One-dimensional models of radiation transfer in heterogeneous canopies: a review, re-evaluation, and improved modelBrian Bailey, María Ponce De León & E. Scott Krayenhoff
This dataset contains the project files and data output for the publication: Bailey, Brian; Ponce de León, María; Krayenhoff, E. Scott (2019), One-dimensional models of radiation transfer in heterogeneous canopies: A review, re-evaluation, and improved model. The file main.cpp contains the main program that sets up and runs the simulations. Output files are stored in the 'output' directory. The current version of the Helios source code can be downloaded at https://www.github.com/PlantSimulationLab/Helios
Bacteria isolated from bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds associated with animal signalingMei Yamaguchi, Guillaume Jospin, Holly Ganz, David Coil, Jonathan Eisen, Adrienne Cho, Thant Zaw, Mitchell McCartney & Cristina Davis
Anal sacs are an important odor producing organ found across the mammalian Order Carnivora. Secretions from the anal sac may be used as chemical signals by animals for behaviors ranging from defense to species recognition to signaling reproductive status. In addition, a recent study suggests that domestic cats utilize short-chain free fatty acids in anal sac secretions for individual recognition. The fermentation hypothesis is the idea that symbiotic microorganisms living in association with animals contribute...
Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)Paul Gepts
Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris, the progenitor of common bean (P. vulgaris), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and...
Self-driving vehicles, as a revolution in mobility, are emerging and developing rapidly. However, public attitudes toward this new unproven technology are still uncertain. Given the significant influence of attitude toward a new technology on the intention to use it, the question arises as to why some people are in favor of this technology whereas others are not. Additionally, questions about the key attitudes influencing self-driving technology acceptance, where these attitudes come from, and how they...
Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of EvolutionMichael Hardigan, Mitchell Feldmann, Anne Lorant, Kevin Bird, Steven Knapp, Patrick Edger, Glenn Cole, Charlotte Acharya & Randi Famula
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a...
Measurements from the Fire Influence on Regional and Global Environments Experiment (FIREX) Fire Lab Mini Chamber ExperimentChristopher Cappa, Christopher Lim, David Hagan & Jesse Kroll
All experiments were conducted during the Fire Influence on Regional to Global Environments Experiment (FIREX) lab study, which took place at the Missoula Fire Sciences Lab in Missoula, MT, USA during November, 2016. Experiments focused on refining our understanding of emissions and short timescale processing. The focus was on measuring fuels or combustion conditions that are characteristic of the western U.S. that may be under-sampled by the fire research community. Numerous types of biomass were...
Data from: Evolution of sexually dimorphic pheromone profiles coincides with increased number of male-specific chemosensory organs in Drosophila prolongataYige Luo, Yuewei Zhang, Jean-Pierre Farine, Jean-François Ferveur, Santiago Ramírez & Artyom Kopp
Binary communication systems that involve sex-specific signaling and sex-specific signal perception play a key role in sexual selection and in the evolution of sexually dimorphic traits. The driving forces and genetic changes underlying such traits can be investigated in systems where sex-specific signaling and perception have emerged recently and show evidence of potential coevolution. A promising model is found in Drosophila prolongata, which exhibits a species-specific increase in the number of male chemosensory bristles. We...
Global food systems rely on irrigated agriculture, and most of these systems in turn depend on fresh sources of groundwater. In this study, we demonstrate that groundwater development, even without overdraft, can transform a fresh, open basin into an evaporation dominated, closed-basin system, such that most of the groundwater, rather than exiting via stream baseflow and lateral subsurface flow, exits predominantly by evapotranspiration from irrigated lands. In these newly closed hydrologic basins, just as in...
Effect of Drought Stress on the Genetic Architecture of Photosynthate Allocation and Remobilization in Pods of Common Bean (Phaseolus vulgaris L.), a Key Species for Food SecurityPaul Gepts, Jorge Carlos Berny Mier Y Teran, Enéas R. Konzen, Antonia Palkovic, Siu M. Tsai, Idupulapati M. Rao & Stephen Beebe
Background: Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed...
Supporting data for the manuscript: Observations and modeling of the surface seiches of Lake Tahoe, USADerek Roberts, S. Geoffrey Schladow & Alexander Forrest
This data set was created to make the data associated with the manuscript Observations and modeling of the surface seiches of Lake Tahoe, USA, accepted for publication in Aquatic Sciences, publically available per journal convention. The publication abstract is shown below: A rich array of spatially complex surface seiche modes exists in lakes. While the amplitude of these oscillations is often small, knowledge of their spatio-temporal characteristics is valuable for understanding when they might be...
Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?Paul Gepts, Saarah Kuzay & Paige Hamilton
Core collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris) core collection of the USDA Western Regional Plant Introduction Station was one of the first ones to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a SNP platform and new...
