104 Works

Structure and distribution of chalky deposits in the Pacific oyster using x-ray computed tomography (CT)

Roxanne Banker & Dawn Sumner
Oysters are unusual among bivalves in that they possess chambers, often filled with soft, chalky calcite, that are irregularly scattered throughout the shell. Because the function of these so-called chalky deposits is still unclear, evaluating the growth and distribution of chalk is important for elucidating the ecological function of this unique shell trait. Specimens of the Pacific oyster Magallana gigas, an oyster well known for chalk expression, were grown in Bodega Harbor, Bodega Bay, CA....

Genetic structure in a cnidarian symbiont is correlated with geographic location, environment, and host species

Brendan Cornwell & Luis Hernández
Corals and cnidarians form symbioses with dinoflagellates across a wide range of habitats from the tropics to temperate zones. Notably, these partnerships create the foundation of coral reef ecosystems and are at risk of breaking down due to climate change. This symbiosis couples the fitness of the partners, where adaptations in one species can benefit the holobiont. However, the scales over which each partner can match their current - and future - environment are largely...

Data for project: A quantitative investigation into the impact of partially automated vehicles on vehicle miles travelled in California

Scott Hardman
We investigate travel changes in partially automated electric vehicles. Partial automation can control vehicle speed and steering using sensors that monitor the external environment. We use survey results from survey responses including 940 users of partial automation, including 628 who have Tesla Autopilot and 312 with systems from other automakers. Autopilot users report using automation more than users of other partial automation systems. Autopilot has the largest impact on travel, notably 36% of Autopilot users...

Data from: The utility of climatic water balance for ecological inference depends on vegetation physiology assumptions

Derek Young, Sean Jeronimo, Derek Churchill, Van Kane & Andrew Latimer
This repository contains the data and code supporting the analyses in the corresponding paper in Global Ecology and Biogeography (GEB). The abstract of the paper is as follows: Background: In modeling and explaining spatial vegetation patterns, ecologists have increasingly favored the use of climatic water balance variables, including actual evapotranspiration (AET) and climatic water deficit (CWD), for representing the hydrologic and energetic environment experienced by plants. Much of the interest in these variables lies in...

The effects of sunlight and slope on the lichen community of the Sweeney Granite Mountains reserve

Kha Cung, , & Samantha Spiegel
Lichen communities are essential to their ecosystems as they provide a means of nitrogen fixation, suitable growing conditions, and resources to other organisms across diverse environments. Their community structure can be impacted by changes in abiotic factors such as temperature, pollution, precipitation, and sunlight. It is widely assumed that lichen prefer to grow on the northern faces of their substrates because it is believed they experience less desiccation and UV radiation from sunlight exposure. This...

Population structure of Drosophila suzukii and signals of multiple invasions in the continental United States

Joanna Chiu
Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. In this study, we sequenced whole genomes of 237 individual...

California Drinking Water Source Assessment Program – UC Davis Information Center for the Environment

Leah Walker & Paul Collins
The California Drinking Water Source Assessment Program (DWSAP) was developed by the California Department of Public Health (CDPH) to provide information to communities that wish to develop local programs to protect their sources of drinking water. ICE was contracted with CDPH in 1999 to provide a wide range of technical services in support of this program, including the development of a statewide, standardized protocol to GPS all drinking water sources and treatment facilities in the...

Population and community-level impacts of increased fire frequency in serpentine chaparral

Miranda Martin, Casey Pfahler, Francesca Shackleford & Emily Wapman
Wildfires are natural processes that revitalize the native biodiversity of many habitats by clearing landscapes and creating sunlight rich areas with low competition. This process occurs in the serpentine chaparral of California, which is home to a variety of fire obligate seeders, including whiteleaf manzanita (Arctostaphylos viscida) and MacNab cypress (Cupressus macnabiana), as well as fire facultative seeders such as chamise (Adenostoma fasciculatum). In our study, we surveyed serpentine chaparral habitats in sites with different...

Pictures of unmanned aerial vehicle (UAV) experiments on testing paper

Shuting Liao, Li-Yu Liu, Ting-An Chen, Kuang-Yu Chen & Fushing Hsieh
Our computational developments and analyses on experimental images are designed to evaluate the effectiveness of chemical spraying via unmanned aerial vehicle (UAV). Our evaluations are in accord with the two perspectives of color-complexity: color variety within a color system and color distributional geometry on an image. First, by working within RGB and HSV color systems, we develop a new color-identification algorithm relying on highly associative relations among three color-coordinates to lead us to exhaustively identify...

