80 Works

Minimum Depth to Groundwater for the Coastal San Francisco Bay Area

Ellen Plane, Kristina Hill & Kris May
This dataset shows estimated values for minimum depth to groundwater in the coastal Bay Area. The estimation is based on an interpolation that uses ground elevation data and minimum depth to water values measured at monitoring wells in the nine Bay Area counties over the past 20 years. NOTE: The most recently uploaded data file (August 24, 2018) has the highest accuracy in the interpolation. Please use this file rather than the older versions. A...

Data from: Stimulus discriminability may bias value-based probabilistic learning

Iris Schutte, Heleen A. Slagter, Anne G.E. Collins, Michael J. Frank, J. Leon Kenemans & Anne G. E. Collins
Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of...

Data from: Population genetic and field ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian

Ian J. Wang & H. Bradley Shaffer
The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field ecological studies. However, empirical assessments of the concordance between direct field ecological and indirect population genetic studies...

Data from: Museum specimen data reveal emergence of a plant disease may be linked to increases in the insect vector population

Adam R. Zeilinger, Giovanni Rapacciuolo, Daniel Turek, Peter T. Oboyski, Rodrigo P. P. Almeida & George K. Roderick
The emergence rate of new plant diseases is increasing due to novel introductions, climate change, and changes in vector populations, posing risks to agricultural sustainability. Assessing and managing future disease risks depends on understanding the causes of contemporary and historical emergence events. Since the mid-1990s, potato growers in the western United States, Mexico, and Central America have experienced severe yield loss from Zebra Chip disease and have responded by increasing insecticide use to suppress populations...

Data from: Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia) drepanolobium

John H. Boyle, Dino J. Martins, Julianne Pelaez, Paul M. Musili, Staline Kibet, S. Kimani Ndung'u, David Kenfack & Naomi E. Pierce
1. The Acacia drepanolobium (also known as Vachellia drepanolobium) ant-plant symbiosis is considered a classic case of species coexistence, in which four species of tree-defending ants compete for nesting space in a single host tree species. Coexistence in this system has been explained by trade-offs in the ability of the ant associates to compete with each other for occupied trees versus the ability to colonize unoccupied trees. 2. We seek to understand the proximal reasons...

Data from: Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns

Paul G. Wolf, Tanner A. Robison, Matthew G. Johnson, Michael A. Sundue, Weston L. Testo & Carl J. Rothfels
Premise of the study: Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one...

Data from: Complex coevolution of wing, tail, and vocal sounds of courting male bee hummingbirds

Christopher J. Clark, Jimmy A. McGuire, Elisa Bonaccorso, Jacob S. Berv & Richard O. Prum
Phenotypic characters with a complex physical basis may have a correspondingly complex evolutionary history. Males in the ‘bee’ hummingbird clade court females with sound from tail-feathers, which flutter during display dives. On a phylogeny of 35 species, flutter sound frequency evolves as a gradual, continuous character on most branches. But on at least six internal branches fall two types of major, saltational changes: mode of flutter changes, or the feather that is the sound source...

Dataset for Large-Scale Analysis of Modern Code Review Practices and Software Security in Open Source Software

Christopher Thompson
Dataset for my thesis titled "Large-Scale Analysis of Modern Code Review Practices and Software Security in Open Source Software. Contains: Labeled issues data used to train and test the quantifier models. Post-quantification datasets the analyses were performed on. Scripts (R, Python) for all analyses performed.

Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United States

K. K. McLauchlan, L. M. Gerhart, J. J. Battles, J. M. Craine, A. J. Elmore, P. E. Higuera, M. C. Mack, B. E. McNeil, D. M. Nelson, N. Pederson & S. S. Perakis
Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing demand for N, the element limiting primary productivity in temperate forests, which could be reducing N availability. To determine the long-term, integrated effects of global changes...

