155 Works

Towards the introgression of PvPdh1 for increased resistance to pod shattering in common bean

Travis Parker, Lorenna Lopes De Sousa, Talissa De Oliveira Floriani, Antonia Palkovic & Paul Gepts
Some varieties of common bean (Phaseolus vulgaris L.) suffer from pod shattering, which can severely reduce yields, especially in arid conditions. The PvPdh1 locus on chromosome Pv03 has recently been described as a major locus controlling pod shattering in common bean and could be used to mitigate pod shattering in the future. Despite this, the role of a possible second locus on chromosome Pv08 remains unclear and patterns of dominance and epistasis between alleles of...

Data from: The global distribution of grass functional traits within grassy biomes

Emma Jardine, Colin Osborne, Gavin Thomas, Caroline Lehmann & Elisabeth Forrestel
Aim: The sorting of functional traits along environmental gradients is an important driver of community and landscape scale patterns of functional diversity. However, the significance of environmental factors in driving functional gradients within biomes and across continents remains poorly understood. Here, we evaluate the relationship of soil nutrients and climate to leaf traits in grasses (Poaceae) that are hypothesised to reflect different strategies of resource-use along gradients of resource availability. Location: Global Taxon: Poaceae Methods:...

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...

Data from: Biogeography of ocean acidification: differential field performance of transplanted mussels to upwelling-driven variation in carbonate chemistry

Bruce Menge, Francis Chan, Jeremy Rose, Eric Sanford, Peter Raimondi, Carol Blanchette & Tarik Gouhier
Ocean acidification (OA) represents a serious challenge to marine ecosystems. Laboratory studies addressing OA indicate broadly negative effects for marine organisms, particularly those relying on calcification processes. Growing evidence also suggests OA combined with other environmental stressors may be even more deleterious. Scaling these laboratory studies to ecological performance in the field, where environmental heterogeneity may mediate responses, is a critical next step toward understanding OA impacts on natural communities. We leveraged an upwelling-driven pH...

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: 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...

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...

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...

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...

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...

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...

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...

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: 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...

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...

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...

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.

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...

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...

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...

Rancho Seco vernal pool community data

Julia Michaels
Disturbance often increases local-scale (α) diversity by suppressing dominant competitors. However, widespread disturbances may also reduce biotic heterogeneity (β diversity) by making the identities and abundances of species more similar among patches. Landscape-scale (γ) diversity may also decline if disturbance-sensitive species are lost. California’s vernal pool plant communities are species-rich due in part to two scales of β diversity: (1) within pools, as species composition changes with depth (referred to here as vertical β diversity),...

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...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Output Management Plan


  • University of California, Davis
  • University of California, Berkeley
  • Oregon State University
  • Stanford University
  • University of Minnesota
  • University of Georgia
  • University of California, Merced
  • University of Tennessee at Knoxville
  • University of Colorado Boulder
  • University of Florida