36 Works

Data from: Local range boundaries versus large-scale tradeoffs: climatic and competitive constraints on tree growth

Leander D. L. Anderegg & Janneke HilleRisLambers
Species often respond to human‐caused climate change by shifting where they occur on the landscape. To anticipate these shifts, we need to understand the forces that determine where species currently occur. We tested whether a long‐hypothesised trade‐off between climate and competitive constraints explains where tree species grow on mountain slopes. Using tree rings, we reconstructed growth sensitivity to climate and competition in range centre and range margin tree populations in three climatically distinct regions. We...

Data from: Multi-omics investigation reveals benzalkonium chloride disinfectants alter sterol and lipid homeostasis in the mouse neonatal brain

Josi M. Herron, Kelly M. Hines, Hideaki Tomita, Ryan P. Seguin, Julia Yue Cui & Libin Xu
Lipids are critical for neurodevelopment; therefore, disruption of lipid homeostasis by environmental chemicals is expected to have detrimental effects on this process. Previously, we demonstrated that the benzalkonium chlorides (BACs), a class of commonly used disinfectants, alter cholesterol biosynthesis and lipid homeostasis in neuronal cell cultures in a manner dependent on their alkyl chain length. However, the ability of BACs to reach the neonatal brain and alter sterol and lipid homeostasis during neurodevelopment in vivo...

Data for tree mortality calibration of satellite and LiDAR-derived fire severity estimates.

N. Macriss, T.J. Furniss, S.M.A. Jeronimo, E. L. Crowley, O. W. Germain, S. Germain, V. R. Kane, A. J. Larson & James A. Lutz
The 55 JFSP plots were established to capture forest types, fire histories, and severity levels beyond those found within the YFPD. The plots were square 50 m × 50 m plots established in Pinus ponderosa, Pinus jeffreyi, and Abies concolor – Pinus lambertiana forest types between 1,431 m and 2,250 m elevation. Plots were installed post-fire based on a randomly chosen locations stratified by burn severity levels as calculated from the differenced Normalized Burn Ratio...

Data from: Leaf shape tracks transitions across forest-grassland boundaries in the grass family (Poaceae)

Timothy Jay Gallaher, Dean C. Adams, Lakshmi Attigala, Sean V. Burke, Joseph M. Craine, Melvin R. Duvall, Phillip C. Klahs, Emma Sherratt, William P. Wysocki & Lynn G. Clark
Grass leaf shape is a strong indicator of their habitat. Linear leaves predominate in open areas and more ovate leaves distinguish forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the...

Data from: Multi-year genetic sampling indicates maternal gene flow via colony emigrations in the army ant Eciton burchellii parvispinum

Thomas W. Soare, Anjali Kumar, Kerry A. Naish & Sean O'Donnell
Sex-biased dispersal occurs when one sex disperses more frequently or farther than the opposite sex. In ants, dispersal is often male-biased and males typically contribute more strongly to gene flow within and among ant populations. However, army ants may offer an exceptional case of female-biased dispersal because army ant colonies (particularly species in the Neotropical genus Eciton) routinely emigrate among nest sites. We hypothesized that maternal mobility via successive colony emigrations would reduce the relative...

Data from: S-cone photoreceptors in the primate retina are functionally distinct from L and M cones

Jacob Baudin, Juan M. Angueyra, Raunak Sinha & Fred Rieke
Daylight vision starts with signals in three classes of cone photoreceptors sensitive to short (S), middle (M), and long (L) wavelengths. Psychophysical studies show that perceptual sensitivity to rapidly varying inputs differs for signals originating in S cones versus L and M cones; notably, S-cone signals appear perceptually delayed relative to L- and M-cone signals. These differences could originate in the cones themselves or in the post-cone circuitry. To determine if the cones could contribute...

Data from: Indirect legacy effects of an extreme climactic event on a marine megafaunal community

Robert Nowicki, Michael Heithaus, Jordan Thomson, Derek Burkholder, Kirk Gastrich & Aaron Wirsing
While extreme climactic events (ECEs) are predicted to become more frequent, reliably predicting their impacts on consumers remains challenging– particularly for large consumers in marine environments. Many studies that do evaluate ECE effects focus primarily on direct effects, though indirect effects can be equally or more important. Here, we investigate the indirect impacts of the 2011 “Ningaloo Niño” marine heatwave ECE on a diverse megafauna community in Shark Bay, Western Australia. We use an 18...

Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence -- simulation data

Hossein Parishani, Michael Pritchard, Christopher Bretherton, Matthew Wyant & Marat Khairoutdinov
This data set contains the simulation outputs used in the study summarized below: Systematic biases in the representation of boundary layer (BL) clouds are a leading source of uncertainty in climate projections. A variation on superparameterization (SP) called ‘‘ultraparameterization’’ (UP) is developed, in which the grid spacing of the cloud-resolving models (CRMs) is fine enough (250x20 m) to explicitly capture the BL turbulence, associated clouds, and entrainment in a global climate model capable of multiyear...

