230 Works

The Chemical Reaction Network Toolbox, Windows Version

Martin Feinberg, Phillipp Ellison, Haixia Ji & Daniel Knight
The Chemical Reaction Network Toolbox provides computer-supported assistance for the analysis of the behavior of complex chemical reaction networks. Its use and theoretical underpinnings are described, for example, in the monograph "Foundations of Chemical Reaction Network Theory" by Martin Feinberg, published in 2019 by Springer-Nature. The download is a zip file containing the Toolbox, a user's guide, and some sample network files.

Data for: The long-term impacts of deer herbivory in determining temperate forest stand and canopy structural complexity

Samuel Reed, Alejandro Royo, Alexander Fotis, Kathleen Knight, Charles Flower & Peter Curtis
1. Ungulates place immense consumptive pressure on forest vegetation globally, leaving legacies of reduced biodiversity and simplified vegetative structure. However, what remains unresolved is whether browse-induced changes occurring early in succession ultimately manifest themselves in the developed forest canopy. Understanding the development and persistence of these legacies is critical as canopy structure is an important determinant of forest ecosystem functions like carbon sequestration and wildlife habitat. 2. We measured how white-tailed deer (Odocoileus virginianus) browse...

Data from: A maximalist approach to the systematics of a biological control agent: Gryon aetherium Talamas, sp. nov. (Hymenoptera, Scelionidae)

Zachary Lahey
A morphological and molecular analysis of Gryon Haliday (Platygastroidea, Scelionidae) was conducted to provide a taxonomic and phylogenetic context for a species under evaluation as a biological control agent of Bagrada hilaris (Burmeister) (Hemiptera, Pentatomidae). Our analysis revealed that Gryon is polyphyletic and that the biological control agent is not G. gonikopalense, a name that was tentatively applied to this species in 2019. We here describe this species as new, Gryon aetherium Talamas sp. nov.,...

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

Population genetic structure and demographic history of the lone star tick, Amblyomma americanum (Ixodida: Ixodidae): new evidence supporting old records

Paula Lado, Megan Smith, Bryan Carstens & Hans Klompen
Range expansions are a potential outcome of climate change. Population genetic structure and demography can be used as tools to evaluate hypotheses on changes in geographic distribution. In this study we explored the genetic variability, population genetic structure, demographic history, and habitat suitability of Amblyomma americanum, a North American tick species that is a known vector of several pathogenic microorganisms. We used a novel double digestion restriction site-associated DNA sequencing (dd-RAD seq), and we discovered...

Mammals on mountainsides revisited: trait-based tests of assembly reveal the importance of abiotic filters

Brooks Kohli, Richard Stevens, Eric Rickart & Rebecca Rowe
Aim: Mountains provide uniquely informative systems for examining how biodiversity is distributed and identifying the causes of those patterns. Elevational patterns of species richness are well-documented for many taxa but comparatively few studies have investigated patterns in multiple dimensions of biodiversity along mountainsides, which can reveal the underlying processes at play. Here, we use trait-based diversity patterns to determine the role of abiotic filters and competition in the assembly of communities of small mammals across...

Data from: Benefits of turbid river plume habitat for Lake Erie yellow perch (Perca flavescens) recruitment determined by juvenile to larval genotype assignment

Lucia B. Carreon-Martinez, Ryan P. Walter, Timothy B. Johnson, Stuart A. Ludsin & Daniel D. Heath
Nutrient-rich, turbid river plumes that are common to large lakes and coastal marine ecosystems have been hypothesized to benefit survival of fish during early life stages by increasing food availability and (or) reducing vulnerability to visual predators. However, evidence that river plumes truly benefit the recruitment process remains meager for both freshwater and marine fishes. Here, we use genotype assignment between juvenile and larval yellow perch (Perca flavescens) from western Lake Erie to estimate and...

Data from: Do ecological communities disperse across biogeographic barriers as a unit?

