152 Works

A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera

Ingrid Jordon-Thaden, James Beck, Catherine Rushworth, Michael Windham, Nicolas Diaz, Jason Cantley, Chris Martine & Carl Rothfels
Premise of the study: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of broad datasets with taxonomic and geographic sampling not otherwise possible. Here we evaluate the utility of a basic restriction site-associated DNA (ddRADseq) protocol with DNAs from four genera extracted from both silica-dried and herbarium tissue. Methods: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (ddRADseq) protocol. The...

Data from: The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks

Hai-Dong Li, Linfang Tang, Chenxi Jia, Marcel Holyoak, Jochen Fründ, Xiaoqun Huang & Zhihsu Xiao
Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species’ functional roles in bird-plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird-plant interactions involving birds feeding only on the tree or both on and under the...

Data from: Consumer responses to experimental pulsed subsidies in isolated vs. connected habitats

Amber Wright, Jonah Piovia-Scott, Louie H. Yang, David A. Spiller & Thomas W. Schoener
Increases in consumer abundance following a resource pulse can be driven by diet shifts, aggregation, and reproductive responses, with combined responses expected to result in faster response times and larger numerical increases. Previous work in plots on large Bahamian islands has shown that lizards (Anolis sagrei) increased in abundance following pulses of seaweed deposition, which provide additional prey (i.e., seaweed detritivores). Numerical responses were associated with rapid diet shifts and aggregation, followed by increased reproduction....

Data from: Wildfire reveals transient changes to individual traits and population responses of a native bumble bee (Bombus vosnesenskii)

John Mola, Michael Miller, Sean O'Rourke & Neal Williams
1. Fire-induced changes in the abundance and distribution of organisms, especially plants, can alter resource landscapes for mobile consumers driving bottom-up effects on their population sizes, morphologies, and reproductive potential. We expect these impacts to be most striking for obligate visitors of plants, like bees and other pollinators, but these impacts can be difficult to interpret due to the limited information provided by forager counts in the absence of survival or fitness proxies. 2. Increased...

Data from: Behavioral changes in calves 11 days after cautery disbudding: effect of local anesthesia

Cassandra Tucker, Sarah Adcock & Danielle Cruz
Hot-iron disbudding results in painful burn wounds that take weeks to heal. Spontaneous behaviors indicative of pain are apparent in the immediate hours after disbudding, but whether they occur later in the healing process is unknown. To evaluate whether ongoing pain was present around the time the necrotic tissue loosens from the scalp, we tested the effect of administration of local anesthetic 11 d after the procedure. Disbudded female Holstein and Jersey calves (n=24) were...

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)....

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...

zigzag: A Hierarchical Bayesian Mixture Model for Inferring the Expression State of Genes in Transcriptomes

Ammon Thompson, Michael May, Brian Moore & Artyom Kopp
Transcriptomes are key to understanding the relationship between genotype and phenotype. The ability to infer the expression state (active or inactive) of genes in the transcriptome offers unique benefits for addressing this issue. For example, qualitative changes in gene expression may underly the origin of novel phenotypes, and expression states are readily comparable between tissues and species. However, inferring the expression state of genes is a surprisingly difficult problem, owing to the complex biological and...

Phenotypic plasticity and community composition interactively shape trophic interactions

Denon Start
Trait variation defines and underpins biodiversity, yet we are only beginning to understand how processes acting across biological scales (individuals to whole communities) interact to produce trait differences and their consequences, particularly over short time scales. First, species often differ widely in their mean phenotype, meaning that changes in community composition can alter average trait values of a guild. Second, phenotypic plasticity alters the trait values of individuals, and the net effect of plasticity can...

Utilizing Highway Rest Areas for Electric Vehicle Charging: Economics and Impacts of Renewable Energy Penetration in California

Behdad Kiani, Joan Ogden, F. Alex Sheldon & Lauren Cordano
California policy is incentivizing rapid adoption of zero emission electric vehicles for light duty and freight applications. In this project, we explored how locating charging facilities at California’s highway rest stops, might impact electricity demand, grid operation, and integration of renewables like solar and wind into California’s energy mix. Assuming a growing population of electric vehicles to meet state goals, we estimated state-wide growth of electricity demand, and identified the most attractive rest stop locations...

Data from: An initial comparative genomic autopsy of wasting disease in sea stars

Dannise V. Ruiz‐Ramos, Lauren M. Schiebelhut, Katharina J. Hoff, John P. Wares & Michael N. Dawson
Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here we take a forensic genomic approach to discover candidate genes that may help explain...

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: The effect of early burn injury on sensitivity to future painful stimuli in dairy heifers

Sarah Adcock & Cassandra Tucker
Animals that experience painful procedures as neonates are more sensitive to pain later in life. We evaluated whether disbudding with a heated iron at 3 (n=12), 35 (n=9), or 56 (n=20) d of age affected heifers’ pain responses to vaccine injections at 11 mo of age. Heifers responded to the injection procedure with struggling and changes in eye temperature and heart rate variability compared to a sham procedure the day before, and still had a...

Decoupled jaws promote trophic diversity in Cichlid fishes

Edward Burress, Christopher Martinez & Peter C Wainwright
Functional decoupling of oral and pharyngeal jaws is widely considered to have expanded the ecological repertoire of cichlid fishes. But, the degree to which the evolution of these jaw systems is decoupled and whether decoupling has impacted trophic diversification remains unknown. Focusing on the large Neotropical radiation of cichlids, we ask whether oral and pharyngeal jaw evolution is correlated and how their evolutionary rates respond to feeding ecology. In support of decoupling, we find relaxed...

