500 Works

Malicious Pathogen-spreading During COVID-19

P.B. Crabb
Among the distressing events of the early months of the COVID-19 pandemic in 2020 was the appearance of news reports of atypical acts of aggression all over the world. This study tested the hypothesis that the aversive conditions of the early months of the pandemic triggered a type of interpersonal aggression that may be called aggressive pathogen-spreading: spitting, coughing, and sneezing bodily fluids on a target person with the goal of causing distress and/or infection....

Data from: Opening the door to the past: accessing phylogenetic, pathogen, and population data from museum curated bees

Anthony D. Vaudo, Megan L. Fritz & Margarita M. López-Uribe
Tens of thousands of insects are deposited in collections every year as a result of survey-based studies that aim to investigate ecological questions. DNA-based techniques can expand the utility of these collections to explore their demographic and evolutionary history, temporal changes in their abundance, and pathogen dynamics. Using museum collections of the non-model bee species Eucera (Peponapis) pruinosa Say 1837 (Hymenoptera: Apidae: Eucerini), we developed a standard minimally-destructive and budget-friendly protocol to extract DNA and...

Data from: Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts

Daniel James Thornhill, Allison M. Lewis, Drew C. Wham & Todd Christopher LaJeunesse
Bursts in species diversification are well documented among animals and plants, yet few studies have assessed recent adaptive radiations of eukaryotic microbes. Consequently, we examined the radiation of the most ecologically dominant group of endosymbiotic dinoflagellates found in reef-building corals, Symbiodinium Clade C, using nuclear ribosomal (ITS2), chloroplast (psbAncr), and multilocus microsatellite genotyping. Through a hierarchical analysis of high-resolution genetic data, we assessed whether ecologically distinct Symbiodinium, differentiated by seemingly equivocal rDNA sequence differences, are...

Data from: Resource limitation prevents the emergence of drug resistance by intensifying within-host competition

Nina Wale, Derek G. Sim, Matthew J. Jones, Rahel Salathe, Troy Day & Andrew F. Read
Slowing the evolution of antimicrobial resistance is essential if we are to continue to successfully treat infectious diseases. Whether a drug-resistant mutant grows to high densities, and so sickens the patient and spreads to new hosts, is determined by the competitive interactions it has with drug-susceptible pathogens within the host. Competitive interactions thus represent a good target for resistance management strategies. Using an in vivo model of malaria infection, we show that limiting a resource...

Data from: ‘Manipulation’ without the parasite: altered feeding behaviour of mosquitoes is not dependent on infection with malaria parasites

Lauren J. Cator, Justin George, Simon Blanford, Courtney C. Murdock, Thomas C. Baker, Andrew F. Read & Matthew B. Thomas
Previous studies have suggested that Plasmodium parasites can manipulate mosquito feeding behaviours such as probing, persistence and engorgement rate in order to enhance transmission success. Here, we broaden analysis of this ‘manipulation phenotype’ to consider proximate foraging behaviours, including responsiveness to host odours and host location. Using Anopheles stephensi and Plasmodium yoelii as a model system, we demonstrate that mosquitoes with early stage infections (i.e. non-infectious oocysts) exhibit reduced attraction to a human host, whereas...

Data from: Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral

Daniel T. Pettay, Jorge H. Pinzón, Drew C. Wham & Todd C. LaJeunesse
Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral-algal symbioses. The fine-scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intra-colony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in...

Data from: The influence of symbiotic bacteria on reproductive strategies and wing polyphenism in pea aphids responding to stress

Miguel L. Reyes, Alice M. Laughton, Benjamin James Parker, Hannah Wichmann, Maretta Fan, Daniel Sok, Jan Hrcek, Tarik Acevedo & Nicole M. Gerardo
1. Environmental stressors can be key drivers of phenotypes, including reproductive strategies and morphological traits. The response to stress may be altered by the presence of microbial associates. For example, in aphids, facultative (secondary) bacterial symbionts can provide protection against natural enemies and stress induced by elevated temperatures. Furthermore, aphids exhibit phenotypic plasticity, producing winged (rather than wingless) progeny that may be better able to escape danger, and the combination of these factors improve the...

Data from: Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data

Frances E. Buderman, Duane R. Diefenbach, Mary J. Casalena, Christopher S. Rosenberry & Bret D. Wallingford
The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data...

Data from: Cascading effects of host plant inbreeding on the larval growth, muscle molecular composition, and flight capacity of an adult herbivorous insect.