Jordan D. Satler & Bryan C. Carstens
Biogeographic barriers have long been implicated as drivers of biological diversification, but how these barriers influence co-occurring taxa can vary depending on factors intrinsic to the organism and in their relationships with other species. Due to the interdependence among taxa, ecological communities present a compelling opportunity to explore how interactions among species may lead to a shared response to historical events. Here we collect single nucleotide polymorphism (SNP) data from five commensal arthropods associated with...

Data from: Historical species distribution models predict species limits in western Plethodon salamanders

Tara A. Pelletier, Charlie Crisafulli, Steve Wagner, Amanda J. Zellmer & Bryan C. Carstens
Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range,...

Data from: Particle backtracking improves breeding subpopulation discrimination and natal-source identification in mixed populations

Michael E. Fraker, Eric J. Anderson, Reed M. Brodnik, Lucia Carreon-Martinez, Kristen M. DeVanna, Brian J. Fryer, Daniel D. Heath, Julie M. Reichert & Stuart A. Ludsin
We provide a novel method to improve the use of natural tagging approaches for subpopulation discrimination and source-origin identification in aquatic and terrestrial animals with a passive dispersive phase. Our method integrates observed site-referenced biological information on individuals in mixed populations with a particle-tracking model to retrace likely dispersal histories prior to capture (i.e., particle backtracking). To illustrate and test our approach, we focus on western Lake Erie’s yellow perch (Perca flavescens) population during 2006–2007,...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Sub-lethal effects on fish provide insight into a biologically-relevant threshold of hypoxia

Allison R. Hrycik, L. Zoe Almeida & Tomas O. Hӧӧk
Hypoxia (low dissolved oxygen) is a mounting concern for aquatic ecosystems as its prevalence increases with rising anthropogenic nutrient inputs. Hypoxia is most commonly defined as 2.0 mg l–1 of dissolved oxygen, although this level varies widely across studies and agency regulations. Such definitions may be too conservative, as ecologically-relevant non-lethal effects (e.g. consumption and growth) of hypoxia on important aquatic species, such as fish, often occur at oxygen levels much higher than 2.0 mg...

Data from: Assembly patterns of mixed-species avian flocks in the Andes

Gabriel J. Z. Colorado, Amanda D. Rodewald & Gabriel J. Colorado
The relative contribution of deterministic and stochastic processes in the assembly of biotic communities is a central issue of controversy in community ecology. However, several studies have shown patterns of species segregation that are consistent with the hypothesis that deterministic factors such as competition and niche-partitioning structure species assemblages in animal communities. Community assembly provides a theoretical framework for understanding these processes, but it has been seldom applied to social aggregations within communities. In this...

Data from: Locomotor endurance predicts differences in realized dispersal between sympatric sexual and unisexual salamanders

Robert D. Denton, Katherine R. Greenwald & H. Lisle Gibbs
Dispersal is the central mechanism that determines connectivity between populations yet few studies connect the mechanisms of movement with realized dispersal in natural populations. To make such a link, we assessed how physiological variation among individuals predicted dispersal in natural populations of unisexual (all-female) and sexual Ambystoma salamanders on the same fragmented landscape in Ohio. Specifically, we assessed variation in a trait that influences long-distance animal movement (locomotor endurance) and determined whether variation in endurance...

Data from: An echinoderm Lagerstätte from the Upper Ordovician (Katian), Ontario: taxonomic re-evaluation and description of new dicyclic camerate crinoids

Selina R. Cole, William I. Ausich, David F. Wright & Joseph M. Koniecki
The Upper Ordovician (lower Katian) Bobcaygeon and Verulam formations from the Lake Simcoe region of Ontario contain a highly diverse echinoderm assemblage that is herein recognized as a Konservat-Lagerstätte. Although fossil crinoids have long been recognized from these formations, the fauna has not received a comprehensive taxonomic evaluation since Springer’s classic 1911 monograph. Recent extensive collection and preparation of new material from the Bobcaygeon and Verulam formations near Brechin, Ontario recovered numerous exceptionally preserved crinoid...