Genital morphology and the mechanics of copulation in the millipede genus Pseudopolydesmus (Diplopoda: Polydesmida: Polydesmidae)Xavier Zahnle, Petra Sierwald, Stephanie Ware & Jason Bond
Mate choice, copulation, genital morphology, and sperm storage are not very well understood in millipedes. The use of three-dimensional x-ray computed tomography (µCT) provides new morphological data regarding millipede reproductive systems in both the female and male, including chitinous sclerites and membranes, muscles, glands, oviducts, and sperm conduits. Here we present a complete integrated account of the morphology and function of the female genital organs in the family Polydesmidae (Diplopoda: Polydesmida) using µCT, UV fluorescence...
This survey data is from a study exploring the potential to promote lower-emissions air travel by providing consumers with information about the carbon emissions of possible flight choices in the context of online flight search and booking. We surveyed over 450 faculty, researchers, and staff at the University of California, Davis, and asked them to choose among hypothetical flight options for a domestic and an international university-related business trip. Emissions estimates for different flight alternatives...
Recently, it was suggested that North America has lost nearly 30% of its avifauna since the 1970s. To mitigate such avian population declines, many birds in California are protected under the Migratory Bird Treaty Act and California Fish and Game Code. Avian presence, therefore, at Caltrans infrastructure projects, especially bridge construction, has caused costly delays. To avoid this conflict and understand population-specific migration and nesting patterns, we used Anna’s hummingbird, Calypte anna, (a species whose...
This tabular data can be used to evaluate perceived bicycling comfort on distinct state highways in California. The highway settings are primarily urban, but vary in traffic conditions, lane configurations, speeds, and bicycling infrastructure. The data include survey responses to video clips of these state highways along with a series of additional survey data that co-varies with the video survey responses.
Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in a genetically diverse strawberry populationSteven Knapp, Dominique Pincot, Michael Hardigan, Glenn Cole, Peter Henry, Thomas Gordon & Randi Famula
Verticillium wilt, a soil-borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a challenge since the disease was first reported on strawberry in the early 1900s. The empirical evidence suggests that genetic gains have not been negligible and that the genetics of resistance to this pathogen is quantitative. While resistant cultivars have been developed, a comparatively small percentage are highly resistant,...
Domestic Well Vulnerability to Drought Duration and Unsustainable Groundwater Management in California's Central ValleyRichard Pauloo, Helen Dahlke, Graham Fogg, Herve Guillon, Amanda Fencl & Alvar Escriva-Bou
Millions of Californians access drinking water via domestic wells, which are vulnerable to drought and unsustainable groundwater management. Groundwater overdraft and the possibility of longer drought duration under climate change threatens domestic well reliability, yet we lack tools to assess the impact of such events. Here, we leverage 943,469 well completion reports and 20 years of groundwater elevation data to develop a spatially-explicit domestic well failure model covering California's Central Valley. Our model successfully reproduces...
Abstract Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display some atavistic characteristics that were advantageous to their wild ancestors, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in a domesticated grain legume, common bean (Phaseolus vulgaris). We compared three methods to evaluate the PD phenotype and identified multiple, unlinked genetic regions controlling PD using a biparental population and two...
Data and analysis code for \"Forest recovery following extreme drought in California, USA: natural patterns and effects of pre-drought management\"Derek Young, Marc Meyer, Becky Estes, Shana Gross, Amarina Wuenschel, Christina Restaino & Hugh Safford
This repository contains data and code for the paper "Forest recovery following extreme drought in California, USA: natural patterns and effects of pre-drought management" by Young et al., published in Ecological Applications. The abstract of the paper is as follows. Rising temperatures and more frequent and severe droughts are driving increases in tree mortality in forests around the globe. However, in many cases, the likely trajectories of forest recovery following drought-related mortality are poorly understood....
Assessment of the effect of UV and visible light on the chemical properties of soils. Raw data of chemical properties measured in a laboratory study of a soils exposed to light.
Sociodemographic data for battery electric vehicle owning households in California (From NCST Project \"Understanding the Early Adopters of Fuel Cell Vehicles\")Scott Hardman
Sociodemographic data for fuel cell and battery electric vehicle owning households in California
Purified and Cy5-labeled Trichoderma reesei Cel7A and its variants (Cel7A catalytic domain, catalytically deficient E212Q mutant and the catalytic domain of E212Q) interacting at the surface of crystalline cellulose fibrils were imaged by Total Internal Reflectance Fluorescence Microscopy (TIRFM).
Genomes From Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic AssignmentDavid Coil, Guillaume Jospin, Jonathan Eisen, Aaron Darling, Collin Wallis, Ian Davis, Stephen Harris, Lucy Holcombe & Ciaran O'Flynn
Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy...
University of California, Davis38
United States Department of Agriculture2
University of Sao Paulo2
California Lutheran University2
University of Washington1
University of Eastern Finland1
Washington State University Vancouver1
Field Museum of Natural History1
Turku PET Centre1
Los Alamos National Laboratory1