65 Works

Data from: Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Paul D. Blischak, Maribeth Latvis, Diego F. Morales-Briones, Jens C. Johnson, Verónica S. Di Stilio, Andrea D. Wolfe & David C. Tank
Premise of the Study: Targeted enrichment strategies for phylogenomic inference are a time‐ and cost‐efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results: We present Fluidigm2PURC, an open source Python utility for processing paired‐end Illumina data from double‐barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling...

Data from: Root responses to elevated CO2, warming, and irrigation in a semi-arid grassland: integrating biomass, length, and life span in a 5‐year field experiment

Kevin E. Mueller, Daniel R. LeCain, M. Luke McCormack, Elise Pendall, Mary Carlson & Dana M. Blumenthal
1.Plant roots mediate the impacts of environmental change on ecosystems, yet knowledge of root responses to environmental change is limited because few experiments evaluate multiple environmental factors and their interactions. Inferences about root functions are also limited because root length dynamics are rarely measured. 2.Using a five‐year experiment in a mixed‐grass prairie, we report the responses of root biomass, length, and lifespan to elevated carbon dioxide (CO2), warming, elevated CO2 and warming combined, and irrigation....

Data from: Integrating abundance and diet data to improve inferences of food web dynamics

Jake M. Ferguson, , Brianna H. Witteveen, John B. Hopkins & Briana H. Witteveen
1. Both population abundances and chemical tracers are useful tools for studying consumer-resource interactions. Food web models parameterized with abundances are often used to understand how interactions structure communities and to inform management decisions of complex ecological systems. Unfortunately, collecting abundance data to parameterize these models is often expensive and time-consuming. Another approach is to use chemical tracers to estimate the proportional diets of consumers by relating the tracers in their tissues to those found...

Data from: High specialization and limited structural change in plant‐herbivore networks along a successional chronosequence in tropical montane forest

Conor M. Redmond, John Auga, Bradley Gewa, Simon T. Segar, Scott E. Miller, Kenneth Molem, George D. Weiblen, Phillip T. Butterill, Gibson Maiyah, Amelia S.C. Hood, Martin Volf, Leonardo R. Jorge, Yves Basset, Vojtech Novotny, Philip T. Butterill & Amelia S. C. Hood
Secondary succession is well‐understood, to the point of being predictable for plant communities, but the successional changes in plant‐herbivore interactions remains poorly explored. This is particularly true for tropical forests, despite the increasing importance of early successional stages in tropical landscapes. Deriving expectations from successional theory, we examine properties of plant‐herbivore interaction networks while accounting for host phylogenetic structure along a succession chronosequence in montane rainforest in Papua New Guinea. We present one of the...

Data from: Is it the song or the singers? Acoustic and social experiences shape adult reproductive tactics and condition

Susan L. Balenger, Elizabeth Bastiaans & Marlene Zuk
When sexual signals are perceived during growth and development they can provide information regarding the social conditions likely to be encountered as an adult. Perception of cues related to the presence and density of future mates and potential competitors can result in altered adult phenotypes. Previous studies have shown that adult male Teleogryllus oceanicus field crickets from a Kauai, Hawaii population reared alone and without hearing conspecific song are more phonotactic than those reared with...

Data from: Activation recovery interval imaging of premature ventricular contraction

Ting Yang, Long Yu, Qi Jin, Liqun Wu & Bin He
Dispersion of ventricular repolarization due to abnormal activation contributes to the susceptibility to cardiac arrhythmias. However, the global pattern of repolarization is difficult to assess clinically. Activation recovery interval (ARI) has been used to understand the properties of ventricular repolarization. In this study, we developed an ARI imaging technique to noninvasively reconstruct three-dimensional (3D) ARI maps in 10 premature ventricular contraction (PVC) patients and evaluated the results with the endocardial ARI maps recorded by a...

Data from: Expression of additive genetic variance for fitness in a population of partridge pea in two field sites

Seema Nayan Sheth, Mason W. Kulbaba, Rachel E. Pain & Ruth G. Shaw
Despite the importance of adaptation in shaping biological diversity over many generations, little is known about populations’ capacities to adapt at any particular time. Theory predicts that a population's rate of ongoing adaptation is the ratio of its additive genetic variance for fitness, VA (W), to its mean absolute fitness, W̅. We conducted a transplant study to quantify W̅ and standing VA (W) for a population of the annual legume Chamaecrista fasciculata in one field...