Project factors and conservation outcome data for SeaDoc Society-funded research projects

Monica LeFlore, Peter Sebastian, Joseph K. Gaydos & David Bunn
This dataset reflects project factors and conservation success of 20 years of research funded by the academically-based marine conservation group the Sea Doc Society (UC Davis School of Veterinary Medicine). These data were compiled through interviews with Principal investigators and co-investigators, and SeaDoc Society's records.

Perspective piece: Comparison of eastern and western North American monarch butterflies

Micah Freedman
Monarch butterflies are a species of conservation priority due to declining overwintering populations in both eastern and western North America. Declines in western overwintering monarchs—more than 99.9% since monitoring began—are especially acute. However, the degree to which western monarchs are a distinct biological entity is uncertain. In this review, we focus on phenotypic and genetic differentiation between eastern and western monarchs, with the goal of informing researchers and policy-makers who are interested in monarch conservation....

Morphology and herbivory of Egregia menziesii at sites from California to Washington

Nicholas Burnett, Eric Armstrong, Rosemary Romero, Charlotte Runzel & Richelle Tanner
Herbivores can drastically alter the morphology of macroalgae by directly consuming tissue and by inflicting structural wounds. Wounds, in particular, can result in large amounts of tissue breaking away from macroalgae, amplifying the damage initially caused by herbivores. Herbivores that commonly wound macroalgae often only occur over a portion of a macroalga’s lifespan or geographic range. However, we know little about the influence of these periodic or regional occurrences of herbivores on the large-scale seasonal...

Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom

Celine Caseys, Gongjun Shi, Nicole Soltis, Raoni Gwinner, Jason Corwin, Susanna Atwell & Daniel Kliebenstein
Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host...

The deep sea is a hot spot of fish body shape evolution

Christopher Martinez
Deep sea fishes have long captured our imagination with striking adaptations to life in the mysterious abyss, raising the possibility that this cold, dark ocean region may be a key hub for physiological and functional diversification. We explore this idea through an analysis of body shape evolution across ocean depth zones in over 3,000 species of marine teleost fishes. We find that the deep ocean contains twice the body shape disparity of shallow waters, driven...

A preliminary framework for magmatism in modern continental back-arc basins and its application to the Triassic-Jurassic tectonic evolution of the Caucasus

Dylan Vasey, Eric Cowgill & Kari Cooper
In contrast to intraoceanic back-arc basins, extension within a continental back-arc basin initiates within continental rather than oceanic lithosphere. The geochemical characteristics of magmatic rocks within continental back-arc basins are poorly understood relative to their intraoceanic counterparts. Here, we compile published geochemical data from five modern continental back-arc basins – the Okinawa Trough, Bransfield Strait, Tyrrhenian Sea, Patagonia plateau, and Aegean Sea/Western Anatolia – to establish a geochemical framework for continental back-arc magmatism. This analysis...

Rice-recombinant butyrylcholinesterase (rrBChE) production dataset

Shuting Liao, Kantharakorn Macharoen, Karen McDonald, Somen Nandi & Debashis Paul
We propose a method for analyzing the variability in smooth, possibly nonlinear, functionals associated with a set of product production trajectories measured under different experimental conditions. The key challenge is to make meaningful inference on these parameters across different experimental conditions when only a limited number of measurements in time are collected for each treatment, and when there are only a few, or no, replicates available. For this purpose we adopt a modeling approach by...

Long-term changes in composition of old-growth mixed evergreen forests in Mendocino County

, Charlie Schiebl, Gabriel Perez & John Salib
Abiotic factors have caused changes in old-growth California forests. These changes may be indicators of environmental stressors such as decreases in precipitation, increases in temperature, and changes in historic fire regimes. We aim to examine these changes by doing a 40-year follow-up study on Ashley Boren’s 1981 undergraduate thesis, conducted at Angelo Coast Reserve in Mendocino County, California. The purpose of this study is to examine whether or not the predictions made in 1981 would...

Phylogeny, Evolution, and Biogeography of the North American Trapdoor Spider family Euctenizidae (Araneae: Mygalomorphae) and the discovery of a new ‘Endangered Living Fossil’ along California’s Central Coast

Jason E. Bond, Chris A. Hamilton, Rebecca L. Godwin, Joel M. Ledford & James. Starrett
We report here the discovery of a remarkable new monotypic mygalomorph spider genus, known only from one geographical location along the central coast of California. The single relict species comprising Cryptocteniza kawtakn. gen. n. sp., is morphologically distinct and geographically isolated from other related genera, with its closest phylogenetic relatives found much further to the east in New Mexico and Arizona. Using a phylogenomic approach employing anchored hybrid enrichment, we reconstruct the evolutionary history of...

