S. Wegmann, Matthew McKown, Nick D. Holmes, Bernie R. Tershy, Rodolfo Dirzo, Stefan Kropidlowski, Donald A. Croll & Alexander S. Wegmann
Rat eradication has become a common conservation intervention in island ecosystems and its effectiveness in protecting native vertebrates is increasingly well documented. Yet, the impacts of rat eradication on plant communities remain poorly understood. Here we compare native and non-native tree and palm seedling abundance before and after eradication of invasive rats (Rattus rattus) from Palmyra Atoll, Line Islands, Central Pacific Ocean. Overall, seedling recruitment increased for five of the six native trees species examined....

Data from: Community-wide consequences of sexual dimorphism: evidence from nectar microbes in dioecious plants

Kaoru Tsuji & Tadashi Fukami
Intra-specific trait variation is receiving renewed interest as a factor affecting the structure of multi-species communities within and across trophic levels. One pervasive form of intra-specific trait variation is sexual dimorphism in animals and plants, which might exert large effects particularly on the communities of host-associated organisms, but the extent of these effects is not well understood. We investigated whether host-associated microbial communities developed differently in the floral nectar of female and male individuals of...

Data from: Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy

Philip Lei Tzou, Soo-Yon Rhee, Sergei L. Kosakovsky Pond, Justen Manasa & Robert W. Shafer
Most HIV-1-infected individuals with virological failure (VF) on a pharmacologically-boosted protease inhibitor (PI)-containing regimen do not develop PI-resistance protease mutations. One proposed explanation is that mutations in HIV-1 gag or gp41 cytoplasmic domain might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with VF on a PI-containing regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from...

Data from: Timing of host feeding drives rhythms in parasite replication

Kimberley F. Prior, Daan R. Van Der Veen, Aidan J. O'Donnell, Katherine Cumnock, David Schneider, Arnab Pain, Amit Subudhi, Abhinay Ramaprasad, Samuel S. C. Rund, Nicholas J. Savill, Sarah E. Reece & Aidan J. O’Donnell
Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence...

Data from: Temperature drives Zika virus transmission: evidence from empirical and mathematical models

Blanka Tesla, Leah Demakovsky, Erin Mordecai, Sadie Ryan, Matthew Bonds, Calistus Ngonghala, Melinda Brindley & Courtney Murdock
Temperature is a strong driver of vector-borne disease transmission. Yet, for emerging arboviruses we lack fundamental knowledge on the relationship between transmission and temperature. Current models rely on the untested assumption that Zika virus responds similarly to dengue virus, potentially limiting our ability to accurately predict the spread of Zika. We conducted experiments to estimate the thermal performance of Zika virus (ZIKV) in field-derived Aedes aegypti across eight constant temperatures. We observed strong, unimodal effects...

Data from: Oxygen, temperature and the deep-marine stenothermal cradle of Ediacaran evolution

Thomas H. Boag, Richard G. Stockey, Leanne E. Elder, Pincelli M. Hull & Erik A. Sperling
Ediacaran fossils document the early evolution of complex megascopic life, contemporaneous with geochemical evidence for widespread marine anoxia. These data suggest early animals experienced frequent hypoxia. Research has thus focused on the concentration of molecular oxygen (O2) required by early animals, while also considering the impacts of climate. One model, the Cold Cradle hypothesis, proposed the Ediacaran biota originated in cold, shallow-water environments due to increased O2 solubility. First, we demonstrate using principles of gas...

Data from: Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies

Alison Ravenscraft, Michelle Berry, Tobin Hammer, Kabir Peay & Carol Boggs
The relationship between animals and their gut flora is simultaneously one of the most common and most complex symbioses on Earth. Despite its ubiquity, our understanding of this invisible but often critical relationship is still in its infancy. We employed adult Neotropical butterflies as a study system to ask three questions: First, how does gut microbial community composition vary across host individuals, species and dietary guilds? Second, how do gut microbiota compare to food microbial...

Model output from N isotope global inverse model

Taylor Martin, Francois Primeau & Karen Casciotti
Global inverse nitrogen isotope model in MATLAB. Nitrogen cycle tracers include PON, DON, NO3, and NO2 for 14N and 15N. Model output optimized to three different combinations of isotope effects for nitrate reduction (eNAR), nitrite oxidation (eNXR), and nitrite reduction (eNIR) is also available.

