51 Works

Data from: AMAS: a fast tool for large alignment manipulation and computing of summary statistics

Marek L. Borowiec
The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present...

Data from: Haplotype-phased synthetic long reads from short-read sequencing

James A. Stapleton, Jeongwoon Kim, John P. Hamilton, Ming Wu, Luiz C. Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus Brown, Christina Chan, C. Robin Buell & Timothy A. Whitehead
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences...

Data from: Long-term climate and competition explain forest mortality patterns under extreme drought

Derek J. N. Young, Jens T. Stevens, J. Mason Earles, Jeffrey Moore, Adam Ellis, Amy L. Jirka & Andrew M. Latimer
Rising temperatures are amplifying drought-induced stress and mortality in forests globally. It remains uncertain, however, whether tree mortality across drought-stricken landscapes will be concentrated in particular climatic and competitive environments. We investigated the effects of long-term average climate [i.e. 35-year mean annual climatic water deficit (CWD)] and competition (i.e. tree basal area) on tree mortality patterns, using extensive aerial mortality surveys conducted throughout the forests of California during a 4-year statewide extreme drought lasting from...

Data from: Ecological intensification and arbuscular mycorrhizas: a meta-analysis of tillage and cover crop effects

Timothy M. Bowles, Louise E. Jackson, Malina Loeher & Timothy R. Cavagnaro
1. Reliance on ecosystem services instead of synthetic, non-renewable inputs is increasingly seen as key to achieving food security in an environmentally sustainable way. This process, known as ecological intensification, will depend in large part on enhancing below-ground biological interactions that facilitate resource use efficiency. Arbuscular mycorrhizas (AM), associations formed between the roots of most terrestrial plant species and a specialized group of soil fungi, provide valuable ecosystem services, but the full magnitude of these...

Data from: Ocean acidification alters the response of intertidal snails to a key sea star predator

Brittany M. Jellison, Aaron T. Ninokawa, Tessa M. Hill, Eric Sanford & Brian Gaylord
Organism-level effects of ocean acidification (OA) are well recognized. Less understood are OA's consequences for ecological species interactions. Here, we examine a behaviourally mediated predator–prey interaction within the rocky intertidal zone of the temperate eastern Pacific Ocean, using it as a model system to explore OA's capacity to impair invertebrate anti-predator behaviours more broadly. Our system involves the iconic sea star predator, Pisaster ochraceus, that elicits flee responses in numerous gastropod prey. We examine, in...

Data from: There’s no place like home: the contribution of direct and extended phenotypes on the expression of spider aggressiveness

Pierre-Olivier Montiglio & Nicholas DiRienzo
Architectural constructions allow animals to modify their environment in order to improve their reproductive success. Constructions also modulate the expression of individual behavior, ultimately affecting the presence and importance of animal personality within populations. The exact impact of constructions on personality is seldom investigated. We quantified experimentally the impact of web characteristics on individual foraging behavior in the Western black widow spider (Latrodectus hesperus). We assayed aggressiveness toward a prey cue, and boldness while individuals...

PLoS One Dodder Data January 2013

Shahla Farzan
An increasing body of evidence now indicates that parasitic species can have ecosystem-level impacts on species diversity patterns, trophic energy flow, and food web stability. Plant parasitic dodders (Cuscuta spp.) are globally distributed holoparasites that form a direct physical connection to host vascular tissue. As a hypergeneralist plant parasite, field dodder (Cuscuta campestris) can connect the phloem and xylem of widely divergent species simultaneously. Using C. campestris as a live bridge between plants, this study...

Data from: The underappreciated role of life history in mediating the functional consequences of biodiversity change

Matthew E.S. Bracken, Susan L. Williams & Matthew E. S. Bracken
Biodiversity is changing on both global and local scales, motivating research to understand the consequences of these changes for how communities and ecosystems function. Here, we explore the role of life history strategies in mediating biodiversity and ecosystem functioning. In particular, we evaluate how the composition, biomass (% cover), and richness of perennial (persistence ≥ 1 year) and ephemeral (persistence < 1 year) species change along a gradient of increasing seaweed species richness on a...

Data from: A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site

Erin A. Becker, Andrew I. Yao, Phillip M. Seitzer, Tobias Kind, Ting Wang, Rich Eigenheer, Katie S. Y. Shao, Vladimir Yarov-Yarovoy & Marc T. Facciotti
Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a...

Data from: Meniscus ascent by thrips (Thysanoptera)

Víctor Manuel Ortega-Jiménez, Sarahi Arriaga-Ramirez & Robert Dudley
Meniscus climbing using a fixed body posture has been well documented for various aquatic and neustonic insects, but is not known from small flying insects that inadvertently become trapped on water surfaces. Here, we show that thrips (order Thysanoptera) can ascend a meniscus by arching their non-wetting bodies to translate head-first and upward along a water surface; if initially oriented backwards, they can turn by 180° to ascend head-first, and climb upward on a surrounding...

Data from: Microhabitat partitioning in seagrass mesograzers is driven by consistent species choices across multiple predator and competitor contexts

Moritz D. Lürig, Rebecca J. Best & John J. Stachowicz
Explanations for the coexistence of multiple species from the same functional group or taxonomic clade frequently include fine-scale resource partitioning. However, despite the hypothesized importance of niche partitioning, we know relatively little about the underlying mechanisms. For example, differences in resource use may be fixed consequences of organism traits, or they may be achieved via context-dependent behaviors. In this study we investigated mechanisms of microhabitat partitioning using eight species of marine mesograzers inhabiting seagrass and...

