203 Works

Supporting Information: Toward learned chemical perception of force field typing rules

Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael K. Gilson, Michael R. Shirts, John D. Chodera & David L. Mobley
The Open Force Field Initiative seeks to to automate force field development in order to advance force fields and improve accuracy (openforcefield.org). An important part of this effort includes automating the determination of chemical perception --- that is, the way force field parameters are assigned to a molecule based on chemical environment. We developed a novel technology for this purpose, termed SMARTY. It generalizes atom typing by using direct chemical perception with SMARTS strings adopting...

Training and Support for Student Library Employees in a Tiered Reference Service Model: Supporting Materials

Brian Quigley, Jeffery Loo, Lisa Ngo, Susan Powell, Samantha Teplitzky, Anna Sackmann & Kortney Rupp
To cultivate students’ reference skills, the Engineering and Physical Sciences Division of the UC Berkeley Library developed an active training program based upon a dynamic online reference manual continuously improved with student feedback. We evaluate the effectiveness of our training program and share procedures and tools for enhancing student training. Students were given a pre-test of reference skills and self-efficacy prior to attending an annual training session. One month afterwards, we distributed a post-test and...

Drivers and projections of global surface temperature anomalies at the local scale

Susanne Benz, Steven Davis & Jennifer Burney
More than half of the world’s population now lives in urban areas, and trends in rural-to-urban migration are expected to continue through the end of the century. Although cities create efficiencies that drive innovation and economic growth, they also alter the local surface energy balance, resulting in urban temperatures that can differ dramatically from surrounding areas. Here we introduce a global 1-km resolution data set of seasonal and diurnal anomalies in urban surface temperatures relative...

Data from: The role of feeding morphology and competition in governing the diet breadth of sympatric stomatopod crustaceans

Maya S. DeVries
Competition for food drives divergence and specialization in feeding morphology. Stomatopod crustaceans have two kinds of highly specialized feeding appendages: either elongate spear-like appendages (spearers) used to ambush soft-bodied evasive prey or hammer-like appendages (smashers) that produce extremely high forces used both to break hard-shelled prey and to capture evasive prey. To evaluate associations between appendage type and feeding ecology, the diet of two small smasher and spearer species (size range: 21–27 mm) that co-occur...

Data from: Gradual loading ameliorates maladaptation in computational simulations of vein graft growth and remodelling

Abhay Bangalore Ramachandra, Jay D. Humphrey & Alison L. Marsden
Vein graft failure is a prevalent problem in vascular surgeries, including bypass grafting and arteriovenous fistula procedures in which veins are subjected to severe changes in pressure and flow. Animal and clinical studies provide significant insight, but understanding the complex underlying coupled mechanisms can be advanced using computational models. Towards this end, we propose a new model of venous growth and remodelling (G&R) based on a constrained mixture theory. First, we identify constitutive relations and...

Data from: A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E.G. Briggs, Rich Mooi & Greg W. Rouse
Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a...

Data from: Limited trophic partitioning among sympatric delphinids off a tropical oceanic atoll

Hillary Young, Katherine Nigro, Douglas J. McCauley, Lisa T. Ballance, Erin M. Oleson & Simone Baumann-Pickering
Understanding trophic relationships among marine predators in remote environments is challenging, but it is critical to understand community structure and dynamics. In this study, we used stable isotope analysis of skin biopsies to compare the isotopic, and thus, trophic niches of three sympatric delphinids in the waters surrounding Palmyra Atoll, in the Central Tropical Pacific: the melon-headed whale (Peponocephala electra), Gray’s spinner dolphin (Stenella longirostris longirostris), and the common bottlenose dolphin (Tursiops truncatus). δ15N values...

Data from: Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation

Oscar Beijbom, Peter J. Edmunds, Chris Roelfsema, Jennifer Smith, David I. Kline, Benjamin Neal, Matthew J. Dunlap, Vincent Moriarty, Tung-Yung Fan, Chih-Jui Tan, Stephen Chan, Tali Treibitz, Anthony Gamst, B. Greg Mitchell, David Kriegman & Benjamin P. Neal
Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and...

