55 Works

Data from: Next generation lineage discovery: a case study of tuberous Claytonia L.

Thomas R. Stoughton, Ricardo Kriebel, Diana D. Jolles & Robin L. O'Quinn
PREMISE OF THE STUDY: Species formation is an intuitive endpoint of reproductive isolation, but circumscribing taxa that arise during speciation can be difficult because of gene flow, morphological continuity, hybridization or polyploidization, and low sequence variation among newly diverged lineages. Nonetheless, species complexes are ubiquitous and their classification is essential for understanding how diversity influences ecosystem function. METHODS: We used modern sequencing technology to identify lineages of perennial Claytonia L., and assessed correspondence between genetic...

Data from: Inference of adaptive shifts for multivariate correlated traits

Paul Bastide, Cecile Ane, Stéphane Robin & Mahendra Mariadassou
To study the evolution of several quantitative traits, the classical phylogenetic comparative framework consists of a multivariate random process running along the branches of a phylogenetic tree. The Ornstein-Uhlenbeck (OU) process is sometimes preferred to the simple Brownian Motion (BM) as it models stabilizing selection toward an optimum. The optimum for each trait is likely to be changing over the long periods of time spanned by large modern phylogenies. Our goal is to automatically detect...

Data from: Phylogeography, population genetics, and distribution modeling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change.

Daniel Spalink, Ron MacKay & Kenneth J. Sytsma
A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modeling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as...

Data from: Social brain volume is associated with in-degree social network size among older adults

Seyul Kwak, Won-Tak Joo, Yoosik Youm & Jeanyung Chey
The social brain hypothesis proposes that large neocortex size evolved to support cognitively demanding social interactions. Accordingly, previous studies have observed that larger orbitofrontal and amygdala structures predict the size of an individual's social network. However, it remains uncertain how an individual's social connectedness reported by other people is associated with the social brain volume. In this study, we found that a greater in-degree network size, a measure of social ties identified by a subject's...

Data from: Genetic analysis of sugarcane mosaic virus resistance in the Wisconsin Diversity Panel of maize

Timothy J. Gustafson, Natalia De Leon, Shawn M. Kaeppler & William F. Tracy
Sugarcane mosaic virus (SCMV) and Maize dwarf mosaic virus can cause yield loss in maize (Zea mays L.). Previous studies identified two key genomic regions controlling host resistance: Scmv1 on chromosome 6 and Scmv2 on chromosome 3. In this study a diverse set of 578 inbreds adapted to a northern US Corn Belt environment, was inoculated at the three-leaf stage with SCMV and rated for presence of virus symptoms at 7, 10, 14, 21, 28,...

Data from: Harvesting effects on wild bee communities in bioenergy grasslands depend on nesting guild

Brian J. Spiesman, Ashley Bennett, Rufus Isaacs & Claudio Gratton
Conversion of annual crops to native perennial grasslands for bioenergy production may help conserve wild bees by enhancing nest and food resources. However, bee response to the disturbance of biomass harvesting may depend on their nesting location, thus their vulnerability to nest destruction, and the response of the forb community on which they forage. Moreover, because bees have long foraging ranges, effects of local harvesting may depend on the amount of natural habitat in the...

Data from: Crop rotational diversity enhances belowground communities and functions in an agroecosystem

L. K. Tiemann, A. S. Grandy, E. E. Atkinson, E. Marin-Spiotta & M. D. McDaniel
Biodiversity loss, an important consequence of agricultural intensification, can lead to reductions in agroecosystem functions and services. Increasing crop diversity through rotation may alleviate these negative consequences by restoring positive aboveground–belowground interactions. Positive impacts of aboveground biodiversity on belowground communities and processes have primarily been observed in natural systems. Here, we test for the effects of increased diversity in an agroecosystem, where plant diversity is increased over time through crop rotation. As crop diversity increased...

Data from: Genetic dissection of hybrid male sterility across stages of spermatogenesis

Denise J. Schwahn, Richard J. Wang, Michael A. White & Bret A. Payseur
Hybrid sterility is a common form of reproductive isolation between nascent species. Although hybrid sterility is routinely documented and genetically dissected in speciation studies, its developmental basis is rarely examined, especially in generations beyond the F1. To identify phenotypic and genetic determinants of hybrid male sterility from a developmental perspective, we characterized testis histology in 312 F2 hybrids generated by intercrossing inbred strains of Mus musculus domesticus and M. m. musculus, two subspecies of house...

Data from: Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: implications for gene discovery

Scott A. Woolbright, Brian J. Rehill, Richard L. Lindroth, Stephen P. DiFazio, Gregory D. Martinsen, Mathew S. Zinkgraf, Gerard J. Allan, Paul Keim, Thomas G. Whitham & Matthew S. Zinkgraf
Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0...

Data from: Development and validation of a weather-based warning system to advise fungicide applications to control dollar spot on turfgrass

Damon L. Smith, James P. Kerns, Nathan R. Walker, Andrea F. Payne, Brandon Horvath, John C. Inguagiato, John E. Kaminski, Maria Tomaso-Peterson & Paul L. Koch
Dollar spot is one of the most common diseases of golf course turfgrass and numerous fungicide applications are often required to provide adequate control. Weather-based disease warning systems have been developed to more accurately time fungicide applications; however, they tend to be ineffective and are not currently in widespread use. The primary objective of this research was to develop a new weather-based disease warning system to more accurately advise fungicide applications to control dollar spot...

Data from: Dynamic colonization history in a rediscovered Isle Royale carnivore

Philip J. Manlick, Mark C. Romanksi & Jonathan N. Pauli
Island ecosystems are globally threatened, and efforts to restore historical communities are widespread. Such conservation efforts should be informed by accurate assessments of historical community composition to establish appropriate restoration targets. Isle Royale National Park is one of the most researched island ecosystems in the world, yet little is actually known about the biogeographic history of most Isle Royale taxa. To address this uncertainty and inform restoration targets, we determined the phylogeographic history of American...

Data from: Seed traits, not density or distance from parent, determine seed predation and establishment in an Afrotropical forest

Cooper Rosin & John R. Poulsen
Seed predators drive patterns in seed mortality and seedling establishment and are posited to contribute to the maintenance of plant species diversity through several mechanisms. Negative density dependence and spatially-restricted recruitment are apparently widespread in Neotropical forests, but are little studied in Afrotropical forests, where generalist vertebrates may contribute more to seed mortality than do specialized invertebrates and fungi. We experimentally assessed the roles of seed density and distance from the parent tree for ten...

Data from: Hungry for the queen: honeybee nutritional environment affects worker pheromone response in a life stage‐dependent manner

Alexander Walton, Adam G. Dolezal, Marit A. Bakken & Amy L. Toth
1.Animal nutritional state can profoundly affect behavior, including an individual's tendency to cooperate with others. We investigated how nutritional restriction at different life stages affects cooperative behavior in a highly social species, Apis mellifera honey bees. 2.We found that nutritional restriction affects a worker's queen pheromone response, a behavioral indicator of investment in group vs. individual reproduction. Nutritional restriction at the larval stage led to reduced ovary size and increased queen pheromone response, whereas nutritional...

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: Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels

Matheus Baseggio, Matthew Murray, Maria Magallanes-Lundback, Nicholas Kaczmar, James Chamness, Edward Buckler, Margaret Smith, Dean DellaPenna, William Tracy, Michael Gore, Margaret E. Smith, Michael A. Gore, William F. Tracy & Edward S. Buckler
Sweet corn (Zea mays L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels, but makes limited contribution to daily intake of vitamin E and antioxidants. We performed a genome-wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes associated with natural variation for tocochromanols and vitamin E in fresh kernels. Concordant with prior studies in...

Data from: Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding

Joseph L. Gage, Michael R. White, Jode W. Edwards, Shawn Kaeppler & Natalia De Leon
Inflorescence capacity plays a crucial role in reproductive fitness in plants, and in production of hybrid crops. Maize is a monoecious species bearing separate male and female flowers (tassel and ear, respectively). The switch from open-pollinated populations of maize to hybrid-based breeding schemes in the early 20th century was accompanied by a dramatic reduction in tassel size, and the trend has continued with modern breeding over the recent decades. The goal of this study was...

Data from: Eprinomectin from a sustained release formulation adversely affected dung breeding insects

Christine C. Nieman, Kevin D. Floate, Rolf-Alexander During, Andre P. Heinrich, Daniel K. Young & Daniel M. Schaefer
The insecticidal activity of parasiticide residues in dung of cattle treated with a sustained release eprinomectin formulation was examined, and an improved eprinomectin dung residue extraction method is presented. Emergent insect abundance and richness were significantly reduced in all post-treatment intervals (7, 14, 28, 56, 84, 112, and 140 d), relative to pre-treatment. Emergent insect diversity was reduced for between 84 and 112 d post-treatment. Collembola were not affected by residues. Chemical analyses subsequently documented...

