426 Works

Data from: Using an arbitrary moment predictor to investigate the optimal choice of prognostic moments in bulk cloud microphysics schemes

Adele A. Igel
Most bulk cloud microphysics schemes predict up to three standard properties of hydrometeor size distributions, namely, the mass mixing ratio, number concentration, and reflectivity factor in order of increasing scheme complexity. However, it is unclear whether this combination of properties is optimal for obtaining the best simulation of clouds and precipitation in models. In this study, a bin microphysics scheme has been modified to act like a bulk microphysics scheme. The new scheme can predict...

Data from: Conditioned place preference reveals ongoing pain in calves 3 weeks after disbudding

Sarah Adcock & Cassandra Tucker
Hot-iron disbudding, a routine procedure that prevents horn bud growth through cauterization, is painful for calves. The resulting burns remain sensitive to touch for weeks, but it is unknown whether calves experience ongoing, non-evoked pain. We evaluated conditioned place preference for analgesia in 44 calves disbudded or sham-disbudded 6 hours (Day 0) or 20 days (Day 20) before testing (n = 11/treatment). Calves were conditioned to associate the effects of a lidocaine cornual nerve block...

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

Nicole Soltis, Celine Caseys, Wei Zhang, Jason Corwin, Susanna Atwell & Daniel Kliebenstein
In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described while little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide...

Phylogenies of fungi isolated from the seagrass, Zostera marina

Cassandra Ettinger & Jonathan Eisen
Fungi in the marine environment are often neglected, despite that they having critical roles on land as decomposers, pathogens or beneficial endophytes. We used culture-dependent methods to survey the fungi associated with the seagrass, Zostera marina, and then placed these sequences in the fungal tree of life. Four different sequence alignments were generated, (1) an alignment to investigate seagrass isolates in the Basidiomycota and Zygomycota phyla, (2) an alignment to investigate seagrass isolates in the...

Automated vehicles and central business district parking: the effects of drop-off-travel on traffic flow and vehicle emissions

Huajun Chai & Caroline Rodier
The potential for automated vehicles (AVs) to reduce parking to allow for the conversion of on-and off-street parking to new uses, such as new space for walk, bike, and shared -micro-mobility services, and housing), has sparked significant interest among urban planners. AVs could drop-off and pick-up passengers in areas where parking costs are high or limited. Personal AVs could return home or park in less expensive locations and shared AVs could serve other passengers. However,...

Data from: Naïve domestic Bos Taurus calves recognize the scent of a canine predator

Sarah J. J. Adcock & Cassandra B. Tucker
Wild ungulates can recognize certain predators without previous experience, but this innate ability may be relaxed under domestication. Using naïve dairy calves, Bos taurus, we examined the effects of exposure to a predator odour (coyote, Canis latrans, urine) and two control odours (deer urine and water) on (1) latency to approach a milk food reward, (2) exploration, vigilance and locomotor play, (3) magnitude of the startle response to a sudden noise delivered upon arrival at...

Dataset: Spatiotemporal analysis of freight patterns in Southern California

Daniel Rivera-Royero, Miguel Jaller, John Harvey, Changmo Kim & Jeremy Lea
There has been general trend to shift the location of warehouses and distribution facilities away from consumer markets (logistics sprawl) in Southern California. This shift has a negative impact on cost and the environment because freight vehicles have to travel longer to reach their destinations. However, during the last decade, this trend has not continued at the same pace, and it may have even reversed. Two main factors potentially explain this phenomenon: the 2008-2009 economic...

Multiple and extra-pair mating in a pair-living hermaphrodite, the intertidal limpet Siphonaria gigas

Jessica Schaefer, John Christy & Peter Marko
Pair-living is a common social system found across animal taxa, and the relationship between pair-living and reproduction varies greatly among species. Siphonaria gigas, hermaphroditic pulmonate gastropods, often live in pairs in the rocky intertidal zone of the tropical Eastern Pacific. Combining genetic parentage analysis using four polymorphic microsatellite loci with behavioral observations from a 10-week field study, we provide the first description of the mating system of a Siphonaria species incorporating genetic data. S. gigas...

Global human influence maps reveal clear opportunities in conserving Earth’s remaining intact terrestrial ecosystems

Jason Riggio, Jonathan E. M. Baillie, Steven Brumby, Erle Ellis, Christina M. Kennedy, James R. Oakleaf, Alex Tait, Therese Tepe, David M. Theobald, Oscar Venter, James E.M. Watson & Andrew P. Jacobson
Leading up to the 2020 Convention on Biological Diversity there is momentum around setting bold conservation targets. Yet it remains unclear how much of Earth’s land area remains without significant human influence and where this land is located. We compare four recent global maps of human influences across Earth’s land, Anthromes, Global Human Modification, Human Footprint, and Low Impact Areas, to answer these questions. Despite using various methodologies and data, these different spatial assessments independently...