Data from: Climate-niche factor analysis: a spatial approach to quantifying species vulnerability to climate change

D. Scott Rinnan & Josh Lawler
Climate change vulnerability assessments are an important tool for understanding the threat that climate change poses to species and populations, but do not generally yield insight into the spatial variation in vulnerability throughout a species' habitat. We demonstrate how to adapt the method of ecological-niche factor analysis (ENFA) to objectively quantify aspects of species sensitivity to climate change. We then expand ENFA to quantify aspects of exposure and vulnerability to climate change as well, using...

Data from: Functional coupling in the evolution of suction feeding and gill ventilation of sculpins (Perciformes: Cottoidei)

Stacy C. Farina, Matthew L. Knope, Katherine A. Corn, Adam P. Summers & William E. Bemis
Suction feeding and gill ventilation in teleosts are functionally coupled, meaning that there is an overlap in the structures involved with both functions. Functional coupling is one type of morphological integration, a term that broadly refers to any covariation, correlation, or coordination among structures. Suction feeding and gill ventilation exhibit other types of morphological integration, including functional coordination (a tendency of structures to work together to perform a function) and evolutionary integration (a tendency of...

Data from: Quantifying habitat use of migratory fish across riverscapes using space-time isotope models

Sean R. Brennan, Timothy J. Cline & Daniel E. Schindler
1.Migratory animals pose difficult challenges to conservation and management because identifying critical habitats used throughout their lives is rarely possible. Endogenous tracers (e.g., isotope ratios) recorded in sequentially growing biogenic tissues, however, represent a potential source of unique insights at the more elusive temporal and spatial scales central to understanding the ecology of mobile species. To this end, a general probabilistic framework has emerged that quantitatively compares predictive models of isotopic variation across landscapes (called...

Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)

Adam Leache, Daniel Portik, Danielle Rivera, Mark-Oliver Rodel, Johannes Penner, Václav Gvoždík, Eli Greenbaum, Gregory Jongsma, Caleb Ofori-Boateng, Marius Burger, Edem Eniang, Rayna Bell & Matthew Fujita
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA)...

Seasonal and directional dispersal behavior in an ongoing dove invasion

David Slager
Range expansions require the dispersal of individual organisms, but dispersal behavior is notoriously difficult to study. Eurasian Collared-Doves have colonized both Europe and North America this century, with both initial invasions proceeding northwestward via "jump" dispersal. The European population has reached carrying capacity, but in the Americas, where exponential population growth continues, little is known about dispersal behavior. I queried citizen science field notes to investigate Eurasian Collared-Dove dispersal behavior in North America along the...

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

Data from: HIV infection is an independent risk factor for decreased 6-minute walk test distance

Tom E. Robertson, Mehdi Nouraie, Shulin Qin, Kristina A. Crothers, Cathy J. Kessinger, Deborah McMahon, Divay Chandra, Lawrence A. Kingsley, Ruth M. Greenblatt, Laurence Huang, Meghan F. Fitzpatrick & Alison Morris
Background: Ambulatory function predicts morbidity and mortality and may be influenced by cardiopulmonary dysfunction. Persons living with HIV (PLWH) suffer from a high prevalence of cardiac and pulmonary comorbidities that may contribute to higher risk of ambulatory dysfunction as measured by 6-minute walk test distance (6-MWD). We investigated the effect of HIV on 6-MWD. Methods: PLWH and HIV-uninfected individuals were enrolled from 2 clinical centers and completed a 6-MWD, spirometry, diffusing capacity for carbon monoxide...

Data from: Environmental gradients determine the potential for ecosystem engineering effects

Joshua B. Grinath, Loralee Larios, Laura R. Prugh, Justin S. Brashares & Katharine N. Suding
Understanding processes that determine biodiversity is a fundamental challenge in ecology. At the landscape scale, physical alteration of ecosystems by organisms, called ecosystem engineering, enhances biodiversity worldwide by increasing heterogeneity in resource conditions and enhancing species coexistence across engineered and non-engineered habitats. Engineering-diversity relationships can vary along environmental gradients due to changes in the amount of physical structuring created by ecosystem engineering, but it is unclear how this variation is influenced by the responsiveness of...

Data from: Past tree influence and prescribed fire exert strong controls on reassembly of mountain grasslands after tree removal

Charles B. Halpern, Joseph A. Antos, Shan Kothari & Annette M. Olson
Woody-plant encroachment represents a global threat to grasslands. Although the causes and consequences of this regime shift have received substantial attention, the processes that constrain reassembly of the grassland state remain poorly understood. We experimentally tested two potentially important controls on reassembly—the past influence of trees and the effects of fire—in conifer-invaded grasslands (mountain meadows) of western Oregon. Previously, we had reconstructed the history of tree invasion at fine spatial and temporal resolution. Using small...

Data from: Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska

Wesley A. Larson, Tyler H. Dann, Morten T. Limborg, Garrett J. McKinney, Jim E. Seeb & Lisa W. Seeb
Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and...