Web Scale Discovery and Resource Usage at the University of California, Berkeley

Lisa Ngo, Ian Knabe & Cody Hennesy
Dataset contains monthly usage data for select ejournal platforms, ebook platforms, and abstract & indexing databases at UC Berkeley from July 2013 through June 2017.

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: Systematic analysis of complex genetic interactions

Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Elizabeth N. Koch, Carles Pons, Andrius Jonas Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo … & Chad L. Myers
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended...

Data from: Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

Ranjan Muthukrishnan, Adam S. Davis, Nicholas R. Jordan & James D. Forester
Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and...

Data from: The role of diversification in the continental scale community assembly of the American oaks (Quercus)

Jeannine Cavender-Bares, Shan Kothari, José Eduardo Meireles, Matthew A. Kaproth, Paul S. Manos & Andrew L. Hipp
Premise of the study: Evolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effects that influence regional species pools and the composition of communities. We consider the consequences of the diversification process in shaping trait evolution and assembly of oak-dominated communities throughout the continental U.S. Methods: Within the US oaks, we tested for phylogenetic and functional trait patterns...

Data from: Quantifying how constraints limit the diversity of viable routes to adaptation

Samuel Yeaman, Aleeza C. Gerstein, Kathryn A. Hodgins, Michael C. Whitlock & Sam Yeaman
Convergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints...

Data from: Cracking the case: seed traits and phylogeny predict time to germination in prairie restoration species

Rebecca S. Barak, Taran M. Lichtenberger, Alyssa Wellman-Houde, Andrea T. Kramer & Daniel J. Larkin
1. Traits are important for understanding how plant communities assemble and function, providing a common currency for studying ecological processes across species, locations, and habitat types. However, most studies relating species traits to community assembly rely upon vegetative traits of mature plants. Seed traits, which are understudied relative to whole-plant traits, are key to understanding assembly of plant communities. This is particularly true in restored communities, which are typically started from seed, making germination a...

Data from: Edaphic factors, successional status, and functional traits drive habitat associations of trees in naturally regenerating tropical dry forests

Leland K. Werden, Justin M. Becknell & Jennifer S. Powers
1. Many studies have examined individual environmental drivers of tropical tree species distributions, but edaphic and successional gradients have not been considered simultaneously. Furthermore, determining how functional traits influence species distributions along these gradients may help to elucidate mechanisms behind community assembly. 2. To assess the influence of environmental filtering on tropical dry forest (TDF) tree species distributions we used forest inventory data from sites with large edaphic and successional gradients in NW Costa Rica....

Data from: Little plant, big city: a test of adaptation to urban environments in common ragweed (Ambrosia artemisiifolia)

Amanda J. Gorton, David A. Moeller & Peter Tiffin
A full understanding of how cities shape adaptation requires characterizing genetically-based phenotypic and fitness differences between urban and rural populations under field conditions. We used a reciprocal transplant experiment with the native plant common ragweed, (Ambrosia artemisiifolia), and found that urban and rural populations have diverged in flowering time, a trait that strongly affects fitness. Although urban populations flowered earlier than rural populations, plants growing in urban field sites flowered later than plants in rural...

Data from: Social living simultaneously increases infection risk and decreases the cost of infection

Vanessa O. Ezenwa, Katherine E.L. Worsley-Tonks & Katherine E. L. Worsley-Tonks
Elevated parasite infection risk is considered to be a near universal cost of social living. However, living in groups may also provide benefits that reduce the negative impacts of infection. These potential ‘tolerance’ benefits of living socially are theoretically possible, but have rarely been described. In this study, we used an anthelmintic treatment experiment in wild Grant’s gazelles (Nanger granti), who are commonly infected with gastrointestinal nematodes (GIN), to show that social living confers both...

Data from: Variation in home-field advantage and ability in leaf litter decomposition across successional gradients

G.F. Ciska Veen, Ashley D. Keiser, Wim H. Van Der Putten, David A. Wardle & G. F. Ciska Veen
1. It is increasingly recognized that interactions between plants and soil (a)biotic conditions can influence local decomposition processes. For example, decomposer communities may become specialized in breaking down litter of plant species that they are associated with, resulting in accelerated decomposition, known as ‘home-field advantage’ (HFA). Also, soils can vary inherently in their capacity to degrade organic compounds, known as ‘ability’. However, we have a poor understanding how environmental conditions drive the occurrence of HFA...