Data from: Retracted: Individual and group performance suffers from social niche disruption

Kate L. Laskowski, Pierre-Olivier Montiglio & Jonathan N. Pruitt
THE ASSOCIATED ARTICLE HAS BEEN RETRACTED. Further use of this data is not recommended. See https://www.journals.uchicago.edu/doi/abs/10.1086/708066 The social niche specialization hypothesis predicts that animal personalities emerge as a result of individuals occupying different social niches within a group. Here we track individual personality and performance, and collective performance among groups of social spiders where we manipulated the familiarity of the group members. We show that individual personalities, as measured by consistent individual differences in boldness...

Data from: Discovery of metabolic biomarkers for Duchenne Muscular Dystrophy within a natural history study

Simina M. Boca, Maki Nishida, Michael Harris, Shruti Rao, Amrita K. Cheema, Kirandeep Gill, Haeri Seol, Lauren P. Morgenroth, Erik Henricson, Craig McDonald, Jean K. Mah, Paula R. Clemens, Eric P. Hoffman, Yetrib Hathout & Subha Madhavan
Serum metabolite profiling in Duchenne muscular dystrophy (DMD) may enable discovery of valuable molecular markers for disease progression and treatment response. Serum samples from 51 DMD patients from a natural history study and 22 age-matched healthy volunteers were profiled using liquid chromatography coupled to mass spectrometry (LC-MS) for discovery of novel circulating serum metabolites associated with DMD. Fourteen metabolites were found significantly altered (1% false discovery rate) in their levels between DMD patients and healthy...

Data from: Community traits affect plant–plant interactions across climatic gradients

Stella M. Copeland & Susan P. Harrison
Plant abundances and demography often vary along gradients of environmental stress, and neighboring plants can amplify or diminish such variation. We asked to what degree the effects of neighboring plants on a focal species can be explained by the traits and abundances of species in the surrounding community. We studied a common understory herb, Trientalis latifolia, across climatic gradients created by topography in the Siskiyou Mountains, southwestern Oregon. We compared Trientalis fitness along these gradients...

Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

Michael R. May, Sebastian Hoehna & Brian R. Moore
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching...

Data from: Calling in sick: impacts of fever on intra-urban human mobility

T. Alex Perkins, Valerie A. Paz-Soldan, Steven T. Stoddard, Amy C. Morrison, Brett M. Forshey, Kanya C. Long, Eric S. Halsey, Tadeusz J. Kochel, John P. Elder, Uriel Kitron, Thomas W. Scott & Gonzalo M. Vazquez-Prokopec
Pathogens inflict a wide variety of disease manifestations on their hosts, yet the impacts of disease on the behaviour of infected hosts are rarely studied empirically and are seldom accounted for in mathematical models of transmission dynamics. We explored the potential impacts of one of the most common disease manifestations, fever, on a key determinant of pathogen transmission, host mobility, in residents of the Amazonian city of Iquitos, Peru. We did so by comparing two...

Data from: Trophic sensitivity of invasive predator and native prey interactions: integrating environmental context and climate change

Brian S. Cheng, Lisa M. Komoroske & Edwin D. Grosholz
Climate change is predicted to intensify the impacts of invasive species by enhancing their performance relative to their native counterparts. However, few studies have compared the performance of invasive predators and native prey, despite the fact that non-native predators are well known to disrupt native communities. The ‘trophic sensitivity hypothesis’ suggests that predators are less tolerant of increasing environmental stress than their prey, whereas the ‘tolerant invaders hypothesis’ suggests that invaders are more tolerant than...

Data from: Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon

Mariah H. Meek, Melinda R. Baerwald, Molly R. Stephens, Alisha Goodbla, Michael R. Miller, Katharine M. H. Tomalty & Bernie May
Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large-scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single-nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled...

Data from: Adaptation to an invasive host is driving the loss of a native ecotype

Meredith L. Cenzer
Locally adapted populations are often used as model systems for the early stages of ecological speciation, but most of these young divergent populations will never become complete species. The maintenance of local adaptation relies on the strength of natural selection overwhelming the homogenizing effects of gene flow; however, this balance may be readily upset in changing environments. Here I show that soapberry bugs (Jadera haematoloma) have lost adaptations to their native host plant (Cardiospermum corindum)...

Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory

Erin Conlisk, Rebecca Swab, Alejandra Martínez-Berdeja & Matthew P. Daugherty
Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In...

Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

Brian Helmuth, Francis Choi, Allison Matzelle, Jessica L. Torossian, Scott L. Morella, K. A. S. Mislan, Lauren Yamane, Denise Strickland, P. Lauren Szathmary, Sarah Gilman, Alyson Tockstein, Thomas J. Hilbish, Michael T. Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher D. G. Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa M. Foley, Angela Johnson, Megan Poole, Mae M. Noble … & Gerardo Zardi
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements...

Data from: Spider phylogenomics: untangling the spider tree of life

Jason Bond, Nicole L. Garrison, Juanita Rodriguez, Ingi Agnarsson, Jonathan A. Coddington, Charles E. Griswold, Christopher A. Hamilton, Marshal Hedin, Kevin Kocot, Joel M. Ledford & Jason E. Bond
Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes...

Data from: Ecomorphological convergence in planktivorous surgeonfishes

Sarah T. Friedman, Samantha A. Price, Andrew S. Hoey & Peter C. Wainwright
Morphological convergence plays a central role in the study of evolution. Often induced by shared ecological specialization, homoplasy hints at underlying selective pressures and adaptive constraints that deterministically shape the diversification of life. Though midwater zooplanktivory has arisen in adult surgeonfishes (family Acanthuridae) at least four independent times, it represents a clearly specialized state, requiring the capacity to swiftly swim in midwater locating and sucking small prey items. While this diet has commonly been associated...

Data from: Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses

Jason P. Sexton, Matthew B. Hufford, Ashley Bateman, David B. Lowry, Harald Meimberg, Sharon Y. Strauss, Kevin J. Rice & