33 Works

Data from: A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error

Jesus A. Ballesteros & Prashant P. Sharma
Horseshoe crabs (Xiphosura) are traditionally regarded as sister to the clade of terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent phylogenomic analyses, but the non-monophyly of Arachnida has consistently been disregarded as artifactual. We reevaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic dataset to date, expanding outgroup sampling and including data from whole genome sequencing projects. In spite of uncertainty in theplacement of some arachnid clades, all analyses show...

Data from: Monitoring vultures in the 21st century: the need for standardized protocols

Paula L. Perrig, Sergio A. Lambertucci, Emiliano Donadio, Julian Padro & Jonathan N. Pauli
This article calls on scientists, managers and organizations focused on vulture conservation to promote and use standardized monitoring programs based on sampling of molted feathers.

Fluorescent biomarkers demonstrate prospects for spreadable vaccines to control disease transmission in wild bats

Kevin Bakker, Tonie Rocke, Rachel Abbott, Carlos Tello, Jorge Carrera, William Valderrama, Carlos Shiva, Nestor Falcon, Jorge Osorio & Daniel Streicker
Vaccines that autonomously transfer among individuals have been proposed as a strategy to control infectious diseases within wildlife populations. However, understanding rates of spread and epidemiological efficacy in real world systems remain elusive. Here, we investigated whether topical vaccines that transfer among bats through social contacts can control vampire bat rabies, a medically and economically important zoonosis in Latin America. Field experiments in 3 Peruvian bat colonies which used fluorescent biomarkers as a proxy for...

Estimating correlations among demographic parameters in population models

Thomas Riecke, Alan Leach, James Sedinger, Benjamin Sedinger & Perry Williams
Estimating correlations among demographic parameters is critical to understanding population dynamics and life-history evolution, where correlations among parameters can inform our understanding of life-history trade-offs, result in effective applied conservation actions, and shed light on evolutionary ecology. The most common approaches rely on the multivariate normal distribution, and its conjugate inverse Wishart prior distribtion. However, the inverse Wishart prior for the covariance matrix of multivariate normal distributions has a strong influence on posterior distributions. As...

Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Rachel H. Toczydlowski & Donald M. Waller
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within...

Data from: Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance

Marie Duhamel, Joe Wan, Laura Bogar, Richard Segnitz, Nora Duncritts & Kabir Peay
Because interactions between plants and microbial organisms can influence species diversity and rates of nutrient cycling, how plants shape microbial communities is fundamental to understanding the structure of ecosystems. Despite this, the spatial and temporal scales over which plants influence microbial communities is poorly understood, particularly whether past abiotic or biotic legacies strongly constrain microbial community development. We examined biogeochemical cycling and microbial community structure in a coastal landscape where historical patterns of vegetation transition...

Data from: Reduced IgG titers against pertussis in rheumatoid arthritis: evidence for a citrulline-biased immune response and medication effects

Caitlyn L. Holmes, Chloe G. Peyton, Amy M. Bier, Tobias Z. Donlon, Fauzia Osman, Christie M. Bartels & Miriam A. Shelef
Background: The antibody response to pertussis vaccination in rheumatoid arthritis is unknown, a concerning omission given the relatively low efficacy of the pertussis vaccine, a rise in pertussis infections, and a general increased susceptibility to infection in rheumatoid arthritis. Additionally, the contributions from an intrinsically dysregulated immune system in rheumatoid arthritis and immune-suppressing medications to the response to pertussis vaccination is poorly defined. This study examines antibody titers against pertussis in vaccinated rheumatoid arthritis patients...

Data from: Land-use and climatic causes of environmental novelty in Wisconsin since 1890

John W. Williams, Kevin D. Burke, Michael S. Crossley, Daniel A. Grant & Volker C. Radeloff
Multiple global change drivers are increasing the present and future novelty of environments and ecological communities. However, most assessments of environmental novelty have focused only on future climate and were conducted at scales too broad to be useful for land management or conservation. Here, using historical county-level datasets of agricultural land use, forest composition, and climate, we conduct a regional-scale assessment of environmental novelty for Wisconsin landscapes from ca. 1890 to 2012. Agricultural land-use data...

Data from: Top-down effects of repatriating bald eagles hinder jointly recovering competitors

Jennyffer Cruz, Steven K. Windels, Wayne E. Thogmartin, Shawn M. Crimmins, Leland H. Grim, James H. Larson & Benjamin Zuckerberg
1. The recovery of piscivorous birds around the world is touted as one of the great conservation successes of the 21st century, but for some species, this success was short-lived. Bald eagles, ospreys, and great blue herons began repatriating Voyageurs National Park, USA, in the mid-20th century. However, after 1990, only eagles continued their recovery, while osprey and heron recovery failed for unknown reasons. 2. We aimed to evaluate whether top-down effects of bald eagles,...

Data from: Energy landscape for the insertion of amphiphilic nanoparticles into lipid membranes: a computational study

Reid C. Van Lehn & Alfredo Alexander-Katz
Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown to enter cells via a non-endocytic, non-disruptive pathway that could be valuable for biomedical applications. The same NPs were also found to insert into a series of model cell membranes as a precursor to cellular uptake, but the insertion mechanism remains unclear. Previous simulations have demonstrated that an amphiphilic NP can insert into a single leaflet of a planar lipid bilayer, but in this configuration all charged...

Data from: Genome-wide association analysis of stalk biomass and anatomical traits in maize

Mona Mazaheri, Marlies Heckwolf, Brieanne Vaillancourt, Joseph L. Gage, Brett Burdo, Sven Heckwolf, Kerrie Barry, Anna Lipzen, Camila Bastos Ribeiro, Thomas J. Y. Kono, Heidi F. Kaeppler, Edgar P. Spalding, Candice N. Hirsch, C. Robin Buell, Natalia De Leon & Shawn M. Kaeppler
Background: Maize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk...

Data from: Influence of climate change and post-delisting management on long-term population viability of the conservation-reliant Kirtland’s warbler

Donald Brown, Deahn Donner, Christine A. Ribic & Carol Bocetti
Rapid global climate change is resulting in novel abiotic and biotic conditions and interactions. Identifying management strategies that maximize probability of long-term persistence requires an understanding of the vulnerability of species to environmental changes. We sought to quantify the vulnerability of Kirtland’s Warbler (Setophaga kirtlandii), a rare Neotropical migratory songbird that breeds almost exclusively in the Lower Peninsula of Michigan and winters in the Bahamian Archipelago, to projected environmental changes on the breeding and wintering...

Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Matheus Baseggio, Matthew Murray, Maria Magallanes-Lundback, Nicholas Kaczmar, James Chamness, Edward Buckler, Margaret Smith, Dean DellaPenna, William Tracy & Michael Gore
Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome-wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging from light to dark yellow in endosperm color to elucidate the genetic basis...

Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel

Joseph L. Gage, Brieanne Vaillancourt, John P. Hamilton, Norma C. Manrique-Carpintero, Timothy J. Gustafson, Kerrie Barry, Anna Lipzen, William F. Tracy, Mark A. Mikel, Shawn M. Kaeppler, C. Robin Buell & Natalia De Leon
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence/absence variations (PAVs). In this study, we present the draft de novo genome assembly of PHJ89, an Oh43-type inbred line. Using three separate reference genome assemblies (B73, PH207, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate...

Data from: Linking plant genes to insect communities: identifying the genetic bases of plant traits and community composition

Hilary L. Barker, Jennifer F. Riehl, Carolina Bernhardsson, Kennedy Rubert-Nason, Liza Holeski, Pär K. Ingvarsson & Richard L. Lindroth
Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen, endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To...

Data from: Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

Ricardo Kriebel, Bryan T. Drew, Chloe P. Drummond, Jesús Guadalupe González Gallegos, Ferhat Celep, Mohamed M. Mahdjoub, Jeffrey P. Rose, Chun-Lei Xiang, Guo-Xiong Hu, Jay B. Walker, Emily M. Lemmon, Alan R. Lemmon & Kenneth J. Sytsma
Premise of the Study: A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega‐genus Salvia. Methods: A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of...

Ordered phylogenomic subsampling enables diagnosis of systematic errors in the placement of the enigmatic arachnid order Palpigradi

Jesús Ballesteros, Carlos Santibáñez López, Ľubomír Kováč, Efrat Gavish-Regev & Prashant Sharma
The miniaturized arachnid order Palpigradi has ambiguous phylogenetic affinities, due to its odd combination of plesiomorphic and derived morphological traits. This lineage has never been sampled in phylogenomic datasets because of its small body size and fragility of most species, a sampling gap of immediate concern to recent disputes over arachnid monophyly. To redress this gap, we sampled a population of the cave-inhabiting species Eukoenenia spelaea from Slovakia and inferred its placement in the phylogeny...

Data from: Forest structure and snow depth alter the movement patterns and subsequent expenditures of a forest carnivore, the Pacific marten

Marie Martin, Katie Moriarty & Jonathan Pauli
Energetic balance is central to the survival and persistence of free-ranging animals. Quantifying expenditures and identifying factors that drive energetics informs our understanding of species’ ecology and their responses to shifting environmental conditions. Approaches used to estimate energetic expenditures of free-ranging species, such as doubly-labelled water (DLW), are precise but difficult to implement. Global positioning system (GPS) collars and accelerometers have emerged as alternatives for estimating expenditures, but these techniques have few applications in terrestrial...