Data from: Is biodiversity energy-limited or unbounded? A test in fossil and modern bivalves

Craig R. McClain, Noel A. Heim, Matthew L. Knope & Jonathan L. Payne
The quantity of biomass in an ecosystem is constrained by energy availability. It is less clear, however, how energy availability constrains taxonomic and functional diversity. Competing models suggest biodiversity is either resource-limited or far from any bound. We test the hypothesis that functional diversity in marine bivalve communities is constrained by energy availability, measured as particulate organic carbon (POC) flux, in the modern oceans. We find that POC flux predicts the relative prevalence of ecological...

Data from: Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster

Emily L. Behrman, Virginia M. Howick, Martin Kapun, Fabian Staubach, Alan O. Bergland, Dmitri A. Petrov, Brian P. Lazzaro & Paul S. Schmidt
Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes across a range of taxa. Here, we use immune defence in natural populations of Drosophila melanogaster to understand the rate of evolution in natural populations and the genetics underlying rapid change. We probed the immune system using the natural...

Data from: Community composition and diversity of Neotropical root-associated fungi in common and rare trees

John W. Schroeder, Jessica T. Martin, Diego F. Angulo, Jomar M. Barbosa, Ramón Perea, Itzel Arias-Del Razo, Esther Sebastián-González & Rodolfo Dirzo
Interactions between plants and root-associated fungi can affect the assembly, diversity, and relative abundances of tropical plant species. Host-symbiont compatibility and some degree of host specificity are prerequisites for these processes to occur, and these prerequisites may vary with host abundance. However, direct assessments of whether specificity of root-associated fungi varies with host abundance are lacking. Here, in a diverse tropical forest in Los Tuxtlas, Mexico, we couple DNA metabarcoding with a sampling design that...

Data from: Scale‐dependent spatial patterns in benthic communities around a tropical island seascape

Eoghan A. Aston, Gareth J. Williams, J. A. Mattias Green, Andrew J. Davies, Lisa M. Wedding, Jamison M. Gove, Jean-Baptiste Jouffray, Timothy T. Jones & Jeanette Clark
Understanding and predicting patterns of spatial organization across ecological communities is central to the field of landscape ecology, and a similar line of inquiry has begun to evolve sub‐tidally among seascape ecologists. Much of our current understanding of the processes driving marine community patterns, particularly in the tropics, has come from small‐scale, spatially‐discrete data that are often not representative of the broader seascape. Here we expand the spatial extent of seascape ecology studies and combine...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: CO2 enrichment and soil type additively regulate grassland productivity

H. Wayne Polley, Michael J. Aspinwall, Harold P. Collins, Anne E. Gibson, Richard A. Gill, Robert B. Jackson, Virginia L. Jin, Albina R. Khasanova, Lara G. Reichmann & Philip A. Fay
Atmospheric CO2 enrichment usually increases aboveground productivity (ANPP) of grassland vegetation, but the magnitude of the ANPP-CO2 response differs among ecosystems. Soil properties affect ANPP via multiple mechanisms and vary over topographic to geographic gradients, but have received little attention as potential modifiers of the ANPP-CO2 response. We assessed effects of three soil types, sandy loam, silty clay, and clay, on the ANPP response of perennial C3/C4 grassland communities to a subambient to elevated CO2...

Data from: Abiotic and habitat drivers of tick vector abundance, diversity, phenology and human encounter risk in southern California

Andrew J. MacDonald
The distribution, abundance and seasonal activity of vector species, such as ticks and mosquitoes, are key determinants of vector-borne disease risk, and are strongly influenced by abiotic and habitat conditions. Despite the numerous species of tick vectors in the heavily populated North American West Coast, all but Ixodes pacificus, the primary vector of the Lyme disease spirochete, is poorly characterized with regard to seasonal activity patterns and fine scale drivers of distribution and abundance, particularly...

Registration Year

  • 2018
    44

Resource Types

  • Dataset
    44

Affiliations

  • Stanford University
    44
  • University of California, Santa Barbara
    5
  • University of Michigan-Ann Arbor
    3
  • University of Chicago
    3
  • Cornell University
    3
  • Bangor University
    2
  • University of Massachusetts Amherst
    2
  • University of Pennsylvania
    2
  • University of Washington
    2
  • University of California System
    2