105 Works

Catastrophes, connectivity and Allee effects in the design of marine reserve networks

Easton White, Marissa Baskett & Alan Hastings
Catastrophic events, like oil spills and hurricanes, occur in many marine systems. One potential role of marine reserves is buffering populations against disturbances, including the potential for disturbance-driven population collapses under Allee effects. This buffering capacity depends on reserves in a network providing rescue effects, setting up a trade-off where reserves need to be connected to facilitate rescue, but also distributed in space to prevent simultaneous extinction. We use a set of population models to...

Data from: A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

William Conner, Emily Delaney, Michael Bronski, Paul Ginsberg, Timothy Wheeler, Kelly Richardson, Brooke Peckenpaugh, Kevin Kim, Masayoshi Watada, Ary Hoffmann, Michael Eisen, Artyom Kopp, Brandon Cooper & Michael Turelli
The Drosophila montium species group is a clade of 94 named species closely related to the model D. melanogaster species group. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times...

Data and Supplemental Material from: A multifunction trade-off has contrasting effects on the evolution of form and function

Katherine Corn, Christopher Martinez, Edward Burress & Peter Wainwright
Trade-offs caused by the use of an anatomical apparatus for more than one function are thought to be an important constraint on evolution. However, whether multifunctionality suppresses diversification of biomechanical systems is challenged by recent literature showing that traits more closely tied to trade-offs evolve more rapidly. We contrast the evolutionary dynamics of feeding mechanics and morphology between fishes that exclusively capture prey with suction and multifunctional species that augment this mechanism with biting behaviors...

Underlying data for: Influence of temporally varying weatherability on CO2-climate coupling and ecosystem change in the late Paleozoic

Jon Richey, Isabel Montañez, Yves Goddéris, Cindy Looy, Neil Griffis & William DiMichele
This dataset contains the primary data used as input parameters in a mechanistic stomatal CO2 model (Franks et al., 2014 (Geophysical Research Letters)) and the Paleosol Barometer Uncertainty Quantifier (i.e., PBUQ; Breecker, 2013 (Geochemistry, Geophysics, Geosystems)), as well as age-adjusted CO2 data from Montañez et al., 2016 (Nature Geoscience). The stomatal parameters were measured by Richey et al., 2020 (Climate Of The Past) and the paleosol parameters are revised from Montañez et al., 2007 (Science)....

Factors affecting acorn predation and infestation in three California oaks

Nicolette Balmaceda, Jovana Durovic, Sierra Montes & Kyler Plouffe
Oak woodlands are in decline due to failed oak recruitment in California. Oak recruitment is heavily impacted by vertebrate herbivory and insect infestation of acorns. Oaks have developed chemical defenses such as tannins to protect acorns from attack. Studies have explored infestation differences in red oaks but have not compared infestation between red oaks and white oaks. We explored how Cydia latiferreana (filbertworm) infestation, Curculio occidentalis (filbert weevil) infestation, and Sciurus griseus nigripes (western gray...

Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra

Jack Cazet, Celina Juliano & Adrienne Cho
During whole-body regeneration, a bisection injury can trigger two different types of regeneration. To understand the transcriptional regulation underlying this adaptive response we characterized transcript abundance and chromatin accessibility during oral and aboral regeneration in the cnidarian Hydra vulgaris. We found that the initial response to amputation at both wound sites is identical and includes widespread apoptosis and the activation of the oral-specifying Wnt signaling pathway. By 8 hours post-amputation, Wnt signaling became restricted to...

The effects of predation-risk on prey stoichiometry: A meta-analysis

Shelby Rinehart & Dror Hawlena
A decade ago, the General Stress Paradigm (GSP) aimed to develop a predictive framework linking predator effects to ecosystem function. The GSP was based on the notion that animals, across taxa, exhibit similar physiological responses to predation risk that divert resources from growth and reproduction [which require N-rich biomolecules (i.e., protein)] to emergency functions [which require C-rich biomolecules (e.g., carbohydrates)]. The GSP predicts that stressed prey should have a greater dietary demand for C-rich resources,...

Physiology trait and growing region climate data compiled from the literature for 34 wine grape cultivars

Megan Bartlett & Gabriela Sinclair
Selection for crop cultivars has largely focused on reproductive traits, while the impacts of global change on crop productivity are expected to depend strongly on the vegetative physiology traits that drive plant resource use and stress tolerance. We evaluated relationships between physiology traits and growing season climate across winegrape cultivars to characterize trait variation across growing regions and elucidate the mechanisms that adapted grapevines to hot, dry conditions. We compiled values from the literature for...

Consistent individual differences in ecto-parasitism of a long-lived lizard host

Eric Payne, David Sinn, Orr Spiegel, Stephan Leu, Caroline Wohlfeil, Stephanie Godfrey, Michael Gardner & Andrew Sih
Individual hosts vary substantially in their parasite loads. However, whether individual hosts have consistently different loads remains uncertain. If so, hosts that have consistently high parasite loads may serve as key reservoirs or super-spreaders. Thus, identifying whether individuals persistently differ in their parasitism and the factors that explain these patterns constitute important issues for disease ecology and management. To investigate these topics, we examined nine years of tick counts in a wild population of sleepy...

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...

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...

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...

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: 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...

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...

Multiple and extra-pair mating in a pair-living hermaphrodite, the intertidal limpet Siphonaria gigas

Jessica Schaefer, John Christy & Peter Marko
Pair-living is a common social system found across animal taxa, and the relationship between pair-living and reproduction varies greatly among species. Siphonaria gigas, hermaphroditic pulmonate gastropods, often live in pairs in the rocky intertidal zone of the tropical Eastern Pacific. Combining genetic parentage analysis using four polymorphic microsatellite loci with behavioral observations from a 10-week field study, we provide the first description of the mating system of a Siphonaria species incorporating genetic data. S. gigas...

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...

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...

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...

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...

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...

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.

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...

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...

Registration Year

  • 2020
    105

Resource Types

  • Dataset
    97
  • Text
    7
  • Software
    1

Affiliations

  • University of California, Davis
    92
  • University of California, Berkeley
    4
  • United States Geological Survey
    3
  • University of Minnesota
    2
  • United States Department of Agriculture
    2
  • University of Florida
    2
  • University of California, Santa Cruz
    2
  • Cornell University
    2
  • SUNY Downstate Medical Center
    1
  • California State University, Northridge
    1