278 Works

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...

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

Michael Hardigan, Mitchell Feldmann, Randi Famula, Michaela Vachev, Mary Madera, Philipp Zerbe, Kristin Mars, Paul Peluso, David Rank, Shujun Ou, Christopher Saski, Charlotte Acharya, Glenn Cole, Alan Yocca, Patrick Edger & Steven Knapp
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the...

The non-traditional Coriolis terms and tropical convective clouds

Matthew Igel
The full, three-dimensional Coriolis force includes the familiar sine-of-latitude terms as well as frequently dropped cosine-of-latitude terms (Nontraditional Coriolis Terms [NCT]). The latter are often ignored because they couple the zonal and vertical momentum equations which in the large-scale limit of weak vertical velocity is considered insignificant almost everywhere. Here, we ask whether equatorial mesoscale clouds which fall outside the large-scale limit are affected by the NCT. A simple scaling indicates that a Lagrangian parcel...

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: 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...

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...

Data from: The effects of temperature on the kinematics of rattlesnake predatory strikes in both captive and field environments

Malachi Whitford, Grace Freymiller, Timothy Higham & Rulon Clark
The outcomes of predator-prey interactions between endotherms and ectotherms can be heavily influenced by environmental temperature, owing to the difference in how body temperature affects locomotor performance. However, as elastic energy storage mechanisms can allow ectotherms to maintain high levels of performance at cooler body temperatures, detailed analyses of kinematics are necessary to fully understand how changes in temperature might alter endotherm-ectotherm predator-prey interactions. Viperid snakes are widely distributed ectothermic mesopredators that interact with endotherms...

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...

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...

Slowing the body slows down time (perception)

Rose De Kock, Weiwei Zhou, Wilsaan Joiner & Martin Wiener
Interval timing is a fundamental component of action, and is interestingly susceptible to motor-related temporal distortions. Several experiments have shown that temporal expansion and compression can occur in systematic ways with modifications of movement direction, speed, and length. These studies have largely shown that movement biases temporal estimates, but have primarily considered self-modulated movement only. However, real-world encounters often include situations in which movement is restricted or perturbed by environmental factors. Thus, in the following...

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...

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 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...

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...

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...

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.

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...

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...

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...

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...

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...

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...

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...

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