308 Works

Abiotic differences and anthropogenic interference affect foothill yellow-legged frog breeding

Sharon Tamir, Anna Szymanska, Amanda Callahan, Gina Lucas & Jeniffer Amezquita
As human presence rapidly introduces novel environmental pressures to native ecosystems, many species experience population declines. Sensitive taxa such as amphibians may be particularly vulnerable to such environmental disturbances. Rana boylii, the foothill yellow-legged frog and a California State Species of Special Concern, serves as a model for understanding the effect of anthropogenic interference, such as changing climate and disturbed habitats, on reproductive success. In this study, we measured egg mass abundance, abiotic characteristics of...

Mendocino meadow memory: legacy effects of land use on plant communities of Angelo Coast Range Reserve

Ary Sanchez-Amaya, Frida Perez, Jena Weinberger & Susan Glasser
Human alteration of landscapes has occurred consistently through actions such as development, tilling, agriculture, and fire management. Human land use can result in a legacy of exotic species dominance and increased competition, with negative impacts on native species richness and soil structure. Meadows within California have been affected by settlement due to their accessibility to humans and soil conditions that are ideal for agriculture. Prior to European settlement, meadows in Angelo Coast Range Reserve (ACRR)...

The adaptive value of leaf quaking in Populus tremuloides

Natalie Kim, Mark Makar, Alexander Osleger & Juliana Shenouda
Some Populus species have evolved a flattened petiole that causes their leaves to quake in mild wind. In this study, we performed one observational study and two experimental studies on quaking aspen (Populus tremuloides) to investigate three predominant hypotheses on the adaptive value of quaking: (1) herbivory reduction, (2) light permeation, and (3) temperature maintenance. Overall, we found less insect herbivory on branches that quake less. We also found that quaking allows more light into...

Life Cycle Modeling of Tech & Strategies for a Sustainable Freight System in California

Hanjiro Ambrose & Alissa Kendall
California’s freight transportation system is a vital part of the state’s economy, but generates a high portion of local pollution in parts of the state with poor air quality. In recognition of these challenges, Executive Order B-32-15 encourages adoption of advanced vehicle technologies and infrastructure, as well as the use of alternative energy and fuels in the freight sector. These measures are echoed in the state’s Sustainable Freight Action Plan. Most emissions reductions from freight...

Sex-specific evolution of relative leg size in Drosophila prolongata results from changes in the intersegmental coordination of tissue growth

David Michael Luecke & Artyom Kopp
Evolution of relative organ size is the most prolific source of morphological diversity, yet the underlying molecular mechanisms that modify growth control are largely unknown. Models where organ proportions have undergone recent evolutionary changes hold the greatest promise for understanding this process. Uniquely among Drosophila species, D. prolongata displays a dramatic, male-specific increase in the size of its forelegs relative to other legs. By comparing leg development between males and females of D. prolongata and...

Impacts of caudal autotomy on personality

Marcus Michelangeli, Brooke Melki-Wegner, Kate Laskowski, Bob Wong & David Chapple
Caudal autotomy, the voluntary shedding of a tail, is a last-ditch strategy used by many lizard species to escape from predators. There are several costs associated with caudal autotomy that may cause lizards to make behavioral adjustments during tail regeneration. These behavioral changes may be dependent upon individual differences in response to autotomy (e.g. trait or state-dependent differences) and/or the degree of tail loss, as many lizards have the capacity to only partially shed their...

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...

Functional variants of DOG1 control seed chilling responses and variation in seasonal life history strategies in Arabidopsis thaliana

Alejandra Martinez-Berdeja, Michelle Stitzer, Mark A. Taylor, Miki Okada, Exequiel Ezcurra, Daniel E. Runcie & Johanna Schmitt
The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life history syndromes, we selected 559 fully-sequenced accessions of the model...

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...

Registration Year

  • 2021
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  • University of California, Davis
  • University of California, Berkeley
  • United States Department of Agriculture
  • San Diego State University
  • United States Geological Survey
  • University of Sao Paulo
  • University of Washington
  • University of Minnesota
  • Oak Ridge National Laboratory
  • University of Wisconsin-Madison