78 Works

Thermal and energetic ion dynamics in Ganymede's magnetosphere

This dataset accompanies the manuscript "Thermal and energetic dynamics in Ganymede's magnetosphere", JGR Space Physics, 2018.

2D attenuation model of Long Valley (CA)

Janire Prudencio, Michael Manga & Taka'aki Taira
We image seismic intrinsic (Qi-1) and scattering (Qs-1) attenuation in Long Valley caldera, California, by analyzing more than 1700 vertical-component waveforms from local earthquakes. Observed energy envelopes are fit to the diffusion model (data files) and seismic attenuation images (anomalies files) are produced using two-dimensional space-weighting functions.

Supporting data for \"Evaluation of version 3.0B of the BEHR OMI NO2 product\"

Joshua Laughner, Qindan Zhu & Ronald Cohen
This dataset contains supporting data for the paper "Evaluation of version 3.0B of the BEHR OMI NO2 product" by Laughner, Zhu, and Cohen. Evaluation of new satellite trace gas products is an important step in proving their usefulness, and, in the case of NO2, is typically done by comparing the satellite-observed vertical column densities to independent measurements taken by aircraft or ground-based spectrometers. Input data required by the satellite retrieval may also be directly compared...

Restoration of incomplete oceanographic datasets

Siavash Ameli & Shawn Shadden
Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data, and are often based on projecting the measurements onto basis functions or a statistical model. Herein, we use an information transport approach inspired from an image processing algorithm. This approach aims to restore gaps in data...

Data from: Mutual fitness benefits arise during coevolution in a nematode-defensive microbe model

Charlotte Rafaluk-Mohr, Ben Ashby, Dylan A. Dahan & Kayla C. King
Species interactions can shift along the parasitism-mutualism continuum. However, the consequences of these transitions for coevolutionary interactions remain unclear. We experimentally coevolved a novel species interaction between Caenorhabditis elegans hosts and a mildly parasitic bacterium, Enterococcus faecalis, with host-protective properties against virulent Staphylococcus aureus. Coinfections drove the evolutionary transition of the C.elegans-E. faecalis relationship towards a reciprocally beneficial interaction. As E. faecalis evolved to protect nematodes against S. aureus infection, hosts adapted by accommodating greater...

Data from: Glucocorticoid-environment relationships align with responses to environmental change in two co-occurring congeners

Talisin T. Hammond, Rupert Palme & Eileen A. Lacey
As more species undergo range shifts in response to climate change, it is increasingly important to understand the factors that determine an organism’s realized niche. Physiological limits imposed by abiotic factors constrain the distributions of many species. Because glucocorticoids are essential to the maintenance of physiological homeostasis, identifying glucocorticoid-environment relationships may generate critical insights into both limits on species distributions and potential responses to environmental change. We explored relationships between variability in baseline glucocorticoids and...

Data from: Bayesian vector transmission model detects conflicting interactions from transgenic disease‐resistant grapevines

Adam R. Zeilinger, Daniel Turek, Daniele Cornara, Anne Sicard, Steven E. Lindow & Rodrigo P. P. Almeida
Effective management of vector-borne plant pathogens often relies on disease-resistant cultivars. While heterogeneity in host resistance and in pathogen population density at the host population level play important and well-recognized roles in epidemiology, the effects of resistance traits on pathogen distribution at the individual host level, and the epidemiological consequences in turn, are poorly understood. Transgenic disease-resistant plants that produce bacterial Diffusible Signaling Factor (DSF) could provide resistance to the vector-borne bacterium Xylella fastidiosa by...

Data from: Genomic analysis of MHC-based mate choice in the monogamous California mouse

Jesyka Meléndez-Rosa, Ke Bi, Elieen A. Lacey & Eileen A Lacey
Variation at Major Histocompatibility Complex (MHC) genes is thought to be an important mechanism underlying mate choice in vertebrates, with individuals typically predicted to prefer MHC-dissimilar reproductive partners. However, analyses based on individual MHC loci have generated contradictory results regarding the role of these genes in mate choice decisions. To provide a more comprehensive assessment of relationships between MHC variation and mating behavior, we used an exome capture strategy to characterize variability at 13 MHC...

