298 Works

Data from: Progressive genome-wide introgression in agricultural Campylobacter coli

Samuel K. Sheppard, Xavier Didelot, Keith A. Jolley, Aaron E. Darling, David J. Kelly, Alison Cody, Frances M. Colles, Norval J.C. Strachan, Iain D. Ogden, Ken Forbes, Nigel P. French, Philip Carter, William G. Miller, Noel D. McCarthy, Robert Owen, Eva Litrup, Michael Egholm, Stephen D. Bentley, Julian Parkhill, Martin C. J. Maiden, Daniel Falush, Jason P. Affourtit, Norval J. C. Strachan, Ben Pascoe & Guillaume Meric
Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been...

Data from: Pest tradeoffs in technology: reduced damage by caterpillars in Bt cotton benefits aphids

Steffen Hagenbucher, Felix L. Wäckers, Felix E. Wettstein, Dawn M. Olson, John R. Ruberson, Jörg Romeis & F. L. Wackers
The rapid adoption of genetically engineered (GE) plants that express insecticidal Cry proteins derived from Bacillus thuringiensis (Bt) has raised concerns about their potential impact on non-target organisms. This includes the possibility that non-target herbivores develop into pests. Although studies have now reported increased populations of non-target herbivores in Bt cotton, the underlying mechanisms are not fully understood. We propose that lack of herbivore-induced secondary metabolites in Bt cotton represents a mechanism that benefits non-target...

Data from: Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

Andrew J. Eckert, Andrew D. Bower, Kathleen D. Jermstad, Jill L. Wegrzyn, Brian J. Knaus, John V. Syring & David B. Neale
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life-history strategies as they influence the effective population size (Ne). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne. An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among...

Data from: A combined parasitological-molecular approach for non-invasive characterization of parasitic nematode communities in wild hosts

Sarah A. Budischak, Eric P. Hoberg, Art Abrams, Anna E. Jolles & Vanessa O. Ezenwa
Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity...

Data from: Global invasion history of the Tropical Fire Ant: a stowaway on the first global trade routes

Dietrich Gotzek, Heather Axen, Andrew Suarez, Sara Helms Cahan, D. DeWayne Shoemaker, Andrew V. Suarez & Heather J. Axen
Biological invasions are largely thought to be contemporary, having recently increased sharply in the wake of globalization. However, human commerce had already become global by the mid-16th century when the Spanish connected the New World with Europe and Asia via their Manila galleon and West Indies trade routes. We use genetic data to trace the global invasion of one of the world's most widespread and invasive pest ants, the Tropical Fire Ant, Solenopsis geminata. Our...

Data from: Disruption of gene expression in hybrids of the fire ants Solenopsis invicta and Solenopsis richteri

Lino Ometto, Kenneth G. Ross, D. DeWayne Shoemaker & Laurent Keller
Transcriptome analysis is a powerful tool for unveiling the distribution and magnitude of genetic incompatibilities between hybridizing taxa. The nature of such incompatibilities is closely associated with the evolutionary histories of the parental species and may differ across tissues and between the sexes. In eusocial insects, the presence of castes that experience divergent selection regimes may result in additional distinct patterns of caste-specific hybrid incompatibilities. We analyzed levels of expression of >14,000 genes in two...

Data from: Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil

Rodrigo N. Graça, Amy L. Ross-Davis, Ned B. Klopfenstein, Mee-Sook Kim, Tobin L. Peever, Philip G. Cannon, Cristina P. Aun, Eduardo S. G. Mizubuti & Acelino C. Alfenas
The rust fungus, Puccinia psidii, is a devastating pathogen of introduced eucalypts (Eucalyptus spp.) in Brazil where it was first observed in 1912. This pathogen is hypothesized to be endemic to South and Central America and to have first infected eucalypts via a host jump from native guava (Psidium guajava). Ten microsatellite markers were used to genotype 148 P. psidii samples from eucalypts and guava plus five additional myrtaceous hosts across a wide geographic range...

Data from: Predator community structure and trophic linkage strength to a focal prey

Jonathan G. Lundgren & Janet K. Fergen
Predator abundance and community structure can increase or decrease the suppression of lower trophic levels, although studies of these interactions under field conditions are relatively few. We investigated how the frequency of consumption (measured using PCR-based gut analysis) is affected by predator abundance, community diversity and evenness under realistic conditions. Soil arthropod communities in sixteen maize fields were measured (number of predators, diversity [Shannon H], and evenness [J]) and predator guts were searched for DNA...