Delimitation of tribes in the subfamily Leptanillinae (Hymenoptera: Formicidae), with a description of the male of Protanilla lini Terayama, 2009

Zachary Griebenow
The subfamily Leptanillinae Emery, 1910 (Hymenoptera, Formicidae) is a clade of cryptic subterranean ants, which is restricted to the tropics and warm temperate regions of the Old World. Due to acquisition bias against the minute and hypogaeic workers, most known leptanilline specimens are male, with four genera described solely from males. The sexes have been associated in only two out of 68 described species, meaning that redundant naming of taxa is likely. Herein the phylogeny...

Data from: Taxonomic revision of the New World members of the Trapdoor spider genus Ummidia Thorell (Araneae,: Mygalomorphae,: Halonoproctidae )

Rebecca Godwin & Jason Bond
This study documents a comprehensive taxonomic treatment of the New World Ummidia species. At the onset of this work the genus comprised 27 species and one subspecies with a cosmopolitan distribution that includes North America, South America, Asia, Northern Africa, and Europe; of these species the majority of the nominal diversity can be attributed to the New World where 20 species have been previously described. Ummidia oaxacana (Chamberlin, 1925) is considered a nomen dubium; U....

Data from: Ectothermy and the macroecology of home range scaling in snakes

Brian Todd & Aaron Nowakowski
Aim: A central question in ecology has been that of why animal home ranges scale more steeply with body size than do metabolic rates. Yet, the generality of this notion has scarcely been tested in non-model species like ectotherms, which have lower metabolic requirements than endotherms and which may therefore have different home range area requirements. Our aim was to examine how home range area scales with body size in snakes and to shed light...

Data for: Environmentally-driven escalation of host egg-rejection decimates success of an avian brood parasite

John Eadie & Bruce Lyon
The black-headed duck (Heteronetta atricapilla) of South America is the only known avian obligate brood parasite with precocial offspring. In Argentina, it relies on two species of coots as primary hosts, which typically reject 35-65% of duck eggs. We show that environmentally-driven increases in host egg-rejection behavior lead to substantial reductions in the reproductive success of the brood parasite. Episodes of flooding and vegetation loss caused dramatic shifts in host egg rejection behavior, resulting in...

VCC User Survey Results

Angela Sanguinetti
PROJECT: Strategies to promote plug-in electric vehicle (PEV) adoption include consumer education about potential energy cost savings. However, the complexity of comparing gasoline and electricity prices makes it difficult to quantify. Vehicle energy cost calculators (VCCs) help consumers navigate this complexity, and research shows they can increase consumer knowledge and positive attitudes about PEVs. At least 12 of these calculators exist, but none appear to be based on behavioral research. They vary in terms of...

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,...

VELB watershed data 2005

Michael Dobbins, Theresa Talley & Marcel Holyoak
The Valley Elderberry Longhorn Beetle (“VELB,” Desmocerus californicus dimorphus) is a rare and cryptic species that is found on or near its host plant, blue elderberry (Sambucus mexicana), and is native to California’s Central Valley. Over the past 100 years, the riparian forests of Central California have shrunk by over 90%, resulting in highly fragmented, and often isolated, remaining VELB habitat patches. This has created the need for robust monitoring and demographic data to assess...

0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains

Roland Faller, Austen Bernardi, Yihan Huang, Bradley Harris, Yongao Xiong, Somen Nandi & Karen McDonald
These are initial and final (75ns) configurations in PDB format of glycosylated ACE2-FC fusion proteins which are promising targets for a COVID-19 therapeutic. Some of them are in interaction witha fragment of the receptor-binding domain (RBD) of the Spike Protein S of the SARS-CoV-2 virus. We used two glycosylation variants for ACE2-FC, variant 1 is fully glycosylated with Man8 glycans, variant 2 is fully glycosylated with GnGnXF3. The Spike RBD is glycosylated with ANaF^6.

Recent bark beetle outbreaks influence wildfire severity in mixed-conifer forests of the Sierra Nevada, California, USA

Rebecca Wayman & Hugh Safford
In temperate forests, elevated frequency of drought related disturbances will likely increase the incidence of interactions between disturbances such as bark beetle epidemics and wildfires. Our understanding of the influence of recent drought and insect-induced tree mortality on wildfire severity has largely lacked information from forests adapted to frequent fire. A recent unprecedented tree mortality event in California’s Sierra Nevada provides an opportunity to examine this disturbance interaction in historically frequent-fire forests. Using field data...

Differing, multi-scale landscape effects on genetic diversity and differentiation in eastern chipmunks

Elizabeth Kierepka, Sara Anderson, Robert Swihart &
Understanding how habitat loss and fragmentation impact genetic variation is a major goal in landscape genetics, but to date, most studies have focused solely on the correlation between intervening matrix and genetic differentiation at a single spatial scale. Several caveats exist in these study designs, among them is the inability to include measures of genetic diversity in addition to differentiation. Both genetic metrics help predict population persistence, but are expected to function at differing spatial...

Pliocene-early Pleistocene geological events structure Pacific martens (Martes caurina)

Ashley Walters, Michael Schwartz, Kristine Pilgrim, Katie Moriarty, Keith Slausen, William Zielinski, Keith Aubry, Benjamin Sacks, Cate Quinn & Michael Young
The complex topography, climate and geological history of Western North America has shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, Davis
  • University of California, Berkeley
  • Oregon State University
  • University of Florida
  • University of Georgia
  • University of Minnesota
  • University of British Columbia
  • Michigan State University
  • University of California, Merced
  • Northwestern University