68 Works

Data from: Larval development in the Pacific oyster and the impacts of ocean acidification: differential genetic effects in wild and domesticated stocks

Evan Durland, Pierre De Wit, Eli Meyer & Chris Langdon
The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO­2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many...

Dehydrated males are less likely to dive into the mating pool

Christopher Friesen, Emily Uhrig & Robert Mason
The hydration state of animals vying for reproductive success may have implications for the tempo and mode of sexual selection, which may be salient in populations that experience increasing environmental fluctuations in water availability. Using red-sided garter snakes as a model system, we tested the effect of water supplementation on courtship, mating behavior, and copulatory plug (CP) production during a drought year. Over three days of mating trials, water-supplemented males (WET males, n = 45)...

Assessing the impact of diffusion model on the turbulent transport and flame structure of premixed lean hydrogen flames: hydrogen data

Aaron Fillo, PETER HAMLINGTON & Kyle Niemeyer
This dataset contains results from direct numerical simulations of premixed, three-dimensional, turbulent hydrogen/air flames, using the multicomponent and mixture-averaged diffusion models. In particular, this dataset contains information about the enstrophy budget and flame structure. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.

Bean CAP Snap Bean Diversity Panel Passport Data

James R. Myers
The accessions used to create the Snap Bean Diversity Panel were 149 snap bean cultivars and germplasm lines selected from North American and European germplasm. This panel was developed with support from the Common Bean Coordinated Agriculture Project (USDA-NIFA grant no. 2009-85606-05964). The accompanying data set contains information, where known, about pod traits and plant growth habit, USDA-NPGS Plant Introduction (PI) number, who bred the cultivar, market class and pod sieve size, plant variety protection...

Hyperspectral reflectance data of wheat in situ and lab scans infected with soilborne wheat mosaic virus

Marja Haagsma, Christina Hagerty, Duncan Kroese & Elizabeth Jachens
Hyperspectral images were taken in a lab setting from wheat leaves and in situ from agricultural wheat fields and disease nursery. The goal of this research was to find infection of soilborne wheat mosaic virus in wheat for early detection using digital imagery, i.e., either hyperspectral or multispectral.

Benthic macroinvertebrates sampled above and below Cougar Dam

Christina Murphy, Sherri Johnson, William Gerth, Todd Pierce & Gregory Taylor
This dataset accompanies the manuscript Unintended consequences of selective water withdrawals from reservoirs alter downstream macroinvertebrate communities in Water Resources Research. Benthic macroinvertebrates were collected from samples taken annually during the first two weeks of August from 2002-2007 and again in 2017 at six sites in the South Fork McKenzie River. Taxonomy of samples collected prior to 2017 have been updated to be consistent with 2017 taxa designations.

Hinkle Creek Benthic Invertebrate Dataset

William Gerth, Judith L. Li, Richard Van Driesche, Janel Sobota, Christina Murphy, Lisa Ganio & Arne Skaugset
This dataset contains records of identified benthic and aquatic emergent invertebrates from pre-timber harvest, post-timber harvest, and reference (no harvest) collection sites in the Hinkle Creek watershed. A variety of fish-bearing tributaries, fishless tributaries, and mainstem creek sites were sampled. Benthic invertebrates were collected using Serber nets and emergent adults were collected with emergence traps. Invertebrates were identified to the lowest practical taxonomic level.

Discharge and suspended sediment a paired watershed study examining the effects of contemporary forest harvesting in the Oregon Coast Range

Jeff Hatten, Catalina Segura, Kevin Bladon, Cody Hale, George G. Ice & John Stednick
Forest harvesting practices can expose mineral soils, decrease infiltration capacities of soils, disturb the stream bank and channel, and increase erosion and fine sediment supply to stream channels. To reduce nonpoint source sediment pollution associated with forest management activities and to maintain the high water quality typically provided from forests, best management practices (BMPs) were developed and implemented. The Alsea Watershed Study was an important early research site that lead to the development of contemporary...

Quantifying temporal variation in dietary niche to reveal drivers of past population declines; stable isotope, harvest trends, and land use

Amanda Cheeseman, Brian Tanis & Elmer Finck
1. Given the long and dynamic history of anthropogenic disturbances to ecosystems, it is difficult to determine the drivers of past population declines. These uncertainties dilute the efficacy of conservation efforts and might hinder species and ecosystem recovery. 2. Niche quantification can be a useful tool for understanding drivers of past population declines. Niche parameters reflect key resources used, providing insight into the conditions needed to achieve population stability. By reconstructing a population’s niche position...

Across borders: external factors and prior behavior influence North Pacific albatross associations with fishing vessels

Rachael Orben, Josh Adams, Michelle Hester, Scott Shaffer, Robert Suryan, Tomohiro Deguchi, Kiyoaki Ozaki, Fumio Sato, Lindsay Young, Corey Clatterbuck, Melinda Conners, David Kroodsma & Leigh Torres
1. Understanding encounters between marine predators and fisheries across national borders and outside national jurisdictions offers new perspectives on unwanted interactions to inform ocean management and predator conservation. Although seabird-fisheries overlap has been documented at many scales, remote identification of vessel encounters has lagged because vessel movement data often is lacking. 2. Here, we reveal albatross-fisheries associations throughout the North Pacific Ocean. We identified commercial fishing operations using Global Fishing Watch data and algorithms to...

Data and scripts from: Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of anostomid fishes

Brian Sidlauskas, Fernando Assega, Bruno Melo, Claudio Oliveira & José Birindelli
The nearly 150 species of Anostomidae comprise one of the most diverse and taxonomically dynamic families of Neotropical freshwater fishes. A recent revision of the enigmatic and poorly diagnosed genus Anostomoides demonstrated that it contains two valid species, each with complicated taxonomic histories; however, that study did not address their phylogenetic placement. Herein, we provide the integrated molecular and morphological data and scripts used to demonstrate their distant evolutionary relationship, and thus the polyphyly of...

Data from: Landscape Context Mediates Avian Habitat Choice in Tropical Forest Restoration

J. Leighton Reid, Chase D. Mendenhall, J. Abel Rosales, Rakan A. Zahawi & Karen D. Holl
Birds both promote and prosper from forest restoration. The ecosystem functions birds perform can increase the pace of forest regeneration and, correspondingly, increase the available habitat for birds and other forest-dependent species. The aim of this study was to learn how tropical forest restoration treatments interact with landscape tree cover to affect the structure and composition of a diverse bird assemblage. We sampled bird communities over two years in 13 restoration sites and two old-growth...

Data from: Natural resistance to worms exacerbates bovine tuberculosis severity independently of worm coinfection

Vanessa Ezenwa, Sarah Budischak, Peter Buss, Mauricio Seguel, Gordon Luikart, Anna Jolles & Kaori Sakamoto
Pathogen interactions arising during coinfection can exacerbate disease severity, for example, when the immune response mounted against one pathogen negatively affects defense of another. It is also possible that host immune responses to a pathogen, shaped by historical evolutionary interactions between host and pathogen, may modify host immune defenses in ways that have repercussions for other pathogens. In this case, negative interactions between two pathogens could emerge even in the absence of concurrent infection. Parasitic...

Raw data from: Experimental evolution can enhance benefits of rhizobia to novel legume hosts

Kenjiro Quides, Alexandra Weisberg, Jerry Trinh, Fathi Salaheldine, Paola Cardenas, Hsu-Han Lee, Ruchi Jariwala, Jeff Chang & Joel Sachs
Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a fullfactorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes...

A method to evaluate body length of live aquatic vertebrates using digital images

Ivan Arismendi, Gwen Bury, Lauren Zatkos & Jeff Snyder
Traditional methods to measure body lengths of aquatic vertebrates rely on anesthetics, and extended handling times. These procedures can increase stress, potentially affecting the animal’s welfare after its release. We developed a simple procedure using digital images to estimate body lengths of coastal cutthroat trout (Oncorhynchus clarkii clarkii) and larval coastal giant salamander (Dicamptodon tenebrosus). Images were post-processed using ImageJ2. We measured more than 1,800 individuals of these two species from 200 pool habitats along...

Time-resolved X-ray microtomography non-equilibrium and quasi-equilibrium two-phase flow in glass beads

Dorthe Wildenschild & Douglas Meisenheimer
This project includes 2 time-resolved X-ray microtomography experiments performed in glass bead packs. The two datasets are differentiated by the flow condition controlling each experiment, non-equilibrium (nonEq) and quasi-equilibrium (quasiEq). Each dataset includes segmented images comprising primary drainage (PD), main imbibition (MI), main drainage (MD), and a few scanning imbibition (SI) and drainage (SD) curves. The quasiEq data also includes some interfacial relaxation data. The tomographic images were collected with a 3.2 um voxel resolution...

An ecoregion-based approach to restoring the world’s intact large mammal assemblages

Carly Vynne, Joe Gosling, Calum Maney, Eric Dinerstein, Andy T. L. Lee, Neil Burgess, Néstor Fernández, Sanjiv Fernando, Harshini Jhala, Yadvendradev Jhala, Reed Noss, Michael Proctor, Jan Schipper, José F. González-Maya, Anup Joshi, David Olson, William J. Ripple & Jens-Christian Svenning
Assemblages of large mammal species play a disproportionate role in the structure and composition of natural habitats. Loss of these assemblages destabilizes natural systems, while their recovery can restore ecological integrity. Here we take an ecoregion-based approach to identify landscapes that retain their historically present large mammal assemblages, and map ecoregions where reintroduction of 1–3 species could restore intact assemblages. Intact mammal assemblages occur across more than one-third of the 730 terrestrial ecoregions where large...

Feather corticosterone reveals developmental challenges in a long‐term study of juvenile northern spotted owls

Ashlee Mikkelsen, Katie Dugger, Kathleen O'Reilly & Damon Lesmeister
1. Corticosterone is a steroid hormone integral to a variety of physiological pathways and is strongly associated with the vertebrate stress–response. In avian species, circulating corticosterone is sequestered into developing feathers and is used as an indicator of energy allocation during feather growth and widely applied in conservation physiology. 2. The northern spotted owl (Strix occidentalis caurina) is a federally threatened old–growth forest obligate of conservation concern endemic to the Pacific Northwest of the United...

Phylogeny of the supertribe Nebriitae (Coleoptera: Carabidae) based on analyses of DNA sequence data

David H. Kavanaugh, David Maddison, W. Brian Simison, Sean D. Schoville, Joachim Schmidt, Arnaud Faille, Wendy Moore, James M. Pflug, Sophie L. Archambeault, Tinya Hoang & Jei-Ying Chen
The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK and wingless) and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI (“barcode” region) and COI (“Pat/Jer” region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted...

Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes

Bruno Melo, Brian Sidlauskas, Thomas Near, Fabio Roxo, Ava Ghezelayagh, Luz Ochoa, Melanie Stiassny, Jairo Arroyave, Jonathan Chang, Brant Faircloth, Daniel MacGuigan, Richard Harrington, Ricardo Benine, Michael Burns, Kendra Hoekzema, Natalia Sanches, Javier Maldonado-Ocampo, Ricardo Castro, Fausto Foresti, Michael Alfaro & Claudio Oliveira
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211...

Postcopulatory sexual selection as a driver of sex- and population-specific kidney mass in garter snakes?

Christopher Friesen, Robert Mason & Emily Uhrig
In lizards and snakes, the kidneys produce seminal fluid in addition to having osmoregulatory functions. Therefore, in response to polyandry, kidney mass should be under selection regimes like those influencing testes. Male red-sided garter snakes deposit a kidney-derived copulatory plug that functions in sperm competition. We first tested for intersexual differences in kidney mass and allometry in one population and found that males had kidneys twice as heavy as those of females, consistent with stronger...

Predicted distribution of a rare and understudied forest carnivore: Humboldt martens (Martes caurina humboldtensis)

Katie Moriarty, Joel Thompson, Matthew Delheimer, Brent Barry, Mark Linnell, Taal Levi, Keith Hamm, Desiree Early, Holly Gamblin, Micaela Szykman-Gunther, Jordan Ellison, Janet Prevey, Jennifer Hartman & Raymond Davis
Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected...

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, Berit Gehrke, Chien-Hsun Huang, Aaron Liston, Hong Ma, Hannah Marx, David Tank & Ya Yang
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone...

Temporal variability of microparticles under the Seattle Aquarium, WA: Documenting the global Covid‐19 pandemic

Lyda S. T. Harris, Laura La Beur, Amy Y. Olsen, Angela Smith, Lindsey Eggers, Emily Pedersen, Jennifer Van Brocklin, Susanne M. Brander & Shawn Larson
Anthropogenic debris including microparticles (MP; <5mm) are ubiquitous in marine environments. The Salish Sea experiences seasonal fluctuations in precipitation, river discharge, sewage overflow events, and tourism– all variables previously thought to have an impact on MP transport and concentrations. Our goals are two-fold: 1) Describe long-term MP contamination data including concentration, type, and size and 2) Determine if seasonal MP concentrations are dependent on environmental or tourism variables in Elliott Bay, Salish Sea. We sampled...

Supplementary Material for: Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation

Felix Vaux, Sandra Bohn, John R. Hyde & Kathleen G. O'Malley
Supplementary Material for: Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation Files include a spreadsheet of samples and sequencing success (Appendix S1), a document containing supplementary methods, references, tables and figures (Appendix S2), lists of identified outlier loci per genome scan program (Appendix S3), full pairwise FST results for the 12 sample areas (Appendix S4), and genetic data files (genepop and vcf genotype files, and fasta consensus files for outlier loci)....

Registration Year

  • 2021

Resource Types

  • Dataset


  • Oregon State University
  • National Council for Air and Stream Improvement
  • Utah State University
  • Humboldt State University
  • United States Geological Survey
  • US Forest Service
  • Sao Paulo State University
  • The Nature Conservancy
  • University of Wollongong
  • University of Minnesota