50 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.

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 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.,...

Pathotype complexity and genetic characterization of Phytophthora sojae populations in Illinois, Indiana, Kentucky, and Ohio

Linda Hebb, Carl A. Bradley, Santiago Xavier Mideros, Darcy E. P. Telenko, Kiersten Wise & Anne Elizabeth Dorrance
Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960’s, but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps gene(s) were still effective and identifying possible population clusters. There...

Diversification of a polyploid complex: the biogeography and acoustic communication evolution of North American gray treefrogs throughout the Quaternary

William Booker, Emily Lemmon, Alan Lemmon, Margaret Ptacek, Alyssa Hassinger, Johannes Schul & H. Carl Gerhardt
Polyploid speciation and whole genome duplications are major drivers of biological diversity. After polyploid species are formed, the interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this...

Phenotype data, genotype input files, and scripts related to adaptation in wild house mice from Western North America

Kathleen Ferris, Andreas Chavez, Taichi Suzuki, Megan Phifer-Rixey, Ke Bi, Michael Nachman & Elizabeth Beckman
Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America....

Raw images for bead aggregation assays - Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent

Michelle Gray, Debadrita Modak, Elakkiya Tamilselvan & Marcos Sotomayor
Intermicrovillar links are formed by two non-classical members of the cadherin superfamily of calcium-dependent cell adhesion proteins: protocadherin-24 (PCDH24, also known as CDHR2) and the mucin-like protocadherin (CDHR5). Images in this data set are for bead aggregations assays used to identify the PCDH24 and CDHR5 domains involved in both heterophilic and homophilic adhesion for human and mouse proteins.

Reevaluating the species status of the southern ghost pipe, Monotropa brittonii (Ericaceae)

Ashley Keesling, John Freudenstein & Michael Broe
Relationships among members of Ericaceae subfamily Monotropoideae have been notoriously difficult to resolve due to convergent evolution in these parasitic plants. All species in this subfamily are fully mycoheterotrophic, meaning they obtain nutrients by parasitizing fungi rather than through photosynthesis. Here, we examine relationships and host specificity in one of the most widespread species in this subfamily, Monotropa uniflora L. We use several lines of evidence to investigate whether there is support for recognizing a...

Adaptation without specialization early in a host shift: fecundity data

Rafael Rodriguez, Thomas Wood, Frank Stearns, Robert Snyder, Kelley Tilmon, Michael Cast, Randy Hunt & Reginald Cocroft
Students of speciation debate the role of performance trade-offs across different environments early in speciation. We tested for early performance trade-offs with a host shift experiment using a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae). In this clade of plant-feeding insects, different species live on different host plants and exhibit strong behavioral and physiological host specialization. After five generations, the experimental host shifts resulted either in no adaptation or in adaptation...

Indoor dust as a matrix for surveillance of COVID-19 outbreaks

Nicole Renninger, Nick Nastasi, Ashleigh Bope, Samuel Cochran, Sarah Haines, Neeraja Balasubrahmaniam, Katelyn Stuart, Aaron Bivins, Kyle Bibby, Natalie Hull & Karen Dannemiller
Ongoing disease surveillance is a critical tool to mitigate viral outbreaks, especially during a pandemic. Environmental monitoring has significant promise even following widespread vaccination among high-risk populations. The goal of this work is to demonstrate molecular SARS-CoV-2 monitoring in bulk floor dust and related samples as a proof-of-concept of a non-invasive environmental surveillance methodology for COVID-19 and potentially other viral diseases. Surface swab, passive sampler, and bulk floor dust samples were collected from rooms of...

Genomic signatures of inbreeding and mutation load in a threatened rattlesnake

Alexander Ochoa & H. Lisle Gibbs
Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long-term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load...

Identifying traits that enable lizard adaptation to different habitats

Flávia Lanna, Guarino Colli, Frank Burbrink & Bryan Carstens
Aim: Species adapt differently to contrasting environments, such as open habitats with sparse vegetation and forested habitats with dense forest cover. We investigated colonization patterns in the open and forested environments in the Diagonal of Open Formations and surrounding rain forests (i.e., Amazon and Atlantic Forest) in Brazil, tested whether the diversification rates were affected by the environmental conditions, and identified traits that enabled species to persist in those environments. Location: South America, Brazil. Taxon:...