Data from: Microbiome interactions shape host fitness

Alison L. Gould, Vivian Zhang, Lisa Lamberti, Eric W. Jones, Benjamin Obadia, Nikolaos Korasidis, Alex Gavryushkin, Jean M. Carlson, Niko Beerenwinkel & William B. Ludington
Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each...

Data from: The Metapopulation Microcosm Plate: a modified 96-well plate for use in microbial metapopulation experiments

Helen Kurkjian & Helen M. Kurkjian
1. Researchers in many sub-fields of ecology and evolutionary biology test hypotheses relating to metapopulation dynamics and landscape spatial structure. Key aspects of these hypotheses are often (a) large numbers of subpopulations and dispersal corridors and (b) their positions relative to each other. Testing such spatial hypotheses using traditional lab equipment and methods can be impractical, unwieldy, expensive, or impossible. 2. The Metapopulation Microcosm Plate (MMP) overcomes these difficulties. This device resembles a 96-well microtiter...

Data from: Native grass ground covers provide multiple ecosystem services in Californian vineyards

Kent M. Daane, Brian N. Hogg, Houston Wilson & Glenn Y. Yokota
1. The mechanisms responsible for the success or failure of agricultural diversification are often unknown. Most studies of arthropod pest management focus on enhancing the effectiveness of natural enemies, but non-crop plants can also improve or hamper pest suppression by changing the host quality of crop plants by reducing or adding available soil nutrients or water. Native perennial ground covers may provide resources and long-term habitat to resident natural enemies and be more compatible than...

Data from: Rapid divergence of mussel populations despite incomplete barriers to dispersal

Diede L. Maas, Stefan Prost, Ke Bi, Lydia L. Smith, Ellie E. Armstrong, Ludi P. Aji, Abdul H.A. Toha, Rosemary G. Gillespie & Leontine E. Becking
Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Data from: Seed ingestion and germination in rattlesnakes: overlooked agents of rescue and secondary dispersal

Randall S. Reiserer, Gordon W. Schuett & Harry W. Greene
Seed dispersal is a key evolutionary process and a central theme in the population ecology of terrestrial plants. The primary producers of most land-based ecosystems are propagated by and maintained through various mechanisms of seed dispersal that involve both abiotic and biotic modes of transportation. By far the most common biotic seed transport mechanism is zoochory, whereby seeds, or fruits containing them, are dispersed through the activities of animals. Rodents are one group of mammals...

Data from: Animals alter precipitation legacies: trophic and ecosystem engineering effects on plant community temporal dynamics

Joshua B. Grinath, Nicolas Deguines, John W. Chesnut, Laura R. Prugh, Justin S. Brashares & Katharine N. Suding
1. Multi-year precipitation ‘legacies’ can have stronger effects on plant community composition than rainfall in the current growing season, but variation in the magnitude of these effects is not fully understood. Direct interactions between plants and animals, such as herbivory, and indirect interactions, such as ecosystem engineering (via changes in the physical environment), may influence precipitation legacies by altering mechanisms of lagged effects. However, the role of direct and indirect plant-animal interactions in determining the...

Data: Researcher Perspectives on the Use and Sharing of Software

Yasmin Alnoamany & John Borghi
We are interested in learning about perceptions, values, and behaviors around the computer software generated as part of the research process. To understand researchers' prespectives on software usage and sharing, we conducted an online survey sent to researchers at academic institutions throughout the United States. We used the Qualtrics platform to distribute our survey. This data set contains the responses of the survey participants after excluding any personally identifying data. All study materials and procedures...

Berkeley High Resolution (BEHR) OMI NO2 - Gridded pixels, daily profiles

Joshua Laughner, Ronald Cohen & Qindan Zhu
The BEHR OMI NO2 product reprocesses tropospheric NO2 columns from the Ozone Monitoring Instrument (OMI) satellite using high resolution a priori NO2 profiles, surface reflectivity, and surface elevation data. This product uses NO2 profiles for the day retrieved, simulated by the WRF-Chem model at 12 km spatial resolution. The use of high spatial resolution NO2 profiles has been shown to better resolve urban/rural differences in NO2 column densities, and the use of day-to-day (rather than...

A Bayesian method of evaluating discomfort due to glare: The effect of order bias from a large glare source

Toby Cheung, Michael Kent, Stefano Schiavon & Aleksandra Lipczyńska
to be confrim

Training and Support for Student Library Employees in a Tiered Reference Service Model: Supporting Materials

Brian Quigley, Jeffery Loo, Lisa Ngo, Susan Powell, Samantha Teplitzky, Anna Sackmann & Kortney Rupp
To cultivate students’ reference skills, the Engineering and Physical Sciences Division of the UC Berkeley Library developed an active training program based upon a dynamic online reference manual continuously improved with student feedback. We evaluate the effectiveness of our training program and share procedures and tools for enhancing student training. Students were given a pre-test of reference skills and self-efficacy prior to attending an annual training session. One month afterwards, we distributed a post-test and...

Effect of non-Schmid Stresses on a-type Screw Dislocation Core Structure and Mobility in Titanium

Max Poschmann
Data summarizing DFT calculations concerning the effects of non-Schmid stresses on dislocation core structure and mobility in titanium.

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Cassandra Ettinger, Laetitia Wilkins, Guillaume Jospin & Jonathan Eisen
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and...

Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

Charles R. Marshall, Seth Finnegan, Erica C. Clites, Patricia A. Holroyd, Nicole Bonuso, Crystal Cortez, Edward Davis, Gregory P. Dietl, Patrick S. Druckenmiller, Ron C. Eng, Christine Garcia, Kathryn Estes-Smargiassi, Austin Hendy, Kathy A. Hollis, Holly Little, Elizabeth A. Nesbitt, Peter Roopnarine, Leslie Skibinski, Jann Vendetti & Lisa D. White
Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology’s first digital revolution – online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a...

Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

Richard W. Hill, Eric J. Armstrong, Kazuo Inaba, Masaya Morita, Martin Tresguerres, Jonathon H. Stillman, Jinae N. Roa & Garfield T. Kwan
The giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However, T. crocea’s mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of...

Data from: Migratory plasticity is not ubiquitous among large herbivores

Hall Sawyer, Jerod A. Merkle, Arthur D. Middleton, Samantha P.H. Dwinnell, Kevin L. Monteith & Samantha P. H. Dwinnell
1. The migratory movements of wild animals can promote abundance and support ecosystem functioning. For large herbivores, mounting evidence suggests that migratory behavior is an individually variable trait, where individuals can easily switch between migrant and resident tactics. The degree of migratory plasticity, including whether and where to migrate, has important implications for the ecology and conservation of large herbivores in a changing world. 2. Mule deer (Odocoileus hemionus) are an iconic species of western...

Data from: The role of red coloration and song in peacock spiders: insights into complex signaling systems

Madeline B. Girard, Michael M. Kasumovic & Damian O. Elias
Research on animal signaling enhances our understanding of links between sensory processing, decision-making, behavior, and evolution. Studies of sexually-selected signals may be particularly informative as mate choice provides access to decision patterns in the way that courtship leads to an easily observable behavioral output in choosers, i.e. mating. Male peacock spiders have some of the most elaborate and varied courtship displays known among animals. Particularly striking to human observers is the diversity of red, orange...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of Minnesota
  • University of Washington
  • Columbia University
  • University of California System
  • Museum of Vertebrate Zoology
  • Dayton Foundation
  • Cornell University
  • Stanford University
  • University of California, San Diego