Multiple Benefits from Agricultural and Natural Land Covers in the Central Valley, CA

Caitlin Peterson, Elias Marvinney & Kristen Dybala
The data and code provided in this repository are associated with the technical report on the "Multiple Benefits from Agricultural and Natural Land Covers" project and were prepared by the authors for the Migratory Bird Conservation Partnership. MBCP partner organizations include The Nature Conservancy, California Audubon, and Point Blue Conservation Science. Executive Summary The Central Valley of California is one of the most heavily modified landscapes in the world, with millions of acres of semi-arid...

Data for: Genetic architecture modulates diet induced hepatic mRNA and miRNA expression profiles

Excel Que, Kristen L. James, Alisha R. Coffey, Tangi L. Smallwood, Jody Albright, M. Nazmul Huda, Daniel Pomp, Praveen Sethupathy & Brian J. Bennett
Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically-relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here we performed global hepatic eQTL and miRNA expression quantitative...

Data and code for simulation study and case study in \"A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity\"

Rahel Sollmann, Mitchell Eaton, William Link, Paul Mulondo, Samuel Ayebare, Sarah Prinsloo & Devin Johnson
This dataset contains the R and JAGS code underlying the simulation study, as well as the data and code underlying the case study on bird occurrence in Murchison Falls National Park, presented in the paper "A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity".

Mean flow direction modulates non-Fickian transport in a heterogeneous alluvial aquifer-aquitard system

Rich Pauloo
Regional-scale groundwater quality degradation from nonpoint source pollution threatens the long-term sustainability of major alluvial aquifer-aquitard systems worldwide. Upscaled models can efficient represent nonpoint source transport, but fail to accurately characterize non-Fickian (anomalous) transport caused by mean flow direction transience. In this study, we demonstrate that hydrogeologic factors explain this failure. Specifically, vertical anisotropy in K and seasonal pumping and recharge in typical alluvial aquifer systems can fundamentally change hydraulic gradients and shift the mean...

Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture

Daniel Swezey, Sara Boles, Kristin Aquilino, Haley Stott, Doug Bush, Andrew Whitehead, Tessa Hill, Eric Sanford, Laura Rogers-Bennett, Tessa Hill & Eric Sanford
Ocean acidification (OA) poses a major threat to marine ecosystems and shellfish aquaculture. A promising mitigation strategy is the identification and breeding of shellfish varieties exhibiting resilience to acidification stress. We experimentally compared the effects of OA on two populations of red abalone (Haliotis rufescens), a marine mollusck important to fisheries and global aquaculture. Results from our experiments simulating captive aquaculture conditions demonstrated that abalone sourced from a strong upwelling region were tolerant of ongoing...

Apis mellifera wing images (Africanized honey bees)

Erin Calfee, Marcelo Agra, María Alejandra Palacio, Santiago Ramírez & Graham Coop
Honey bee wing lengths and vein patterns differ between major genetic lineages. In this dataset we publish forewing images for 276 individual honey bees with mixtures of African and European genetic ancestry of varying proportions. In the associated population genomics study, we compared evolutionary outcomes of the Africanized honey bee invasion in North and South America (California and Argentina). Samples from Argentina were provided by the National Institute of Agricultural Technology (INTA), Argentina.

Pesticide and resource stressors additively impair wild bee reproduction

Clara Stuligross & Neal Williams
Bees and other beneficial insects experience multiple stressors within agricultural landscapes that act together to impact their health and diminish their ability to deliver the ecosystem services on which human food supplies depend. Disentangling the effects of coupled stressors is a primary challenge for understanding how to promote their populations and ensure robust pollination and other ecosystem services. We used a crossed design to quantify the individual and combined effects of food resource limitation and...

Lignification of tomato (Solanum lycopersicum) pericarp tissue during blossom-end rot development

Nicholas Reitz
Blossom-end rot is a physiological disorder causing significant losses in the produce industry each year. Accumulation of reactive oxygen species has been established as a key characteristic of blossom-end rot development. An increase in peroxidase activity and lignin precursor content are also associated with blossom-end rot symptoms, leading to the hypothesis that lignification may be occurring during blossom-end rot development. To investigate the potential involvement of lignification, hydrogen peroxide content, catalase activity, and peroxidase activity...

Data and analysis from: Two centuries of monarch butterfly collections reveal contrasting effects of range expansion and migration loss on wing traits

Micah Freedman, Hugh Dingle, Sharon Strauss & Santiago Ramírez
Migratory animals exhibit traits that allow them to exploit seasonally variable habitats. In environments where migration is no longer beneficial, such as oceanic islands, migration-association traits may be selected against or be under relaxed selection. Monarch butterflies are best known for their continent-scale migration in North America but have repeatedly become established as non-migrants in the tropical Americas and on Atlantic and Pacific Islands. These replicated non-migratory populations provide natural laboratories for understanding the rate...

Data from: Injury alters motivational trade-offs in calves during the healing period

Cassandra Tucker & Sarah Adcock
Injury can produce long-lasting motivational changes that may alter decisions made under risk. Our objective was to determine whether a routine painful husbandry procedure, hot-iron disbudding, affects how calves trade off risk avoidance against a competing motivation (i.e., feeding), and whether this response depends on time since injury. We used a startle test to evaluate this trade-off in calves disbudded 0 or 21 days previously and non-injured control calves. For 3 days, calves were individually...

Data from: Habitat primarily structures seagrass epifaunal communities: a regional-scale assessment in the Chesapeake Bay

Claire Murphy, Jonathan Lefcheck & Robert Orth
Epifaunal invertebrates play an important role in seagrass systems, both by grazing epiphytic algae from seagrass blades and by acting as a major food source for higher trophic levels. However, while many studies have described epifaunal community properties at small spatial scales (1 – 10 m2) and across very large gradients (from continental coastlines to the entire globe), few have examined regional-scale (100 ­– 1000 km2) patterns or, more importantly, disentangled the drivers of these...

Sex and tissue-specific evolution of developmental plasticity in Drosophila melanogaster

Didem Sarikaya
Developmental plasticity influences the size of adult tissues in insects. Tissues can have unique responses to environmental perturbation during development, however, the prevalence of within species evolution of tissue-specific developmental plasticity remains unclear. To address this, we studied the effects of temperature and nutrition on wing and femur size in D. melanogaster populations from a temperate and tropical region. Wings were more sensitive to temperature, while wings and femurs were equally responsive to nutrition in...

Impacts of anthropogenic disturbance and insect abundance on Sonoran Desert bat activity

Amy Sue Law, , Emma McAndrews & Jess Stumpf
Rapid urbanization has been beneficial and detrimental to desert ecosystems. One group of organisms that are sensitive to such anthropogenic disturbance are bats. In this study, we examined bat abundance and composition in the Sonoran Desert in Southern California to assess how the bat community is affected by human disturbance and insect abundance. We observed bat calls and surveyed insect abundance at sites with high and low levels of human impact. We found that there...

Human-wildlife interactions in Anza-Borrego Desert State Park

Ninfa Negrete, Sara Ramirez & Robert Wong
Transportation infrastructure, such as roads and highways, supports human activity but negatively affect wildlife habitat, populations, and entire ecosystems (Bennet et. al 2011). As road networks continue to expand, animals lose habitat and are confined to isolated fragments, with the possibility of being enclosed by roads. Road effects like habitat fragmentation is not well known in state parks. This study aims to examine some of the effects of road disturbance on wildlife in the Anza-Borrego...

Distribution and population estimates of the Borrego sand scorpion (Paruroctonus borregoensis)

Emma Korntheuer, Pearl Rakowski, Jack Choi & Sarkis Kasparian
Scorpions are important to the desert biome as prolific prey items, predators, and habitat modifiers. Our study set out to fill in the knowledge gap pertaining to the abundance and homing behavior of the Borrego dune scorpion, Paruroctonus borregoensi. A mark and recapture was conducted to determine if Borrego sand scorpions display site fidelity and as well as estimate population density in the Anza Borrego Desert in California. The Borrego sand scorpion displays no evidence...

Defensive displays and chemical secretions of darkling beetles in the Mojave Desert

Tania Aguilar, , Meghan Proctor & Athena Schlereth
Many organisms often rely on chemical defenses to deter predators. However, the way in which invertebrates utilize chemical defenses has been relatively understudied. Darkling beetle species of the Eleodes and Coelocnemis genera exhibit defensive posturing followed by malodorous chemical secretions to signal their unpalatability towards potential predators. However, the metabolic costs and trade-offs associated with these mechanisms are unknown. It is also unclear whether certain beetle species utilize chemical defenses more readily than others. We...

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