Data from: Meta-analytic and economic approaches for evaluation of pesticide impact on Sclerotinia stem rot control and soybean yield in the North Central U.S.

Jaime F. Willbur, Paul Mitchell, Mamadou L. Fall, Adam M. Byrne, Scott Chapman, Crystal M. Floyd, Carl A. Bradley, Keith Ames, Martin I. Chilvers, Nathan Kleczewski, Dean Malvick, Brian Mueller, Daren Mueller, Mehdi Kabbage, Shawn P. Conley & Damon Smith
As complete host resistance in soybean has not been achieved, Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum continues to be of major economic concern for farmers. Thus, chemical control remains a prevalent disease management strategy. Pesticide evaluations were conducted in Illinois, Iowa, Michigan, Minnesota, New Jersey, and Wisconsin from 2009 to 2016, for a total of 25 site-years (n = 2057 plot-level data points). These studies were used in network meta-analyses to evaluate the...

Data from: Linking the foraging behavior of three bee species to pollen dispersal and gene flow

Johanne Brunet, Yang Zhao & Murray K. Clayton
Foraging behaviors that impact gene flow can guide the design of pollinator strategies to mitigate gene flow. Reduced gene flow is expected to minimize the impact of genetically engineered (GE) crops on feral and natural populations and to facilitate the coexistence of different agricultural markets. The goal of this study is to link foraging behavior to gene flow and identify behaviors that can help predict gene flow for different bee species. To reach this goal,...

Data from: Meta-analysis of yield response of foliar fungicide-treated hybrid corn in the United States and Ontario, Canada

Kiersten A. Wise, Damon L. Smith, Anna Freije, Daren S. Mueller, Yuba Kandel, Tom Allen, Carl A. Bradley, Emmanuel Byamukama, Martin Chilvers, Travis Faske, Andrew Friskop, Clayton Hollier, Tamra A. Jackson-Ziems, Heather Kelly, Bob Kemerait, Paul Price, Alison Robertson & Albert Tenuta
Background: Foliar fungicide applications to corn (Zea mays) occur at one or more application timings ranging from early vegetative growth stages to mid-reproductive stages. Previous studies indicated that fungicide applications are profitable under high disease pressure when applied during the tasseling to silking growth stages. Few comprehensive studies in corn have examined the impact of fungicide applications at an early vegetative growth stage (V6) compared to late application timings (VT) for yield response and return...

Data from: The mechanisms affecting seedling establishment in restored savanna understories are seasonally dependent

Quinn M. Sorenson & Ellen I. Damschen
1. Globally, agricultural land is increasingly being abandoned with over 200 million hectares recovering from agricultural use. Regeneration of plant communities sharply differ in their structure and composition after agricultural impacts, yet the mechanisms underpinning these dramatic changes are poorly understood. It is critical to determine the relative importance of abiotic and biotic factors that limit plant establishment and success during the recovery process. In particular, belowground competition for resources in soils impacted by former...

Data from: Differing climatic mechanisms control transient and accumulated vegetation novelty in Europe and eastern North America

Kevin Burke, John Williams, Simon Brewer, Walter Finsinger, Thomas Giesecke, David Lorenz & Alejandro Ordonez
Understanding the mechanisms that produce novel ecosystems is of joint interest to conservation biologists and paleoecologists. Here, we define and differentiate transient from accumulated novelty and evaluate four climatic mechanisms proposed to cause species to reshuffle into novel assemblages: high climatic novelty, high spatial rates of change (displacement), high variance among displacement rates for individual climate variables, and divergence among displacement vector bearings. We use climate simulations to quantify climate novelty, displacement, and divergence across...

Climate induced stress and mortality in vervet monkeys

Christopher Young, Tyler Bonnell, Leslie Brown, Marcus Dostie, André Ganswindt, Stefan Kienzle, Richard McFarland, Peter Henzi & Louise Barrett
As the effects of global climate change become more apparent, animal species will become increasingly affected by extreme climate and its effect on the environment. There is a pressing need to understand animal physiological and behavioural responses to climatic stressors. We used the reactive scope model as a framework to investigate the influence of drought conditions on vervet monkey (Chlorocebus pygerythrus) behaviour, physiological stress and survival across 2.5-years in South Africa. Data were collected on...

Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community?

Sean Schoville, Rachel Slatyer, César Nufio & Lauren Buckley
Species responses to environmental change are likely to depend on existing genetic and phenotypic variation, as well as evolutionary potential. A key challenge is to determine whether gene flow might facilitate or impede genomic divergence among populations responding to environmental change, and if emergent phenotypic variation is limited by gene flow rates. A general expectation is that patterns of genetic differentiation in a set of co-distributed species reflect differences in dispersal ability. In less-dispersive species,...

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