280 Works

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: 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: 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: Phylogenomics supports incongruence between ecological specialization and taxonomy in a charismatic clade of buck moths

Julian R. Dupuis, Richard S. Peigler, Scott M. Geib & Daniel Rubinoff
Local adaptation can be a fundamental component of speciation, but its dynamics in relation to gene flow are not necessarily straightforward. Herbivorous taxa with localized host plant or habitat specialization across their geographic range are ideal models for investigating the patterns and constraints of local adaptation and its impact on diversification. The charismatic, day-flying moths of the Hemileuca maia species complex (Lepidoptera: Saturniidae) are such taxa, as they are geographically-widespread, exhibit considerable ecological and morphological...

Data from: Long-term agroecosystem research in the Central Mississippi River Basin: Goodwater Creek Experimental Watershed and regional herbicide water quality data

R. N. Lerch, C. Baffaut, E. J. Sadler & R. J. Kremer
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://doi.org/10.2134/jeq2013.12.0518. Goodwater Creek Experimental Watershed (GCEW) has been the focus area of a long-term effort to document the extent of and to understand the factors controlling herbicide transport. We document the datasets generated in the 20-yr-long research effort to study the transport of herbicides to surface and groundwater in the GCEW. This long-term effort was augmented with a spatially broad effort within...

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: Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

Kaitlin C. Maguire, Douglas J. Shinneman, Kevin M. Potter & Valerie D. Hipkins
Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of...

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: 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: 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: Genetic diversity of Chamaecrista fasciculata (Fabaceae) from the USDA germplasm collection

Erika Bueno, Theodore Kisha, Sonja L. Maki, Eric J. B. Von Wettberg & Susan R. Singer
Objective: Chamaecrista fasciculata is a widespread annual legume across Eastern North America, with potential as a restoration planting, biofuel crop, and genetic model for non-papillinoid legumes. As a non-Papilinoid, C. fasciculata, belongs to the Caesalpiniod group in which nodulation likely arose independently of the nodulation in Papilinoid and Mimosoid legumes. Thus, C. fasciculata is an attractive model system for legume evolution. In this study, we describe population structure and genetic diversity among 32 USDA germplasm...

Data from: Functional responses in habitat selection: clarifying hypotheses and interpretations

Joseph D. Holbrook, Lucretia E. Olson, Nicholas J. DeCesare, Mark Hebblewhite, John R. Squires & Robin Steenweg
A fundamental challenge in habitat ecology and management is understanding the mechanisms generating animal distributions. Studies of habitat selection provide a lens into such mechanisms, but are often limited by unrealistic assumptions. For example, most studies assume that habitat selection is constant with respect to the availability of resources, such that habitat use remains proportional to availability. To the contrary, a growing body of work has shown the fallacy of this assumption, indicating that animals...

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: 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: Spatial, temporal, and experimental: three study design cornerstones for establishing defensible numeric criteria in freshwater ecosystems

Jason M. Taylor, Jeffrey A. Back, Bryan W. Brooks & Ryan S. King
1.Nutrient over‐enrichment increasingly threatens global water resources. Stressor‐response studies specifically designed to identify levels of nutrients strongly associated with undesirable ecological conditions are needed to inform numeric nutrient criteria that protect inland waters. 2.Diatoms are important components of aquatic life, which support higher trophic levels and are sensitive to nutrient enrichment. We tested a framework that relies on stressor‐response modelling of phosphorus (P) enrichment and stream diatom assemblages across many field locations, multiple years and...

Data from: Identification of resistance to bacterial leaf blight in the U.S. Department of Agriculture Collard Collection

Sandra E. Branham, Mark W. Farnham, Shane M. Robinson & W. Patrick Wechter
Bacterial leaf blight incited by Pseudomonas cannabina pv. alisalensis (Pca) is a devastating disease with incidence reports worldwide and a wide host range capable of infecting all commercially valuable Brassica crops. With no chemical control options available, the most effective form of disease control is host plant resistance, but thus far resistant germplasm has only been identified in Brassica juncea L. (mustard greens). We report the first screening of Brassica oleracea L. var. viridis germplasm,...

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: 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: 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: Thermal history of alfalfa leafcutting bees affects nesting and diapause incidence

Kayla Earls, Kendra Greenlee, Monique Porter & Joseph Rinehart
Variable spring temperatures may expose developing insects to sublethal conditions, resulting in long-term consequences. The alfalfa leafcutting bee, Megachile rotundata, overwinters as a prepupa inside a brood cell, resuming development in spring. During these immobile stages of development, bees must tolerate unfavourable temperatures. In this study, we test how exposure to low temperature stress during development affects subsequent reproduction and characteristics of the F1 generation. Developing male and female M. rotundata were exposed to either...

Tree species of wet tropical forests differ in their tissue biochemistry and effects on soil carbon dynamics

Ann Russell, Rachel Marek & Daniel Olk
Given the hypothesized effects on soil organic matter (SOM) of polyphenols in plant tissues, differences among tree species in their biochemical composition could influence the turnover and accrual of SOM in various ways. The extent to which the biochemical composition of leaf and fine-root tissues differ among tropical tree species, and the effects on soil dynamics, are largely undocumented, however. We used cupric oxide analyses of plant tissues and soil in long-term, replicated, mono-dominant 15-yr-old...

Omnivory in predatory ladybird beetles is widespread and driven by an appetite for sterols

Todd Ugine, Stuart Krasnoff & Spencer Behmer
1. Animals maintain physiological and behavioral systems that allow them to detect and consume specific macro- and micronutrients to maximize their fitness. One common physiological system is the nutrient-state-dependent or demand-driven appetite. These systems are well described for macronutrient regulation, but not for micronutrients. 2. Sterols are essential micronutrients that all animals need to survive. They are the backbone of many hormones, important in cell signaling, and an integral component of cell membranes. 3. Lady...

Novel fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

Dominique Pincot, Mitchell Feldmann, Michael Hardigan, Mishi Vachev, Peter Henry, Thomas Gordon, Marta Bjornson, Alan Rodriguez, Nicolas Cobo, Randi Famula, Glenn Cole, Gitta Coaker & Steven Knapp
Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria x ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse...

Data from: Corn stover removal responses on soil test P and K levels in Coastal Plain Ultisols

Jeffrey Novak, James Frederick, Donald Watts, Thomas Ducey & Douglas Karlen
This is digital research data corresponding to a published manuscript, Corn stover removal responses on soil test P and K levels in Coastal Plain Ultisols, in Sustainability. 2021. 13:4401. Corn (Zea mays L.) stover is used as a biofuel feedstock in the U.S. Selection of stover harvest rates for soils is problematic, however, because excessive stover removal may have consequences on plant available phosphorus (P) and potassium (K) concentrations. Our objective was to quantify stover...

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