Wild bumble bee colony abundance, scaled by field size, predicts pollination services

Shelby Fleischer, James Strange, Margarita Lopez-Uribe & Carley McGrady
Although bee visitation rate to flowers is often used to assess both pollination services and bee abundance, the abundance of social species needs to be assessed by quantifying the number of colonies instead of the number of foraging individuals. Because accurately quantifying the number of wild bee colonies can be difficult, the relationship of visitation rates provided by foragers and the abundance of colonies contributing those foragers from the surrounding landscape is poorly documented for...

Evolution of moult-migration is directly linked to aridity of the breeding grounds in North American passerines

Claudie Pageau, Christopher Tonra, Mateen Shaikh, Nancy Flood, Matthew Reudink, Christopher M. Tonra, Nancy J. Flood & Matthew W. Reudink
To avoid energy allocation conflicts, birds generally separate breeding, migration and moult during the annual cycle. North American passerines typically moult on the breeding grounds prior to autumn migration. However, some have evolved a moult-migration strategy in which they delay moult until stopping over during autumn migration. Rohwer et al . (2005) proposed the ‘push–pull hypothesis' as an explanation for the evolution of this moult strategy, but it has not been empirically tested. Poor conditions...

A non-native earthworm shifts the seed predation dynamics of a native weed

Stephen Hovick, Emilie Regnier, Jianyang Liu, S. Kent Harrison & Florian Diekmann
Seed predators both consume and disperse seeds, with important consequences for the population dynamics of many plant species. The net effect of multiple seed predators depends on the relative proportion of the seed pool each predator obtains, and this proportion should reflect species-specific habitat preferences. We studied the effect of the non-native earthworm, Lumbricus terrestris, on seed loss dynamics in the native weed, Ambrosia trifida (giant ragweed). Giant ragweed seeds are predated by mice, but...

The role of shade in maintaining alternative stable states between open- and closed-canopy vegetation

Simon Power, G. Anthony Verboom, William Bond, Kirsten Packer & Michael Cramer
Fire is commonly identified as strong driver of alternative stable states such as adjacent open- versus closed-canopy vegetation types. The absence of open-canopy species from closed-canopy understoreys, where light availability is low and dynamic, however, suggests shade tolerance is an integral determinant of such vegetation boundaries. While the importance of light dynamics between alternative stable states has been acknowledged, the physiological mechanisms behind sun versus shade-tolerance are unclear. Here we investigated the differences in light...

An integrated phylogenetic reassessment of the parasitoid superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) results in a revised familial classification

Chen Huayan, Lahey Zachary, Elijah J. Talamas, Alejandro A. Valerio, Ovidiu A. Popovici, Luciana Musetti, Hans Klompen, Andrew Polaszek, Lubomír Masner, Andrew D. Austin & Norman F. Johnson
The superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) is a diverse group of parasitoid wasps that attack nine orders of insects as well as spiders. They appear to show a clear pattern of host group specificity among genera. A robust phylogeny is essential to understanding the monophyly of and relationships among lower level groups and the pattern of the shifts among host groups. We conducted phylogenetic analyses of Platygastroidea based on four molecular markers (18S, 28S, COI, and...

Supplemental movies for the analysis of biofilm detachment using a novel rotating-disc rheometry method

Erin Gloag
Supplemental Movie 1: Adapted rotating-disc rheometry measurement. Left panel is a recording of the rheometry measurement for an untreated 5 d S. gordonii biofilm. Right panel indicates the corresponding torque – angular velocity data collection. Individual frames from the time-lapse depicting separate biofilm detachment events are displayed in Fig 2. Timestamp is indicated in the top left-hand corner (min : s). Playback rate is at 15 fps. Supplemental Movie 2: Transformed data collection. Left panel...