Data from: AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data

Michael G. Sovic, Anthony C. Fries & H. Lisle Gibbs
An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to...

Data from: Posterior predictive checks of coalescent models: P2C2M, an R package

Michael Gruenstaeudl, Noah M. Reid, Gregory L. Wheeler & Bryan C. Carstens
Bayesian inference operates under the assumption that the empirical data are a good statistical fit to the analytical model, but this assumption can be challenging to evaluate. Here, we introduce a novel r package that utilizes posterior predictive simulation to evaluate the fit of the multispecies coalescent model used to estimate species trees. We conduct a simulation study to evaluate the consistency of different summary statistics in comparing posterior and posterior predictive distributions, the use...

Data from: Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Paul D. Blischak, Laura S. Kubatko & Andrea D. Wolfe
Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty–ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population...

Data from: Community trees: identifying codiversification in the páramo dipteran community

Bryan Charles Carstens, Michael Gruenstaeudl & Noah M. Reid
Groups of codistributed species that responded in a concerted manner to environmental events are expected to share patterns of evolutionary diversification. However, the identification of such groups has largely been based on qualitative, post hoc analyses. We develop here two methods (PPS, K-F ANOVA) for the analysis of codistributed species that, given a group of species with a shared pattern of diversification, allow empiricists to identify those taxa that do not codiversify (i.e., "outlier" species)....

Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

Chathurani Ranathunge, Gregory L. Wheeler, Melody E. Chimahusky, Meaghan M. Kennedy, Jesse I. Morrison, Brian S. Baldwin, Andy D. Perkins & Mark E. Welch
The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted...

Data from: Genetic diversity in migratory bats: results from RADseq data for three tree bat species at an Ohio windfarm

Michael G. Sovic, Bryan C. Carstens & H. Lisle Gibbs
Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs within Lasiurus cinereus (Hoary Bat), L. borealis (Red Bat), and Lasionycteris noctivagans (Silver-Haired Bat) bats found at a wind turbine site in Ohio, and to also estimate demographic parameters in each of these three groups. Our specific goals...

Data from: Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species

Manolo Perez, Isabel A. S. Bonatelli, Evandro Moraes & Bryan C. Carstens
Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches...

Data from: Habitat patch use by fishers in the deciduous forest-dominated landscape of the central Appalachian Mountains, USA

Hance Ellington E., Sean W. Gess, Erin L. Koen, Joe Duchamp, Matthew Lovallo, Matthew R. Dzialak, Jeffrey Larkin, Joseph E. Duchamp & Jeffery L. Larkin
Fishers (Pekania pennanti) are often associated with the coniferous and mixed forests of the northern United States and central Canada, and their ecology has been studied extensively in portions of their distributional range. Recently, natural range expansion and reintroductions have led to recolonization by fishers of portions of the central Appalachian Mountains, USA, where deciduous forest is the dominant vegetation type. We used noninvasive hair snare surveys and microsatellite genetic analysis to detect fishers in...

Data from: Alteration of plant-species assemblages can decrease the transmission potential of malaria mosquitoes

Babak Ebrahimi, Bryan T. Jackson, Julie L. Guseman, Colin M. Przybylowicz, Christopher M. Stone & Woodbridge A. Foster
1. Knowledge of the link between a vector population’s pathogen-transmission potential and its biotic environment can generate more realistic forecasts of disease risk due to environmental change. It also can promote more effective vector control by both conventional and novel means 2. The present study assessed the effect of particular plant-species assemblages differing in nectar production on components of the vectorial capacity of the mosquito Anopheles gambiae s.s., an important vector of African malaria. 3....

Data from: Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

Michael G. Sovic, Anthony C. Fries & H. Lisle Gibbs
Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern...

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