78 Works

Data from: Social structure contains epidemics and regulates individual roles in disease transmission in a group-living mammal

Carly Rozins, Matthew J. Silk, Darren P. Croft, Richard J. Delahay, Dave J. Hodgson, Robbie A. McDonald, Nicola Weber & Mike Boots
Population structure is critical to infectious disease transmission. As a result, theoretical and empirical contact networks models of infectious disease spread are increasingly providing valuable insights into wildlife epidemiology. Analysing an exceptionally detailed data set on contact structure within a high-density population of European badgers Meles meles, we show that a modular contact network produced by spatially structured stable social groups, lead to smaller epidemics, particularly for infections with intermediate transmissibility. The key advance is...

Data from: The impact of bacteriophages on phyllosphere bacterial abundance and composition

Norma M. Morella, Annika L. Gomez, Grant Wang, Michelle S. Leung & Britt Koskella
Interactions between bacteria and bacteriophage viruses (phages) are known to influence pathogen growth and virulence, microbial diversity, and even biogeochemical cycling. Lytic phages in particular infect and lyse their host cells, and can therefore have significant effects on cell densities as well as competitive dynamics within microbial communities. Despite the known impacts of lytic phages on the ecology and evolution of bacteria in free-living communities, little is known about the role of lytic phages in...

Data from: Trait evolution, resource specialization and vulnerability to plant extinctions among Antillean hummingbirds

Bo Dalsgaard, Jonathan D. Kennedy, Benno I. Simmons, Andrea C. Baquero, Ana M. Martín González, Allan Timmermann, Pietro K. Maruyama, Jimmy A. McGuire, Jeff Ollerton, William J. Sutherland & Carsten Rahbek
Species traits are thought to predict feeding specialisation and the vulnerability of a species to extinctions of interaction partners, but the context in which a species evolved and currently inhabits may also matter. Notably, the predictive power of traits may require that traits evolved to fit interaction partners. Furthermore, local abiotic and biotic conditions may be important. On islands, for instance, specialised and vulnerable species are predicted to be found mainly in mountains, whereas species...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Data from: Phenotypic integration between claw and toepad traits promotes microhabitat specialization in the Anolis adaptive radiation

Michael L. Yuan, Marvalee H. Wake & Ian J. Wang
The performance of an organism in its environment frequently depends more on its composite phenotype than on individual phenotypic traits. Thus, understanding environmental adaptation requires investigating patterns of covariation across functionally-related traits. The replicated adaptive radiations of Greater Antillean Anolis lizards are characterized by ecological and morphological convergence, thus providing an opportunity to examine the role of multiple phenotypes in microhabitat adaptation. Here, we examine integrated claw and toepad morphological evolution in relation to habitat...

Discomfort due to glare from a large source: Evaluating stimulus range effects when using the luminance adjustment procedure

Michael Kent, Toby Cheung & Stefano Schiavon
Using the luminance adjustment procedure, we evaluated four discomfort sensation on a Hopkinson-like glare scale: (a), (b), (c) and (d), respectively. Two methodological factors that were beleived to influence the luminance adjustment procedure were investigated. One was the stimulus range bias effect. This describes how the influence of the available range of a variable stimulus (i.e., glare source luminances) influence the setting made to a subjective sensation (i.e., "just uncomfortable" glare). 42 test participants were...

In Situ Transmission Electron Microscopy Data of Dislocations in Imperfectly Attached PbTe Nanocrystal Pairs

Justin Ondry, Matthew Hauwiller & A. Paul Alivisatos
Dataset containing high resolution transmission electron microscopy data of imperfectly attached PbTe nanocrystals. The data contains High Resolution TEM timeseries of images showing the annealing of of well defined b=a/2[110] edge dislocations in PbTe nanocrystal pairs viewed down the<001> zone axis. Depending on the attachment facets of the particles, the dislocations anneal out at different rates. In addition we performed geometric phase analysis on the images to visualize the strain fields surrounding the dislocation cores....

Berkeley High Resolution (BEHR) OMI NO2 - Native pixels, daily profiles

Joshua Laughner, Qindan Zhu & Ron Cohen
The BEHR OMI NO2 product reprocesses tropospheric NO2 columns from the Ozone Monitoring Instrument (OMI) satellite using high resolution a priori NO2 profiles, surface reflectivity, and surface elevation data. This product uses NO2 profiles for the day retrieved, simulated by the WRF-Chem model at 12 km spatial resolution. The use of high spatial resolution NO2 profiles has been shown to better resolve urban/rural differences in NO2 column densities, and the use of day-to-day (rather than...