Data from: Studying long-term, large-scale grassland restoration outcomes to improve seeding methods and reveal knowledge gaps

Matthew J. Rinella, Erin K. Espeland & Bruce J. Moffatt
Studies are increasingly investigating effects of large-scale management activities on grassland restoration outcomes. These studies are providing useful comparisons among currently used management strategies, but not the novel strategies needed to rapidly improve restoration efforts. Here we illustrate how managing restoration projects adaptively can allow promising management innovations to be identified and tested. We studied 327 Great Plains fields seeded after coal mining. We modelled plant responses to management strategies to identify the most effective...

Data from: Inferring invasive species abundance using removal data from management actions

Amy J. Davis, Mevin B. Hooten, Ryan S. Miller, Matthew L. Farnsworth, Jesse Lewis, Michael Moxcey & Kim M. Pepin
Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and...

Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Roswitha Schmickl, Aaron Liston, Vojtěch Zeisek, Kenneth Oberlander, Kevin Weitemier, Shannon C. K. Straub, Richard C. Cronn, Léanne L. Dreyer & Jan Suda
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African...

Data from: SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation

Chao Li, Geoff Waldbieser, Brian Bosworth, Benjamin H. Beck, Wilawan Thongda & Eric Peatman
Blue catfish, Ictalurus furcatus, are valued in the United States as a trophy fishery for their capacity to reach large sizes, sometimes exceeding 45 kg. Additionally, blue catfish × channel catfish (I. punctatus) hybrid food fish production has recently increased the demand for blue catfish broodstock. However, there has been little study of the genetic impacts and interaction of farmed, introduced and stocked populations of blue catfish. We utilized genotyping-by-sequencing (GBS) to capture and genotype...

Data from: Reduced mycorrhizal responsiveness leads to increased competitive tolerance in an invasive exotic plant

Lauren P. Waller, Ragan M. Callaway, John N. Klironomos, Yvette K. Ortega & John L. Maron
Arbuscular mycorrhizal (AM) fungi can exert a powerful influence on the outcome of plant–plant competition. Since some exotic plants interact differently with soil biota such as AM fungi in their new range, range-based shifts in AM responsiveness could shift competitive interactions between exotic and resident plants, although this remains poorly studied. We explored whether genotypes of the annual exotic Centaurea solstitialis (yellow starthistle), collected from populations across the native and non-native ranges, differed in responsiveness...

Data from: Minimally invasive collection of adipose tissue facilitates the study of eco-physiology in small-bodied mammals

Jeff Clerc, Theodore J. Weller, Jeffrey B. Schineller & Joseph M. Szewczak
Adipose tissue is the primary fuel storage for vertebrates and is an important component of energy budgets during periods of peak energetic demands. Investigating the composition of adipose tissue can provide information about energetics, migration, reproduction and other life-history traits. Until now, most field methods for sampling adipose tissue of small-bodied vertebrates have been destructive. Therefore, investigations of adipose tissue in small-bodied vertebrates have been limited in their broadscale application. We developed a field-ready micro-adipose...

Data from: Climate, demography, and zoogeography predict introgression thresholds in Salmonid hybrid zones in Rocky Mountain streams

Michael K. Young, Daniel J. Isaak, Kevin S. McKelvey, Taylor M. Wilcox, Daniel M. Bingham, Kristine L. Pilgrim, Kellie J. Carim, Matthew R. Campbell, Matthew P. Corsi, Dona E. Horan, David L. Nagel, Michael K. Schwartz, Dona L. Horan & David E. Nagel
Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream...

Data from: Pyrodiversity promotes avian diversity over the decade following forest fire

Morgan W. Tingley, Viviana Ruiz-Gutierrez, Robert L. Wilkerson, Christine A. Howell & Rodney B. Siegel
An emerging hypothesis in fire ecology is that pyrodiversity increases species diversity. We test whether pyrodiversity—defined as the standard deviation of fire severity—increases avian biodiversity at two spatial scales, and whether and how this relationship may change in the decade following fire. We use a dynamic Bayesian community model applied to a multi-year dataset of bird surveys at 1106 points sampled across 97 fires in montane California. Our results provide strong support for a positive...

Data from: Tracking global change using lichen diversity: towards a global-scale ecological indicator

Paula Matos, Linda Geiser, Amanda Hardman, Doug Glavich, Pedro Pinho, Alice Nunes, Amadeu M. V. M. Soares, Cristina Branquinho & Amadeu M.V.M. Soares
Lichens have been used to efficiently track major drivers of global change from the local to regional scale since the beginning of the industrial revolution (sulphur dioxide) to the present (nitrogen deposition and climate change). Currently, the challenge is to universalize monitoring methodologies to compare global change drivers’ simultaneous and independent effects on ecosystems and to assess the efficacy of mitigation measures. Because two protocols are now used at a continental scale North America (US)...