Data from: Does habitat fragmentation promote climate-resilient phenotypes?

Christopher E. Latimer, Sheldon J. Cooper, William H. Karasov & Benjamin Zuckerberg
Understanding how individual differences in physiological performance modify behavioral responses to environmental variability and its fitness consequences is key to predicting the vulnerability of species and populations to environmental change. For many species, summit metabolic rate (M); the upper limit to heat production) and basal metabolic rate (BMR; the lower limit related to energy acquisition and processing) often constrain aspects of physiological performance and behavioral activity. We examined the relationship between metabolic phenotypes, foraging behavior,...

Data from: Catch diversification provides multiple benefits in inland fisheries

Shin-Ichiro S. Matsuzaki, Ryuichiro Shinohara, Kei Uchida & Takehiro Sasaki
1. Diversification of fisheries and agroecosystems can increase and stabilize production and revenue, despite unpredictable changes in ecosystems and markets. Recent work suggests that diversification can provide multiple benefits simultaneously, but empirical evidence of relationships between catch or crop diversification and the provision of multiple benefits is scarce. The effect of diversification on multiple benefits may vary temporally and among systems. 2. Using long-term (11–54 years) capture fishery statistics from five Japanese lakes, we examined...

Data from: Minimizing polymerase biases in metabarcoding

Ruth V. Nichols, Christopher Vollmers, Lee A. Newsom, Yue Wang, Peter D. Heintzman, McKenna Leighton, Richard E. Green & Beth Shapiro
DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or “barcode”, from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of...

Data from: Directional selection reduces developmental canalization against genetic and environmental perturbations in Drosophila wings

Benjamin R. Groth, Yuheng Huang, Matthew J. Monette & John E. Pool
Natural selection may enhance or weaken the robustness of phenotypes against genetic or environmental perturbations. However, important aspects of the relationship between adaptive evolution and canalization remain unclear. Recent work showed that the evolution of larger wing size in a high altitude natural population of Drosophila melanogaster was accompanied by decanalized wing development – specifically a loss of robustness to genetic perturbation. But this study did not address environmental robustness, and it compared populations that...

Data from: Non-invasive measurement of metabolic rates in wild, free-living birds using doubly labelled water

Amanda R. Bourne, Andrew E. McKechnie, Susan J. Cunningham, Amanda R. Ridley, Stephan M. Woodborne & William H. Karasov
1. Doubly labelled water (DLW) is routinely used to measure energy expenditure and water turnover in free-ranging animals. Standard methods involve capture, blood sampling for baseline measurement, injection with isotopic tracers, captivity for an equilibration period, post-dose blood sampling, release, and subsequent re-capture for final blood sampling. Single sampling methods that minimise disturbance by reducing capture and handling time have been developed and tested. Sampling faeces rather than blood could further reduce disturbance to study...

Data from: Delaying conservation actions matters for species vulnerable to climate change

Ilona Naujokaitis-Lewis, Lars Y. Pomara & Benjamin Zuckerberg
1. Most climate change adaptation efforts emphasize where to implement management actions, whereas timing remains largely overlooked. The rate of modern climate change introduces urgency in evaluating whether delaying conservation actions compromises their efficacy for reaching important conservation targets. 2. We evaluated the importance of multiple climate change adaptation strategies including timing of actions on preventing extinctions for a threatened climate-sensitive species, the Eastern Massasauga rattlesnake (Sistrurus catenatus). We parameterised a range-wide population viability analysis...

Data from: Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment

Huan Fan, Anthony R. Ives & Yann Surget-Groba
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment-free methods are...

Data from: Independent and interactive effects of plant genotype and environment on plant traits and insect herbivore performance: a meta-analysis with Salicaceae

Hilary L. Barker, Liza M. Holeski & Richard L. Lindroth
1. Ecological research has increasingly highlighted the importance of intraspecific variation in shaping the structure and function of communities and ecosystems. Indeed, the effects of intraspecific variation can match or exceed those of interspecific variation. Previous reviews of intraspecific variation in plant traits across heterogeneous environments have focused primarily on mean phenotypic effects. We propose that a richer and fuller understanding of the ecological causes and consequences of intraspecific variation would be provided by partitioning...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Wisconsin-Madison
  • Michigan State University
  • Northern Arizona University
  • Iowa State University
  • Columbia University
  • Duke University
  • University of Georgia
  • University of Alberta
  • Texas A&M University
  • McGill University