Data and R scripts from: Which factors determine the long-term effect of poor early-life nutrition? A meta-analytic review

L. Zoe Almeida, Stephen Hovick, Stuart Ludsin & Elizabeth Marschall
Early-life conditions can have long-lasting effects (experiential legacies) on an individual’s performance. Experiential legacies are an important source of variation among mature individuals because responses to early-life environments vary widely. Yet, the factors influencing the magnitudes and directions of phenotypic responses to experiential legacies are poorly understood, hindering our ability to predict adult phenotypes and population-level consequences of environmental stressors. To better understand these issues, we examined how experiential legacies varied with the type of...

Community phylogeographic patterns reveal how a barrier filters and structures taxa in North American warm deserts

Kaiya Provost, Edward A. Myers & Brian Smith
Aim: The study of biogeographic barriers has been instrumental in understanding the evolution and distribution of taxa. With the increasing availability of empirical datasets, emergent patterns can be inferred from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data across a barrier and perform spatially-explicit simulations to quantify spatiotemporal patterns of divergence, the influence of species traits on these patterns, and the statistical power needed to differentiate alternative diversification...

Pseudomonas aeruginosa biofilm killing beyond the spacer by antibiotic-loaded calcium sulfate beads: An in vitro study raw data

Paul Stoodley & Jacob Brooks
Introduction: Bacterial biofilms are an important virulence factor in chronic periprosthetic joint infection (PJI) and other orthopedic infection since they are highly tolerant to antibiotics and host immunity. Antibiotics are mixed into carriers such as bone cement and calcium sulfate bone void fillers to achieve sustained high concentrations of antibiotics required to more effectively manage biofilm infections through local release. The effect of antibiotic diffusion from antibiotic-loaded calcium sulfate beads (ALCS-B) in combination with PMMA...

Evolution of winter moulting strategies in European and North American migratory passerines

Claudie Pageau, Jared Sonnleitner, Christopher M. Tonra, Mateen Shaikh & Matthew W. Reudink
Moult is critical for birds as it replaces damaged feathers and worn plumage, enhancing flight performance, thermoregulation, and communication. In passerines, moult generally occurs on the breeding grounds during the post-breeding period once a year. However, some species of migrant passerines that breed in the Nearctic and western Palearctic regions have evolved different moulting strategies that involve moulting on the overwintering grounds. Some species forego moult on the breeding grounds and instead complete their prebasic...

Files used in the analyses from A role of asynchrony of seasons in explaining genetic differentiation in a Neotropical toad

Maria Tereza Thomé
The process of diversification can be studied at the phylogeographic level by attempting to identify the environmental features that promote and maintain population divergence. Here we investigate diversification in Rhinella granulosa, a Neotropical toad from northeastern Brazil, by testing a range of hypotheses that encompass different putative mechanisms reducing gene flow among populations. We sequenced single nucleotide polymorphisms and examined individual predictions related to the role of geographic barriers (rivers), ecological gradients, historical habitat stability,...

10-year trends reveal declining quality of seeded pollinator habitat on reclaimed mines regardless of seed mix diversity

Andrew Lybbert, Sarah Cusser, Keng-Lou Hung & Karen Goodell
Plant-pollinator interactions represent a crucial ecosystem function threatened by anthropogenic landscape alterations. Disturbances that reduce plant diversity are associated with floral resource and pollinator declines. Establishing wildflower plantings is a major conservation strategy targeting pollinators, the success of which depends on long-term persistence of seeded floral communities. However, most pollinator-oriented seeding projects are monitored for a few years, making it difficult to evaluate the longevity of such interventions. Selecting plant species to provide pollinators diverse...

Registration Year

  • 2021

Resource Types

  • Dataset


  • The Ohio State University
  • Thompson Rivers University
  • University of Missouri
  • United States Geological Survey
  • American Museum of Natural History
  • Cornell University
  • Ohio Department of Natural Resources
  • Nationwide Children's Hospital
  • Sun Yat-sen University
  • Estación Biológica de Doñana