Data from: The role of aedeagus size and shape in failed mating interactions among recently diverged taxa in the Drosophila mojavensis species cluster

Maxi Polihronakis Richmond
Background: Investigating the evolution of species-specific insect genitalia is central to understanding how morphological diversification contributes to reproductive isolation and lineage divergence. While many studies evoke some form of sexual selection to explain genitalia diversity, the basis of selection and the mechanism of heterospecific mate exclusion remains vague. I conducted reciprocal mate pair trials in the Drosophila mojavensis species cluster to quantify the frequency of failed insemination attempts, historically referred to as pseudocopulation, between lineages...

Data from: Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade

Elisa Boscari, Anna Barmintseva, Jose Martin Pujolar, P. Doukakis, Nikolai Mugue & Leonardo Congiu
Overexploitation of wild populations due to the high economic value of caviar has driven sturgeons to near extinction. The high prices commanded by caviar on world markets have made it a magnet for illegal and fraudulent caviar trade, often involving low-value farmed caviar being sold as top-quality caviar. We present a new molecular approach for the identification of pure sturgeon species and hybrids that are among the most commercialized species in Europe and North America....

Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

Richard W. Hill, Eric J. Armstrong, Kazuo Inaba, Masaya Morita, Martin Tresguerres, Jonathon H. Stillman, Jinae N. Roa & Garfield T. Kwan
The giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However, T. crocea’s mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of...

Data from: Frost sensitivity of leaves and flowers of subalpine plants is related to tissue type and phenology

Paul J. CaraDonna & Justin A. Bain
Harsh abiotic conditions–such as low temperatures that lead to spring and summer frost events in high-elevation and high-latitude ecosystems–can have strong negative consequences for plant growth, survival, and reproduction. Despite the predicted increase in episodic frost events under continued climate change in some ecosystems, our general understanding of the factors associated with frost sensitivity of reproductive and vegetative plant structures in natural plant communities is limited. The timing of growth and reproduction may be an...

Data from: Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow

Joao Pinto, Alexander Egyir-Yawson, José L. Vicente, Bruno Gomes, Federica Santalomazza, Marta Moreno, Jacques D. Charlwood, Frederic Simard, Nohal Elissa, David Weetman, Martin J. Donnelly, Adalgisa Caccone, Alessandra Della Torre, Caccone A, Simard F, Pinto J, Vicente JL, Gomes B, Elissa N, Weetman D & Donnelly MJ
The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In western Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviours. To investigate patterns of macro-geographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west,...

Data from: The Nearctic Nedubini: the most basal lineage of katydids is resolved among the paraphyletic “Tettigoniinae” (Orthoptera: Tettigoniidae)

Jeffrey A. Cole & Bo Huey Chiang
This study investigated the systematics of the Nearctic shield-back katydids (“Tettigoniinae”), a paraphyletic group thought to include genera from a distinctive Gondwanan tribe, the Nedubini, among an otherwise Holarctic fauna. From exemplars of five genera of Nedubini and the majority of other genera of Nearctic “Tettigoniinae,” five gene regions were sequenced, aligned with publicly available sequence data that represent diverse subfamilies of Tettigoniidae, and subjected to phylogenetic analysis under Bayesian and likelihood criteria. Our results...

Data from: Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

Benjamin E. R. Rubin, Jon G. Sanders, Kyle M. Turner, Naomi E. Pierce & Sarah D. Kocher
Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between...

Data from: Rapid evolution of thermal plasticity in mountain lake Daphnia populations

Hamanda B. Cavalheri, Celia C. Symons, Marika Schulhof, Natalie T. Jones & Jonathan B. Shurin
Populations at risk of extinction due to climate change may be rescued by adaptive evolution or plasticity. Selective agents, such as introduced predators, may enhance or constrain plastic or adaptive responses to temperature. We tested responses of Daphnia to temperature by collecting populations from lakes across an elevational gradient in the presence and absence of fish predators (long-term selection). We subsequently grew these populations at two elevations in field mesocosms over two years (short-term selection),...