Data from: Machine learning for characterization of insect vector feeding

Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski & Stephen L. Lapointe
Insects that feed by ingesting plant and animal fluids cause devastating damage to humans, livestock, and agriculture worldwide, primarily by transmitting pathogens of plants and animals. The feeding processes required for successful pathogen transmission by sucking insects can be recorded by monitoring voltage changes across an insect-food source feeding circuit. The output from such monitoring has traditionally been examined manually, a slow and onerous process. We taught a computer program to automatically classify previously described...

Data from: Density-dependent vulnerability of forest ecosystems to drought

Alessandra Bottero, Anthony W. D'Amato, Brian J. Palik, John B. Bradford, Shawn Fraver, Michael A. Battaglia, Lance A. Asherin & Mike A. Battaglia
Climate models predict increasing drought intensity and frequency for many regions, which may have negative consequences for tree recruitment, growth, and mortality, as well as forest ecosystem services. Furthermore, practical strategies for minimizing vulnerability to drought are limited. Tree population density, a metric of tree abundance in a given area, is a primary driver of competitive intensity among trees, which influences tree growth and mortality. Manipulating tree population density may be a mechanism for moderating...

Data from: Maternal and nourishment factors interact to influence offspring developmental trajectories in social wasps

Jennifer M. Jandt, Sainath Suryanarayanan, John C. Hermanson, Robert L. Jeanne & Amy L. Toth
The social and nutritional environments during early development have the potential to affect offspring traits, but the mechanisms and molecular underpinnings of these effects remain elusive. We used Polistes fuscatus paper wasps to dissect how maternally controlled factors (vibrational signals and nourishment) interact to induce different caste developmental trajectories in female offspring, leading to worker or reproductive (gyne) traits. We established a set of caste phenotype biomarkers in P. fuscatus females, finding that gyne-destined individuals...

Data from: Ecosystem engineering strengthens bottom-up and weakens top-down effects via trait-mediated indirect interactions

Zhiwei Zhong, Xiaofei Li, Dean Pearson, Deli Wang, Dirk Sanders, Yu Zhu & Ling Wang
Trophic interactions and ecosystem engineering are ubiquitous and powerful forces structuring ecosystems, yet how these processes interact to shape natural systems is poorly understood. Moreover, trophic effects can be driven by both density- and trait-mediated interactions. Microcosm studies demonstrate that trait-mediated interactions may be as strong as density-mediated interactions, but the relative importance of these pathways at natural spatial and temporal scales is underexplored. Here, we integrate large-scale field experiments and microcosms to examine the...

Data from: A comparison of individual-based genetic distance metrics for landscape genetics

Andrew J. Shirk, Erin L. Landguth & Samuel A. Cushman
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes, and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between...

Data from: Native grass ground covers provide multiple ecosystem services in Californian vineyards

Kent M. Daane, Brian N. Hogg, Houston Wilson & Glenn Y. Yokota
1. The mechanisms responsible for the success or failure of agricultural diversification are often unknown. Most studies of arthropod pest management focus on enhancing the effectiveness of natural enemies, but non-crop plants can also improve or hamper pest suppression by changing the host quality of crop plants by reducing or adding available soil nutrients or water. Native perennial ground covers may provide resources and long-term habitat to resident natural enemies and be more compatible than...

Data from: Identification of candidate effector genes of Pratylenchus penetrans

Paulo Vieira, Thomas Mayer, Sebastian Eves-Van Den Akker, Dana K. Howe, Inga Zasada, Thomas Baum, Jonathan D. Eisenback, Kathryn Kamo, Thomas R. Maier & Thomas J. Baum
Pratylenchus penetrans is one of the most important species among root lesion nematodes (RLNs) due to the detrimental and economic impact that it causes in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbors a significant number of secreted proteins that play key roles during parasitism. Here we combined spatially and temporally resolved next generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the...

Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Mark Eric Benbow, Philip S. Barton, Michael D. Ulyshen, James C. Beasley, Travis L. DeVault, Michael S. Strickland, Jeffery K. Tomberlin, Heather R. Jordan & Jennifer L. Pechal
Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has...

Registration Year

  • 2022
    12
  • 2021
    19
  • 2020
    49
  • 2019
    25
  • 2018
    48
  • 2017
    25
  • 2016
    36
  • 2015
    28
  • 2014
    18
  • 2013
    12

Resource Types

  • Dataset
    289
  • Text
    9

Affiliations

  • United States Department of Agriculture
    297
  • Cornell University
    25
  • University of Florida
    22
  • University of Montana
    19
  • Oregon State University
    16
  • University of Georgia
    15
  • Colorado State University
    14
  • University of Minnesota
    13
  • University of Washington
    9
  • Iowa State University
    9