Data from: Tree-growth is more sensitive than species distributions to recent changes in climate and acidic deposition in the northeastern United States

Jay W. Wason, Martin Dovciak, Colin M. Beier & John J. Battles
Tree-growth responses to environmental change could provide early detection of shifts in forest composition and help facilitate ecosystem management and conservation. We studied forest tree responses to recent trends in climate and acidic deposition using analyses of tree rings and long-term climate, deposition and forest plot data along an elevational climatic gradient in the northeastern United States. We analyzed how (a) individual growth of dominant species (Picea rubens, Abies balsamea), and (b) spatial distributions of...


Daniella Hirschfeld, Kristina Hill & Ellen Plane
As awareness of climate change increases more projects are beginning to include sea level rise in their planning and design. To better understand cutting edge examples of sea level rise adaptation we examined the current conditions and projected future changes from nine physical sea level rise adaptation projects in the San Francisco Bay.

Data from: Teosinte in Europe – searching for the origin of a novel weed

Miluse Trtikova, Andre Lohn, Rosa Binimelis, Ignacio Chapela, Bernadette Oehen, Niklaus Zemp, Alex Widmer & Angelika Hilbeck
A novel weed has recently emerged, causing serious agronomic damage in one of the most important maize-growing regions of Western Europe, the Northern Provinces of Spain. The weed has morphological similarities to a wild relative of maize and has generally been referred to as teosinte. However, the identity, origin or genetic composition of ‘Spanish teosinte’ was unknown. Here, we present a genome-wide analysis of single-nucleotide polymorphism (SNP) data for Spanish teosinte, sympatric populations of cultivated...

Data from: Adaptation of the pathogen, Pseudomonas syringae during experimental evolution on a native versus alternative host plant

Sean Meaden & Britt Koskella
The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within-host growth rate will vary among host genotypes/species and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also...

Data from: Transgenerational effects alter plant defense and resistance in nature

Jack Colicchio
Trichomes, or leaf hairs, are epidermal extensions that take a variety of forms and perform many functions in plants, including herbivore defense. In this study, I document genetically determined variation, within-generation plasticity, and a direct role of trichomes in herbivore defense for (Mimulus guttatus). After establishing the relationship between trichomes and herbivory, I test for transgenerational effects of wounding on trichome density and herbivore resistance. Patterns of inter-annual variation in herbivore density and the high...

Data from: The seasonal climate niche predicts phenology and distribution of an ephemeral annual plant, Mollugo verticillata

Joe Hereford, Johanna Schmitt & David D. Ackerly
1.Many short-lived species complete their life cycles during brief seasonal windows of favorable environmental conditions. Such species may persist in the face of climate warming by migration to track their seasonal climate niche in space and/or by phenological shifts to track favorable conditions in time within the year. To describe the seasonal climate niche of the short-lived annual Mollugo verticillata in California, we used data from herbarium specimens and historic climate records to estimate environmental...

Forcing files and Model output for \"Contrasting impacts of the South Pacific Split Jet and the Southern Annular Mode modulation on Southern Ocean circulation and biogeochemistry\"

John Chiang, Kathy Tokos, Shih-Yu Lee & Katsumi Matsumoto
This contains the CESM forcing files and ocean model output used in Chiang J.C.H, K. Tokos, S.-Y. Lee, and K. Matsumoto, Contrasting impacts of the South Pacific Split Jet and the Southern Annular Mode modulation on Southern Ocean circulation and biogeochemistry. In revision for Paleoceanography, Oct 2017.

Data from: Parallel Pleistocene amphitropical disjunctions in a parasitic plant and its host

Adam C. Schneider & Abigail J. Moore
PREMISE OF THE STUDY: Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown. METHODS: Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based...

Data from: Trapped within the city: Integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization

André Lourenço, David Álvarez, Ian J. Wang & Guillermo Velo-Antón
Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders...