Data from: Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli

Caroline B. Turner, Brian D. Wade, Justin R. Meyer, Brooke A. Sommerfeld & Richard E. Lenski
Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, much less is known about the rates and directions of evolutionary changes in elemental composition. We measured carbon, nitrogen and phosphorus content of 12 Escherichia coli populations that evolved under controlled carbon-limited, serial-transfer conditions for 50...

Data from: Stress response, gut microbial diversity, and sexual signals correlate with social interactions

Iris I. Levin, David M. Zonana, Bailey K. Fosdick, Se Jin Song, Rob Knight & Rebecca J. Safran
Theory predicts that social interactions are dynamically linked to phenotype. Yet because social interactions are difficult to quantify, little is known about the precise details on how interactivity is linked to phenotype. Here, we deployed proximity loggers on North American barn swallows (Hirundo rustica erythrogaster) to examine intercorrelations among social interactions, morphology and features of the phenotype that are sensitive to the social context: stress-induced corticosterone (CORT) and gut microbial diversity. We analysed relationships at...

Data from: The effect of keystone individuals on collective outcomes can be mediated through interactions or behavioral persistence

Noa Pinter-Wollman, Carl Nick Keiser, Roy Wollman & Jonathan Pruitt
Collective behavior emerges from interactions among group members who often vary in their behavior. The presence of just one or a few keystone individuals, such as leaders or tutors, may have a large effect on collective outcomes. These individuals can catalyze behavioral changes in other group members, thus altering group composition and collective behavior. The influence of keystone individuals on group function may lead to trade-offs between ecological situations, because the behavioral composition they facilitate...

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment-dependent

Ken Thompson, Catherine Peichel, Diana Rennison, Matthew McGee, Arianne Albert, Timothy Vines, Anna Greenwood, Abigail Wark, Yaniv Brandvain, Molly Schumer & Dolph Schluter
Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are 'intrinsic', meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus...

Data accompanying manuscript: Allometric analysis of brain cell number in Hymenoptera suggests ant brains diverge from general trends

R Keating Godfrey, Mira Swartzlander & Gronenberg Wulfila
Many comparative neurobiological studies seek to connect sensory or behavioral attributes across taxa with differences in their brain composition. Such studies can only be interpreted in a meaningful way if the general brain-body relationships are known on a larger taxonomic scale. Recent studies in vertebrates suggest cell number and density may be better correlated with behavioral ability than brain mass or volume, but few estimates of such figures exist for insects. Here we use the...

Data from: Monitoring spawning activity in a southern California marine protected area using molecular identification of fish eggs

Alice E. Harada, Elise A. Lindgren, Maiko C. Hermsmeier, Peter A. Rogowski, Eric Terrill & Ronald S. Burton
In order to protect the diverse ecosystems of coastal California, a series of marine protected areas (MPAs) have been established. The ability of these MPAs to preserve and potentially enhance marine resources can only be assessed if these habitats are monitored through time. This study establishes a baseline for monitoring the spawning activity of fish in the MPAs adjacent to Scripps Institution of Oceanography (La Jolla, CA, USA) by sampling fish eggs from the plankton....

Data from: Electrophoretic mobility confirms reassortment bias among geographic isolates of segmented RNA phages

Samuel L. Díaz-Muñoz, Olivier Tenaillon, Daniel Goldhill, Kristen Brao, Paul E. Turner & Lin Chao
Background: Sex presents evolutionary costs and benefits, leading to the expectation that the amount of genetic exchange should vary in conditions with contrasting cost-benefit equations. Like eukaryotes, viruses also engage in sex, but the rate of genetic exchange is often assumed to be a relatively invariant property of a particular virus. However, the rates of genetic exchange can vary within one type of virus according to geography, as highlighted by phylogeographic studies of cystoviruses. Here...

Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome

Jessica L. Metcalf, Se Jin Song, James T. Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie & Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

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