Data from: Species-specific spatiotemporal patterns of leopard, lion and tiger attacks on humans

Craig Packer, Shweta Shivakumar, Vidya Athreya, Meggan E. Craft, Harshawardhen Dhanwatey, Poonam Dhanwatey, Bhim Gurung, Anup Joshi, Hadas Kushnir, John D.C. Linnell, Nicholas M. Fountain-Jones & John D. C. Linnell
1. Large carnivores of the genus Panthera can pose serious threats to public safety. Although the annual number of attacks on humans is rare compared to livestock depredation, such incidents undermine popular support for wildlife conservation and require immediate responses to protect human life. 2. We used a space-time scan method to perform a novel spatiotemporal analysis of 908 attacks on humans by lions, leopards and tigers to estimate the risks of further attacks in...

Data from: Resilience of seed production to a severe El Niño‐induced drought across functional groups and dispersal types

Michael J. O'Brien, Daniel Peréz-Aviles & Jennifer S. Powers
More frequent and severe El Niño Southern Oscillations (ENSO) are causing episodic periods of decreased rainfall. Although the effects of these ENSO-induced droughts on tree growth and mortality have been well studied, the impacts on other demographic rates such as reproduction are less well known. We use a four-year seed rain dataset encompassing the most severe ENSO-induced drought in more than 30 years to assess the resilience (i.e. resistance and recovery) of the seed composition...

Data from: Sexual signal loss: the link between behavior and rapid evolutionary dynamics in a field cricket

Marlene Zuk, Nathan W. Bailey, Brian Gray & John T. Rotenberry
1. Sexual signals may be acquired or lost over evolutionary time, and are tempered in their exaggeration by natural selection. 2. In the Pacific field cricket, Teleogryllus oceanicus, a mutation (“flatwing”) causing loss of the sexual signal, the song, spread in < 20 generations in two of three Hawaiian islands where the crickets have been introduced. Flatwing (as well as some normal-wing) males behave as satellites, moving towards and settling near calling males to intercept...

Data from: Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests

Bonnie G. Waring, Rachel Adams, Sara Branco & Jennifer S. Powers
Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free‐living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale‐explicit sampling strategy to examine soil N cycling at...

Data from: Anthropogenic increases in nutrients alter sexual selection dynamics: a case study in butterflies

Anne Espeset, Megan E. Kobiela, Kristin L. Sikkink, Tiffany Pan, Colton Roy & Emilie C. Snell-Rood
Anthropogenic increases in nutrient availability offer opportunities to study evolutionary shifts in sexual selection dynamics in real time. A rapid increase in nutrient availability may reduce the utility of condition-dependent ornaments as signals of quality and lessen any nutritional benefits to females from re-mating. We explored these ideas using cabbage white butterflies, focusing on nitrogen as a nutrient, as it is important to this species in not only in ornamentation but also as a key...

Data from: Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest

Erik M. Schilling, Bonnie G. Waring, Jonathan S. Schilling & Jennifer S. Powers
We investigated how forest composition, litter quality, and rainfall interact to affect leaf litter decomposition across three successional tropical dry forests in Costa Rica. We monitored litter stocks and bulk litter turnover in 18 plots that exhibit substantial variation in soil characteristics, tree community structure, fungal communities (including forests dominated by ecto- or arbuscular mycorrhizal host trees), and forest age. Simultaneously, we decomposed three standard litter substrates over a 6-month period spanning an unusually intense...

Data from: Lion population dynamics: do nomadic males matter?

Natalia Borrego, Arpat Ozgul, Rob Slotow & Craig Packer
Key population processes are sometimes driven by male dynamics, but these drivers are often overlooked because of the scale over which they operate. Lions (Panthera leo) provide an ideal case study for investigating factors governing male dynamics and their influence on population sustainability. Lions display sexually selected infanticide, and resident males must defend their offspring from nomads that may have dispersed over long distances; factors affecting male-male competition over large spatial scales can have population...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Minnesota
  • Utah State University
  • Duke University
  • Iowa State University
  • University of Washington
  • Stanford University
  • University of Michigan-Ann Arbor
  • The Ohio State University
  • University of California, Berkeley
  • German Center for Integrative Biodiversity Research