Data from: Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

Erin Conlisk, Cristina Castanha, Matthew J. Germino, Thomas T. Veblen, Jeremy M. Smith, Andrew B. Moyes & Lara M. Kueppers
Understanding how climate warming will affect the demographic rates of different ecotypes is critical to predicting shifts in species distributions. Here we present results from a common garden, climate change experiment in which we measured seedling recruitment of lodgepole pine, a widespread North American conifer that is also planted globally. Seeds from a low-elevation provenance had greater recruitment to their third year (by 323%) than seeds from a high-elevation provenance across sites within and above...

Data from: Caching for where and what: evidence for a mnemonic strategy in a scatter-hoarder

Mikel M. Delgado & Lucia F. Jacobs
Scatter-hoarding animals face the task of maximizing retrieval of their scattered food caches while minimizing loss to pilferers. This demand should select for mnemonics, such as chunking, i.e. a hierarchical cognitive representation that is known to improve recall. Spatial chunking, where caches with the same type of content are related to each other in physical location and memory, would be one such mechanism. Here we tested the hypothesis that scatter-hoarding eastern fox squirrels (Sciurus niger)...

Data from: Residential development alters behavior, movement, and energetics in an apex predator, the puma

Yiwei Wang, Justine A. Smith & Christopher C. Wilmers
Human development strongly influences large carnivore survival and persistence globally. Behavior changes are often the first measureable responses to human disturbances, and can have ramifications on animal populations and ecological communities. We investigated how a large carnivore responds to anthropogenic disturbances by measuring activity, movement behavior, and energetics in pumas along a housing density gradient. We used log-linear analyses to examine how habitat, time of day, and proximity to housing influenced the activity patterns of...

Data from: Variation in thermal niche of a declining river-breeding frog: from counter-gradient responses to population distribution patterns

Alessandro Catenazzi & Sarah J. Kupferberg
When dams or climate change alter the thermal regimes of rivers, conditions can shift outside optimal ranges for aquatic poikilothermic vertebrates. Plasticity in thermal performance and preference, however, may allow temperature-vulnerable fauna to persist under challenging conditions. To determine the effects of thermal regime on Rana boylii (Ranidae), a threatened frog species endemic to rivers of California and Oregon, we quantified tadpole thermal preferences and performance in relation to thermal conditions. We monitored temperature and...

Data from: Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

Dario Copetti, Alberto Burquez, Enriquena Bustamante, Joseph L. M. Charboneau, Kevin L. Childs, Luis E. Eguiarte, Seunghee Lee, Tiffany L. Liu, Michelle M. McMahon, Noah K. Whiteman, Rod A. Wing, Martin F. Wojciechowski & Michael J. Sanderson
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We...

Vegetation Change in the Natural Reserve of Orange County

Katherine Suding, Sara Jo Dickens & Samuel Bedgood
This data set describes vegetation change in 109 areas in the Nature Reserve of Orange County. The authors of this data were mainly interested in the success of artichoke thistle (Cynara cardunculus) control, but it could be approached in many different ways. Surveyors identified and recorded more than 375 plant species from the years 1998, 2008, and 2013.

Causal Evidence for Lateral Prefrontal Cortex Dynamics Supporting Cognitive Control

Derek Nee & Mark D'Esposito
The lateral prefrontal cortex (LPFC) is essential for higher-level cognition, but how its interactions support cognitive control remains elusive. Previously (Nee and D'Esposito, 2016), dynamic causal modeling (DCM) indicated that mid LPFC integrates abstract, rostral and concrete, caudal influences to inform context-appropriate action. Here, we use continuous theta-burst transcranial magnetic stimulation (cTBS) to causally test this model. cTBS was applied to three LPFC sites and a control site in counterbalanced sessions. Behavioral modulations resulting from...

Registration Year

  • 2017

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  • University of California, Berkeley
  • University of California System
  • University of Colorado Boulder
  • University of Washington
  • The University of Texas at Austin
  • University of Michigan-Ann Arbor
  • University of North Carolina
  • Australian National University
  • California Academy of Sciences
  • University of Florida