78 Works

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...

Detailed experimental investigation of air speed field induced by ceiling fans

Shou Liu, Aleksandra Lipczynska, Stefano Schiavon & Edward Arens
Comfort cooling by ceiling fans is cost-effective and energy-efficient compared to compressor-based cooling and fans are commonly used in tropical and subtropical countries. There are however limited data and design tools supporting the design of fan systems, especially for situations where there are multiple fans. In this study, we investigate airflow profiles induced by a single fan and multiple fans using high spatial resolution air speed measurements (5,760 and 20,160 measuring points for the two...

Directed Evolution of AAV for Efficient Gene Delivery to Canine and Primate Retina - Raw counts of variants from deep sequencing

Leah Byrne, Timothy Day, Meike Visel, Deniz Dalkara, Valerie Dufour, Felipe Pompeo Marinho, William Merigan, Gustavo Aguirre, William Beltran, David Schaffer & John Flannery
Efficient AAV-mediated gene delivery remains a significant obstacle to effective retinal gene therapies. Here, we apply the process of directed evolution – guided by deep sequencing and followed by direct in vivo secondary selection of high-performing vectors with a GFP-barcoded library – to create AAV viral capsids with new capabilities to deliver genes to the outer retina in large animals. The resulting vectors resulted in efficient targeting of photoreceptors, bipolar cells, and RPE cells in...

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: Applying ecological site concepts and state-and-transition models to a grazed riparian rangeland

Felix Ratcliff, James Bartolome, Luke Macaulay, Sheri Spiegal & Michael D. White
Ecological sites and state-and-transition models are useful tools for generating and testing hypotheses about drivers of vegetation composition in rangeland systems. These models have been widely implemented in upland rangelands, but comparatively little attention has been given to developing ecological site concepts for rangeland riparian areas, and additional environmental criteria may be necessary to classify riparian ecological sites. Between 2013 and 2016, fifteen study reaches on five creeks were studied at Tejon Ranch in southern...

Data from: The role of history and ecology as drivers of song divergence in Bell’s and Sagebrush sparrows (Artemisiospiza, Aves: Passerellidae)

Benjamin R. Karin, Carla Cicero, Michelle S. Koo, Rauri C.K. Bowie & Rauri C K Bowie
Bell’s and Sagebrush sparrows (Artemisiospiza belli and A. nevadensis) are phenotypically and genetically distinct, but data have yielded contradictory findings for A. belli subspecies. Disjunct populations of A. b. canescens from the San Joaquin Valley and Mojave Desert are phenotypically indistinguishable but diagnosable from Coast Range A. b. belli. However, San Joaquin Valley A. b. canescens shares allozymes and mtDNA with A. b. belli whereas Mojave Desert A. b. canescens is genetically distinct. Furthermore, Great...

Data from: The low but uncertain measured benefits of U.S. water quality policy

David A. Keiser, Catherine L. Kling & Joseph S. Shapiro
US investment to decrease pollution in rivers, lakes, and other surface waters has exceeded $1.9 trillion since 1960, and has also exceeded the cost of most other US environmental initiatives. These investments come both from the 1972 Clean Water Act and the largely voluntary efforts to control pollution from agriculture and urban runoff. This paper reviews the methods and conclusions of about 20 recent evaluations of these policies. Surprisingly, most analyses estimate that these policies’...

Data from: Arachnid aloft: directed aerial descent in neotropical canopy spiders

Stephen P Yanoviak, Yonatan Munk & Robert Dudley
The behaviour of directed aerial descent has been described for numerous taxa of wingless hexapods as they fall from the tropical rainforest canopy, but is not known in other terrestrial arthropods. Here, we describe similar controlled aerial behaviours for large arboreal spiders in the genus Selenops (Selenopidae). We dropped 59 such spiders from either canopy platforms or tree crowns in Panama and Peru; the majority (93%) directed their aerial trajectories towards and then landed upon...

Data from: Partial genomic survival of cave bears in living brown bears

Axel Barlow, James A. Cahill, Stefanie Hartmann, Christoph Theunert, Georgios Xenikoudakis, Gloria G. Fortes, Johanna L. A. Paijmans, Gernot Rabeder, Christine Frischauf, Aurora Grandal-D'Anglade, Ana García-Vázquez, Marine Murtskhvaladze, Urmas Saarma, Peeter Anijalg, Tomaž Skrbinšek, Giorgio Bertorelle, Boris Gasparian, Guy Bar-Oz, Ron Pinhasi, Montgomery Slatkin, Love Dalén, Beth Shapiro & Michael Hofreiter
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the...

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...

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