Shrubland vegetation topographic facets of Southern California

Allan Hollander & Emma Underwood
To approximate the distribution of shrubland species based on their postfire reproductive strategy (resprouter, seeder, and facultative seeder) across Southern California, we created a raster layer subdividing the landscape into a number of different facet classes. This raster dataset is at 30 meters pixel resolution and contains 12 different landscape facet classes based on vegetation and physiography. Specifically, the facets included several different vegetation types based on the California Wildlife Habitat Relations (WHR) classification (three...

Snail mucus increases the CO2 efflux of biological soil crusts

Shelby Rinehart, Netta Shamir Weller & Dror Hawlena
Biological soil crusts (hereafter, biocrusts) are communities of microorganisms that regulate key ecosystem processes such as water distribution, soil erosion, and nutrient cycling in drylands worldwide. The nature of biocrust function can be influenced by multiple environmental factors, including climatic conditions (e.g., precipitation), interactions with plants, and anthropogenic disturbances. Animal regulation of biocrust function has received less research attention, focusing primarily on livestock trampling and to a much lesser extent on biocrust consumption by mesofauna....

Wheat grain yield decreased over the past 35 years, but protein content did not change

Arnold Bloom & Richard Plant
The extent to which rising atmospheric CO2 concentration has already influenced food production and quality is uncertain. Here, we analyzed annual field trials of fall-planted common wheat in California from 1985 to 2019, a period during which global atmospheric CO2 concentration increased 19%. Even after accounting for other major factors (cultivar, location, degree-days, soil temperature, total water applied, nitrogen fertilization, and pathogen infestation), wheat grain yield and protein yield declined 13% over this period, but...

Map script with examples from: Taxonomic revision of the Temnothorax salvini clade (Hymenoptera: Formicidae), with a key to the clades of New World Temnothorax

Matthew Prebus
Temnothorax is a large myrmicine ant genus with a range spanning the northern hemisphere, including the northern half of the Neotropics. Many of the Neotropical species were originally placed in the now defunct genus Macromischa. Recent molecular work has revealed that distinct lineages of Neotropical Temnothorax have arrived by evolutionary convergence at a morphological syndrome with characteristics that were used to diagnose the former genus Macromischa. One such lineage is the salvini clade, which in...

California subalpine forest post-fire diversity and productivity

Emily Brodie
High severity fire may promote or reduce plant understory diversity in forests. However, few empirical studies test long-standing theoretical predictions that productivity may help to explain observed variation in post-fire plant diversity. Support for the influence of productivity on disturbance-diversity relationships is found predominantly in experimental grasslands, while tests over large areas with natural disturbance and productivity gradients are few and have yielded inconsistent results. Here, we measured the response of post-fire understory plant diversity...

Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly

Tingting Zhu, Le Wang, Hélène Rimbert, Juan Rodriguez, Karin Deal, Romain De Oliveira, Frédéric Choulet, Gabriel Keeble-Gagnère, Josquin Tibbits, Jane Rogers, Kellye Eversole, Rudi Appels, Yong Gu, Martin Mascher, Jan Dvorak, Ming-Cheng Luo, Juan C. Rodriguez, Karin R. Deal, Gabriel Keeble‐Gagnère, Yong Q. Gu & Ming‐Cheng Luo
This dataset contains a single whole-genome optical map file (.CMAP) for bread wheat (Triticum aestivum) cv Chinese Spring (CS). The methods for constructing this optical map and the properties of this map are described below. The definition of the CMAP format is documented in https://bionanogenomics.com/wp-content/uploads/2017/03/30039-CMAP-File-Format-Specification-Sheet.pdf. The extracted ultra-high-molecular weight DNA molecules of CS were labeled with the DLE-1 enzyme (Bionano Genomics, San Diego, CA, USA) and were then stained with the Bionano PrepTM DLS Kit...

Environmental metadata for: 2019/2020 biomineral sampling of drainpipes from California public rest areas

Kahui Lim, Harold Leverenz, Cara Wademan & Samantha Barnum
Clogging and odor is strongly associated with ureolytic biomineralization in waterless and low-flow urinal drainage systems in high usage settings. These blockages continue to hinder widespread waterless and low-flow urinal adoption due to subsequent high maintenance requirements and hygiene concerns. Through field observations, hypothesis testing, and multiple regression analysis, this study attempts to characterize, for the first time, the ureolytic activity of the biomineralization found in alternative cated at 9 State-owned restrooms. Multiple regression analysis...

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  • 2021
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  • University of California, Davis
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  • Centre d'Etudes Biologiques de Chizé
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