Dopaminergic mechanisms underlying normal variation in trait anxiety: supplemental

Anne Berry
Trait anxiety has been associated with altered activity within corticolimbic pathways connecting the amygdala and rostral anterior cingulate cortex (rACC), which receive rich dopaminergic input. Though the popular culture uses the term “chemical imbalance” to describe the pathophysiology of psychiatric conditions such as anxiety disorders, we know little about how individual differences in human dopamine neurochemistry are related to variation in anxiety and activity within corticolimbic circuits. We addressed this issue by examining inter-individual variability...

Data from: Valuable habitat and low deforestation can reduce biodiversity gains from development rights markets

Kate J. Helmstedt & Matthew D. Potts
1. Illegal private land deforestation threatens global biodiversity, even in areas with native habitat requirements stipulated by law. Compliance can be improved by allowing landholders to meet legal reserve requirements by buying and selling the rights to have deforested land through a Tradeable Development Rights system (TDR). While this policy mechanism may prevent native habitat area loss, the spatial pattern of reserved areas will shift, creating novel landscape patterns. The resulting altered fragmentation and connectivity...

Data for Cold adaptation does not alter ATP homeostasis during cold exposure in Drosophila melanogaster

Caroline Williams
Data and analysis scripts for Williams et al. 2018 Integrative Zoology:

Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

Craig F. Barrett, Susann Wicke & Chodon Sass
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree...

Data from: Synopsis and taxonomic revision of three genera in the snake tribe Sonorini

Christian L. Cox, Alison R. Davis Rabosky, Iris A. Holmes, Jacobo Reyes-Velasco, Corey E. Roelke, Eric N. Smith, Oscar Flores-Villel, Jimmy A. McGuire & Jonathan A. Campbell
Delimiting species is a crucial goal of integrative biology, and yet can be misled by homoplasy and high levels of morphological variation. The snake tribe Sonorini contains three genera that have long confounded taxonomists: Chilomeniscus, Chionactis and Sonora. Dynamic colour evolution in this group, including rampant geographic variation in colour and colour polymorphism, has led to a chaotic taxonomy. We used mitochondrial and high-throughput nuclear data (ddRADseq) and complete taxonomic sampling of each genus to...

Data from: Opening the file drawer: Unexpected insights from a chytrid infection experiment

Allison Q. Byrne, Thomas J. Poorten, Jamie Voyles, Craig K.R. Willis, Erica Bree Rosenblum & Craig K. R. Willis
Infection experiments are critical for understanding wildlife disease dynamics. Although infection experiments are typically designed to reduce complexity, disease outcomes still result from complex interactions between host, pathogen, and environmental factors. Cryptic variation across factors can lead to decreased repeatability of infection experiments within and between research groups and hinder research progress. Furthermore, studies with unexpected results are often relegated to the “file drawer” and potential insights gained from these experimental outcomes are lost. Here,...

Data from: Consumption of carotenoids not increased by bacterial infection in brown trout embryos (Salmo trutta)

Lucas Marques Da Cunha, Laetitia G.E. Wilkins, Laure Menin, Daniel Ortitz, Véronique Vocat-Mottier, Claus Wedekind & Laetitia G. E. Wilkins
Carotenoids are organic pigment molecules that play important roles in signalling, control of oxidative stress, and immunity. Fish allocate carotenoids to their eggs, which gives them the typical yellow to red colouration and supports their resistance against microbial infections. However, it is still unclear whether carotenoids act mainly as a shield against infection or are used up during the embryos' immune defence. We investigated this question with experimental families produced from wild-caught brown trout (Salmo...

Data from: Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests

Marta A. Skowron Volponi, Donald James McLean, Paolo Volponi & Robert Dudley
Clearwing moths are known for their physical resemblance to hymenopterans, but the extent of their behavioural mimicry is unknown. We describe zigzag flights of sesiid bee mimics which are nearly indistinguishable from those of sympatric bees, whereas sesiid wasp mimics display faster, straighter flights more akin to those of wasps. In particular, the flight of the sesiids Heterosphecia pahangensis, Aschistophleps argentifasciata and Pyrophleps cruentata resembles both Tetragonilla collina and T. atripes stingless bees and, to...

Data from: Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae).

Brian L. Dorsey, Timothy J Gregory, Chodon Sass & Chelsea D. Specht
Premise of the study: Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation thereby becoming separated by topography. Methods: We inferred orthologs from transcriptomes...

Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing

Henrik Krehenwinkel, Susan R. Kennedy, Alexandra Rueda, Athena Lam & Rosemary G. Gillespie
1. The simplicity and cost efficiency of Illumina amplicon sequencing has greatly contributed to the advancement of DNA barcoding and metabarcoding applications. However, current amplicon sequencing based barcoding approaches are usually restricted to short, single-locus fragments, limiting their taxonomic and phylogenetic resolution. 2. Here, we establish a cost efficient and simple multiplex PCR protocol for arthropod systematics by Illumina amplicon sequencing. We introduce primer sets, including several new, generic primers, to reliably amplify nine loci...

Data from: A genotypic trade-off between constitutive resistance to viral infection and host growth rate

Lewis J. Bartlett, Lena Wilfert & Mike Boots
Genotypic trade-offs are fundamental to the understanding of the evolution of life-history traits. In particular, the evolution of optimal host defence and the maintenance of variation in defence against infectious disease is thought to be underpinned by such evolutionary trade-offs. However, empirical demonstrations of these trade-offs that satisfy the strict assumptions made by theoretical models are rare. Additionally, none of these trade-offs have yet been shown to be robustly replicable using a variety of different...

Data from: Collective behavior and colony persistence of social spiders depends on their physical environment

Ambika Kamath, Skylar D. Primavera, Colin M. Wright, Grant N. Doering, Kirsten A. Sheehy, Noa Pinter-Wollman & Jonathan N. Pruitt
The physical environment occupied by group-living animals can profoundly affect their cooperative social interactions and therefore their collective behavior and success. These effects can be especially apparent in human-modified habitats, which often harbor substantial variation in the physical environments available within them. For nest-building animal societies, this influence of the physical environment on collective behavior can be mediated by the construction of nests—nests could either buffer animal behavior from changes in the physical environment or...

Climate, snow, and soil moisture data set for the Tuolumne and Merced River watersheds, California, USA

James Roche, Robert Rice, Xiande Meng, Daniel Cayan, Mike Dettinger, Douglas Alden, Sarina Patel, Megan Mason, Martha Conklin & Roger Bales
UCM sites. Snow depth, soil moisture and soil temperature are measured near the Merced Grove, Gin Flat, Smoky Jack Creek, and Olmsted Quarry with a distributed array of 6-7 sensor nodes at each location. Snow depth is measured in the open, at the drip edge and under canopies, as well as 3-4 other sites representative of an area of 1-2 hectares. Soil moisture and temperature are measured at 10, 30, 60 and 90 cm depths...

Interview Proceedings with Delbert Anderson

Hunter Hall
The following are the proceedings of an interview between Hunter Hall (interviewer) and Delbert Anderson (interviewee). The text has been transcribed from email to this document for legibility. The interview occurred on May 3rd, 2018 and was conducted with intentions to use as primary evidence for Hall’s final paper due for the Music R1B (Spring 2018) course at the University of California, Berkeley.

Berkeley High Resolution (BEHR) OMI NO2 - Gridded pixels, monthly profiles

Joshua Laughner, Qindan Zhu & Ronald Cohen
The BEHR OMI NO2 product reprocesses tropospheric NO2 columns from the Ozone Monitoring Instrument (OMI) satellite using high resolution a priori NO2 profiles, surface reflectivity, and surface elevation data. This product uses NO2 profiles for the day retrieved, simulated by the WRF-Chem model at 12 km spatial resolution. The use of high spatial resolution NO2 profiles has been shown to better resolve urban/rural differences in NO2 column densities, and the use of day-to-day (rather than...

Data from: Origins of East Asian Summer Monsoon Seasonality

John Chiang, Wenwen Kong, Chi-Hua Wu & David Battisti
Climatological model output used in Chiang et al. (2019), "Origins of East Asian Summer Monsoon Seasonality".

3D attenuation model of Long Valley Caldera (CA)

Janire Prudencio & Michael Manga
Unrest at Long Valley caldera, California has been attributed to magma recharge or the ascent of hydrothermal fluids. The difference is critical for assessing volcanic hazard. To better constrain subsurface structures in the upper crust and to help distinguish between these two competing hypotheses for the origin of unrest, we model the 3D seismic attenuation structure by analyzing more than 47000 vertical waveforms with the coda normalization method. We identify high attenuation anomalies in the...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of Minnesota
  • University of Washington
  • Columbia University
  • University of California System
  • Museum of Vertebrate Zoology
  • Dayton Foundation
  • Cornell University
  • Stanford University
  • University of California, San Diego