Scott L. Portman, Rupesh R. Kariyat, Michelle A. Johnston, Andrew G. Stephenson & James H. Marden
A primary function of adult winged insects is dispersal. Limiting larval dietary intake (partial starvation) has been shown to affect the flight muscle metabolism of adult moths reared on artificial diet, but a more ecologically relevant question is whether natural variation in host plant quality can lead to differences in the flight capacity of adult insects. Recent studies have shown that inbreeding compromises plant anti-herbivore defenses. We created inbred and outbred progeny from locally collected...

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: Diagnostic pathways and direct medical costs incurred by new adult pulmonary tuberculosis patients prior to anti-tuberculosis treatment – Tamil Nadu, India

Karun Sandeep Veesa, Kamalabhai Russell John, Patrick K. Moonan, Saravanakumar Puthupalayam Kaliappan, Krishna Manjunath, Karuna D. Sagili, Chinnappareddy Ravichandra, Pradeep Aravindan Menon, Chandrakumar Dolla, Nancy Luke, Kaivan Munshi, Kuryan George & Shantidani Minz
Background: Tuberculosis (TB) patients face substantial delays prior to treatment initiation, and out of pocket (OOP) expenditures often surpass the economic productivity of the household. We evaluated the pre-diagnostic cost and health seeking behaviour of new adult pulmonary TB patients registered at Primary Health Centres (PHCs) in Vellore district, Tamil Nadu, India. Methods: This descriptive study, part of a randomised controlled trial conducted in three rural Tuberculosis Units from Dec 2012 to Dec 2015, collected...

Data from: Calcareous nannoplankton ecology and community change across the Paleocene-Eocene Thermal Maximum

Leah J. Schneider, Timothy J. Bralower, Lee R. Kump & Mark E. Patzkowsky
The Paleocene-Eocene Thermal Maximum (PETM; ca. 55.8 Ma) is thought to coincide with a profound but entirely transient change among nannoplankton communities throughout the ocean. Here we explore the ecology of nannoplankton during the PETM by using multivariate analyses of a global data set that is based upon the distribution of taxa in time and space. We use these results, coupled with stable isotope data and geochemical modeling, to reinterpret the ecology of key genera....

Data from: Sibling species of mutualistic Symbiodinium clade G from bioeroding sponges in the western Pacific and western Atlantic oceans

Blake D. Ramsby, Malcolm S. Hill, Daniel J. Thornhill, Sieuwkje F. Steenuizen, Michelle Achlatis, Allison M. Lewis, Todd C. LaJeunesse & Sieuwkje F. Steenhuizen
Dinoflagellates in the genus Symbiodinium associate with a broad array of metazoan and protistian hosts. Symbiodinium-based symbioses involving bioeroding sponge hosts have received less attention than those involving scleractinian hosts. Certain species of common Cliona harbor high densities of an ecologically restricted group of Symbiodinium, referred to as Clade G. The relationships of these unusual Clade G Symbiodinium with Foraminifera, sponges, and black coral (Antipatharia) are rarely studied. Nonetheless, analyses of genetic evidence indicate that...

Data from: Restoration of pyrethroid susceptibility in a highly resistant Aedes aegypti population

Marissa K. Grossman, Valentin Uc-Puc, Julian Rodriguez, David J. Culter, Levi T. Morran, Pablo Manrique-Saide, Gonzalo M. Vazquez-Prokopec & David J. Cutler
Insecticide resistance has evolved in disease vectors worldwide, creating the urgent need to either develop new control methods or restore insecticide susceptibility to regain the use of existing tools. Here we show that phenotypic susceptibility can be restored in a highly resistant field-derived strain of Aedes aegypti in only ten generations through rearing them in the absence of insecticide.

Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits

Gerrit Angst, Kevin E. Mueller, David M. Eissenstat, Susan Trumbore, Katherine H. Freeman, Sarah E. Hobbie, Jon Chorover, Jacek Oleksyn, Peter B. Reich & Carsten W. Mueller
Rising atmospheric CO2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40‐year‐old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and...

Data from: The significance of prey avoidance behaviour for the maintenance of a predator colour polymorphism

Helena Ajuria Ibarra, Michael Kinahan, Julien Marcetteau, Andrew J.R. Mehigan, Ross O. Ziegelmeier, Tom Reader & Andrew J R Mehigan
The existence of conspicuous colour polymorphisms in animals provides an ideal opportunity to examine the mechanisms which determine genetic and phenotypic variation in populations. It is well known that directional and negative frequency-dependent selection by predators can influence the persistence of colour polymorphisms in their prey, but much less attention has been paid to the idea that prey behaviour could generate selection on predator colour morphs. In this study, we examine the role that avoidance...