Initial application of the noise-sorted scanning clustering algorithm to the analysis of composition-dependent organic aerosol thermal desorption measurements

Christopher Cappa, Ziyue Li, Emma D'Ambro, Siegfried Schobesberger, John Shilling, Felipe Lopez-Hilfiker, Jiumeng Liu, Cassandra Gaston & Joel Thornton
The FIGAERO-CIMS (Filter Inlet for Gases and AEROsols + chemical ionization mass spectrometer) measures thermal desorption profiles for individual ions evolved from evaporation of organic aerosol components. Often, hundreds of individual thermograms are obtained, reflecting the compositional complexity of organic aerosol. We have developed a novel clustering algorithm, Noise-Sorted Scanning Clustering (NSSC), that provides a robust, reproducible analysis of the FIGAERO temperature-dependent mass spectral data. The NSSC allows for determination of thermal profiles for compositionally...

Data from: Climate impacts on the ocean are making the Sustainable Development Goals a moving target traveling away from us

Gerald G. Singh, Nathalie Hilmi, Joey R. Bernhardt, Andres M. Cisneros Montemayor, Madeline Cashion, Yoshitaka Ota, Sevil Acar, Jason M. Brown, Richard Cottrell, Salpie Djoundourian, Pedro C. Gonzalez-Espinosa, Vicky Lam, Nadine Marshall, Barbara Neumann, Nicolas Pascal, Gabriel Reygondeau, Joacim Rocklov, Alain Safa, Laura R. Virto & William Cheung
1. Climate change is impacting marine ecosystems and their goods and services in diverse ways, which can directly hinder our ability to achieve the Sustainable Development Goals, set out under the 2030 Agenda for Sustainable Development. 2. Through expert elicitation and a literature review, we find that most climate change effects have a wide variety of negative consequences across marine ecosystem services, though most studies have highlighted impacts from warming and consequences to marine species....

Extinct plants of North America north of Mexico

Wesley Knapp, Anne Frances, Reed Noss, Robert Naczi, Alan Weakley, George Gann, Bruce Baldwin, James Miller, Patrick McIntyre, Brent Mishler, Gerry Moore, Richard Olmstead, Anna Strong, Daniel Gluesenkamp & Kathryn Kennedy
The recent study by Humphreys et al., reporting extinction of almost 600 plant species globally, represents a groundbreaking effort at compiling direct data on seed plants. We applaud Humphreys et al. for quantifying plant extinctions because they formulate an important and testable hypothesis. However, their study missed many extinctions and rediscoveries of seed plants in the United States and Canada. Our team of experts has been compiling a list of extinct plants of North America...

Data from: Assexon: assembling exon using gene capture data

Hao Yuan, Calder Atta, Luke Tornabene & Chenhong Li
Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not...

Data from: Anatomical diversification of a skeletal novelty in bat feet

Kathryn Elizabeth Stanchak, Jessica Arbour & Sharlene E. Santana
Neomorphic, membrane-associated skeletal rods are found in disparate vertebrate lineages, but their evolution is poorly understood. Here we show that one of these elements—the calcar of bats (Chiroptera)—is a skeletal novelty that has anatomically diversified. Comparisons of evolutionary models of calcar length and corresponding disparity-through-time analyses indicate that the calcar diversified early in the evolutionary history of Chiroptera, as bats phylogenetically diversified after evolving the capacity for flight. This interspecific variation in calcar length and...

Data from: One and two year visual outcomes from the Moorfields age-related macular degeneration database: a retrospective cohort study and an open science resource

Katrin Fasler, Gabriella Moraes, Siegfried K. Wagner, Karsten U. Kortuem, Reena Chopra, Livia Faes, Gabriella Preston, Nikolas Pontikos, Dun Jack Fu, Praveen J. Patel, Adnan Tufail, Aaron Y. Lee, Konstantinos Balaskas & Pearse A. Keane
Objectives: To analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area. Setting: Retrospective, comparative, non-randomised electronic medical record...

Data from: Mesopredators change temporal activity in response to a recolonizing apex predator

Carolyn R. Shores, Justin A. Dellinger, Eric S. Newkirk, Shannon M. Kachel & Aaron J. Wirsing
Apex predators can influence ecosystems through density and behaviorally mediated effects on herbivores and mesopredators. In many parts of the world, apex predators live in, or are returning to, landscapes that have been modified by people, so it is important to understand their ecological role in anthropogenic landscapes. We used motion-activated game cameras to compare the activity patterns of humans and two mesopredators, coyotes (Canis latrans) and bobcats (Lynx rufus), in areas with and without...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of Washington
  • University of Colorado Boulder
  • University of Montana
  • Oregon State University
  • Moorfields Eye Hospital NHS Foundation Trust
  • University of Adelaide
  • University of Eastern Finland
  • Biodiversity Research Institute
  • Stanford University
  • Utah State University