14 Works

Data from: Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams

Rafael P. Leitão, Jansen Zuanon, David Mouillot, Cecília G. Leal, Robert M. Hughes, Philip R. Kaufmann, Sébastien Villéger, Paulo S. Pompeu, Daniele Kasper, Felipe R. De Paula, Silvio F. B. Ferraz & Toby A. Gardner
Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the...

A unifying framework for analyzing temporal changes in functional and taxonomic diversity along disturbance gradients

Erin Larson, N. Leroy Poff, W. Chris Funk, Rachel Harrington, Boris Kondratieff, Scott Morton & Alexander Flecker
Frameworks exclusively considering functional diversity are gaining popularity, as they complement and extend the information provided by taxonomic diversity metrics, particularly in response to disturbance. Taxonomic diversity should be included in functional diversity frameworks to uncover the functional mechanisms causing species loss following disturbance events. We present and test a predictive framework that considers temporal functional and taxonomic diversity responses along disturbance gradients. Our proposed framework allows us to test different multidimensional metrics of taxonomic...

Data from: Evaluating in vitro-in vivo extrapolation of toxicokinetics

John F. Wambaugh, Michael F. Hughes, Caroline L. Ring, Denise K. MacMillan, Jermaine Ford, Timothy R. Fennell, Sherry R. Black, Rodney W. Snyder, Nisha S. Sipes, Barbara Wetmore, Joost Westerhout, R. Woodrow Setzer, Robert Pearce, Jane-Ellen Simmons, Russell S. Thomas, Robert G Pearce, Barbara A Wetmore & Jane Ellen Simmons
Prioritizing the risk posed by thousands of chemicals potentially present in the environment requires exposure, toxicity, and toxicokinetic (TK) data, which are often unavailable. Relatively high throughput, in vitro TK (HTTK) assays and in vitro-to-in vivo extrapolation (IVIVE) methods have been developed to predict TK, but most of the in vivo TK data available to benchmark these methods are from pharmaceuticals. Here we report on new, in vivo rat TK experiments for 26 non-pharmaceutical chemicals...

Data from: Honey bees and neonicotinoid-treated corn seed: contamination, exposure, and effects

Chia-Hua Lin, Douglas Sponsler, Rodney Richardson, Harold Watters, Donna Glinski, W. Matthew Henderson, Jeffrey Minucci, E. Henry Lee, S. Thomas Purucker & Reed Johnson
Most corn (Zea mays) seeds planted in the US in recent years are coated with a seed treatment containing neonicotinoid insecticides. Abrasion of the seed coating generates insecticide-laden planter dust that disperses through the landscape during corn planting and has resulted in many ‘bee-kill’ incidents in North America and Europe. We investigated the linkage between corn planting and honey bee colony success in a region dominated by corn agriculture. Over three years we consistently observed...

Data from: Sex ratio of Western Bluebirds Sialia mexicana is mediated by phenology and clutch size

Andrew Bartlow, Mark Jankowski, Charles Hathcock, Randall Ryti, Steven Reneau & Jeanne Fair
Mothers may produce more of one sex to maximize their fitness if there are differences in the cost of producing each sex or there are differences in their relative reproductive value. We tested if breeding date, clutch size and drought conditions influenced offspring sex ratios in Western Bluebirds (Sialia mexicana) from 1997 to 2017. We found that hatch dates late in the breeding season were associated with the production of more females. When clutch size...

Shape matters: The relationship between cell geometry and diversity in phytoplankton

Alexey Ryabov, Onur Kerimoglu, Irina Olenina, Leonilde Roselli, Alberto Basset, Elena Stanca, Elena Litchman & Bernd Blasius
We compiled the most comprehensive data set of phytoplankton and other marine protists in terms of sizes, shapes, genus, and species names. Samples were obtained from seven globally distributed marine areas: Baltic Sea, North Atlantic (Scotland), Mediterranean Sea (Greece and Turkey), Indo-Pacific (the Maldives), South-western Pacific (Australia), Southern Atlantic (Brazil). See details in Ryabov et al Ecology Letters 'Shape matters: the relationship between cell geometry and diversity in phytoplankton', https://doi.org/10.1111/ele.13680

Data from: Demodifying RNA for transcriptomic analyses of archival formalin-fixed paraffin-embedded samples

Leah C. Wehmas, Charles E. Wood, Remi Gagne, Andrew Williams, Carole Yauk, Mark M. Gosink, Deidre Dalmas, Ruixin Hao, Raegan O'Lone & Susan Hester
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n=6/group) were divided...

The Alginate Immobilization of Metabolic Enzymes (AIME) platform retrofits an estrogen receptor transactivation assay with metabolic competence

Chad Deisenroth, Danica DeGroot, Todd Zurlinden, Andrew Eicher, James McCord, Mi-Young Lee, Paul Carmichael & Russell Thomas
The U.S. EPA Endocrine Disruptor Screening Program utilizes data across the ToxCast/Tox21 high-throughput screening (HTS) programs to evaluate the biological effects of potential endocrine active substances (EAS). A potential limitation to the use of in vitro assay data in regulatory decision-making is the lack of coverage for xenobiotic metabolic processes. Both hepatic- and peripheral-tissue metabolism can yield metabolites that exhibit greater activity than the parent compound (bioactivation) or are inactive (bioinactivation) for a given biological...

Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Ilaria Milano, Massimiliano Babbucci, Alessia Cariani, Miroslava Atanassova, Dorte Bekkevold, Gary R. Carvalho, Montserrat Espiñeira, Fabio Fiorentino, Germana Garofalo, Audrey J. Geffen, Einar E. Nielsen, Rob Ogden, Tomaso Patarnello, Marco Stagioni, Fausto Tinti & Luca Bargelloni
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed...

Data from: Population connectivity and phylogeography of the Mediterranean endemic skate Raja polystigma and evidence of its hybridization with the parapatric sibling R. montagui

Alessia Cariani, ED Farrell, P Carbonara, G Garofalo, M Stagioni, F Tinti, F Fiorentino, N Frodella, A Veloná, R Cannas & MC Follesa
The genetic structure and population connectivity of the Mediterranean endemic speckled skate Raja polystigma were investigated in 10 population samples (N = 232) at 7 exon-primed nuclear microsatellites and at 3 mitochondrial DNA sequence markers. The phylogeographic and population genetic analyses revealed that R. polystigma in the western and central Mediterranean represents a near-panmictic population, with a subtle but significant mitochondrial divergence of the Adriatic deme. Nuclear genotypes revealed that 2.5% of the total individuals...

Data from: Is environmental legislation conserving tropical stream faunas? a large-scale assessment of local, riparian and catchment-scale influences on Amazonian stream fish

Cecília G. Leal, Jos Barlow, Toby Gardner, Robert M. Hughes, Rafael P. Leitão, Ralph Mac Nally, Philip R. Kaufmann, Silvio F. B. Ferraz, Jansen Zuanon, Felipe R. De Paula, Joice Ferreira, James R. Thomson, Gareth D. Lennox, Eurizângela P. Dary, Cristhiana P. Röpke, Paulo S. Pompeu & Toby A. Gardner
1.Agricultural expansion and intensification are major threats to tropical biodiversity. In addition to the direct removal of native vegetation, agricultural expansion often elicits other human-induced disturbances, many of which are poorly addressed by existing environmental legislation and conservation programmes. This is particularly true for tropical freshwater systems, where there is considerable uncertainty about whether a legislative focus on protecting riparian vegetation is sufficient to conserve stream fauna. 2.To assess the extent to which stream fish...

Data from: High-throughput H295R steroidogenesis assay: utility as an alternative and a statistical approach to characterize effects on steroidogenesis

Derik E. Haggard, Agnes L. Karmaus, Matthew T. Martin, Richard S. Judson, R. Woodrow Setzer & Katie Paul Friedman
The U.S. Environmental Protection Agency Endocrine Disruptor Screening Program and the Organization for Economic Co-operation and Development (OECD) have used the human adrenocarcinoma (H295R) cell-based assay to predict chemical perturbation of androgen and estrogen production. Recently, a high-throughput H295R (HT-H295R) assay was developed as part of the ToxCast program that includes measurement of 11 hormones, including progestagens, glucocorticoids, androgens, and estrogens. To date, 2012 chemicals have been screened at one concentration; of these, 656 chemicals...

Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

Katrina West, Michael Travers, Michael Stat, Euan Harvey, Zoe Richards, Joseph DiBattista, Stephen Newman, Alastair Harry, Craig Skepper, Matthew Heydenrych, Michael Bunce, Michael J. Travers, Euan S. Harvey, Zoe T. Richards, Joseph D. DiBattista, Stephen J. Newman & Craig L. Skepper
Aim: Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales, or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break, and evaluate its use as a regional biomonitoring tool in Australia. Location: North-western Australia (NWA) Methods: We applied metabarcoding assays targeting...

Data from: In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

Jon A. Doering, Sehan Lee, Kurt Kristiansen, Linn Evenseth, Mace G. Barron, Ingebrigt Sylte & Carlie A. LaLone
Chemical hazard assessment requires extrapolation of information from model organisms to all species of concern. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed as a rapid, cost effective method to aid cross-species extrapolation of susceptibility to chemicals acting on specific protein targets through evaluation of protein structural similarities and differences. The greatest resolution for extrapolation of chemical susceptibility across species involves comparisons of individual amino acid residues at key positions involved...

Registration Year

  • 2021
  • 2020
  • 2018
  • 2017
  • 2016
  • 2013

Resource Types

  • Dataset


  • Environmental Protection Agency
  • Environmental Protection Agency
  • Oregon State University
  • University of Bologna
  • Federal University of Lavras
  • Universidade Federal de Minas Gerais
  • University of Sao Paulo
  • Environmental Protection Agency
  • Lancaster University
  • University of Cagliari