Data from: Neonicotinoid insecticide travels through a soil food chain, disrupting biological control of non-target pests and decreasing soya bean yield

Margaret R. Douglas, Jason R. Rohr & John F. Tooker
1. Neonicotinoids are the most widely used insecticides world-wide, but their fate in the environment remains unclear, as does their potential to influence non-target species and the roles they play in agroecosystems. 2. We investigated in laboratory and field studies the influence of the neonicotinoid thiamethoxam, applied as a coating to soya bean seeds, on interactions among soya beans, non-target molluscan herbivores and their insect predators. 3. In the laboratory, the pest slug Deroceras reticulatum...

Data from: Persistent chaos of measles epidemics in the prevaccination United States caused by a small change in seasonal transmission patterns

Benjamin D. Dalziel, Ottar N. Bjornstad, Willem G. Van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell & Ottar N. Bjørnstad
Epidemics of infectious diseases often occur in predictable limit cycles. Theory suggests these cycles can be disrupted by high amplitude seasonal fluctuations in transmission rates, resulting in deterministic chaos. However, persistent deterministic chaos has never been observed, in part because sufficiently large oscillations in transmission rates are uncommon. Where they do occur, the resulting deep epidemic troughs break the chain of transmission, leading to epidemic extinction, even in large cities. Here we demonstrate a new...

Data from: Real-time decision-making during emergency disease outbreaks

William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher J. Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari & Michael J. Tildesley
In the event of a new infectious disease outbreak, mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic. In the early stages of such outbreaks, substantial parameter uncertainty may limit the ability of models to provide accurate predictions, and policymakers do not have the luxury of waiting for data to alleviate this state of uncertainty. For policymakers, however, it is the selection...

Data from:A computational study of cancer hyperthermia based on vascular magnetic nanoconstructs

Mahdi Nabil & Paolo Zunino
The application of hyperthermia to cancer treatment is studied using a novel model arising from the fundamental principles of flow, mass and heat transport in biological tissues. The model is defined at the scale of the tumour microenvironment and an advanced computational scheme called the embedded multiscale method is adopted to solve the governing equations. More precisely, this approach involves modelling capillaries as one-dimensional channels carrying flow, and special mathematical operators are used to model...

Data from: Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana

J. Grey Monroe, Cullen McGovern, Jesse R. Lasky, Kelsi Grogan, James Beck & John K. McKay
The evolutionary processes and genetics underlying local adaptation at a specieswide level are largely unknown. Recent work has indicated that a frameshift mutation in a member of a family of transcription factors, C-repeat binding factors or CBFs, underlies local adaptation and freezing tolerance divergence between two European populations of Arabidopsis thaliana. To ask whether the specieswide evolution of CBF genes in Arabidopsis is consistent with local adaptation, we surveyed CBF variation from 477 wild accessions...

Data from: Symbiodinium glynnii sp. nov., a species of stress-tolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean

Drew C. Wham, Gang Ning & Todd C. LaJeunesse
A formal Symbiodinium species taxonomy enhances understanding of the physiology and ecology of coral–dinoflagellate symbioses. Here we formally define a new species of stress tolerant Symbiodinium in Clade D, Symbiodinium glynnii sp. nov. This species exhibits high host specificity for members of the stony coral genus Pocillopora in the Pacific Ocean and can also be found in symbiosis with the coral genera Seriatopora and Montipora. Symbiodinium glynnii is especially common in the Eastern Tropical and...

Data from: Seeing spots: quantifying mother-offspring similarity and assessing fitness consequences of coat pattern traits in a wild population of giraffes (Giraffa camelopardalis)

Derek E. Lee, Douglas R. Cavener & Monica L. Bond
Polymorphic phenotypes of mammalian coat coloration have been important to the study of genetics and evolution, but less is known about the inheritance and fitness consequences of individual variation in complex coat pattern traits such as spots and stripes. Giraffe coat markings are highly complex and variable and it has been hypothesized that variation in coat patterns most likely affects fitness by camouflaging neonates against visually hunting predators. We quantified complex coat pattern traits of...

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

Michael R. McKain, Norman Wickett, Yeting Zhang, Saravanaraj Ayyampalayam, W. Richard McCombie, Mark W. Chase, J. Chris Pires, Claude W. DePamphilis, Jim Leebens-Mack & Claude W. De Pamphilis
PREMISE OF THE STUDY: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next Generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were...

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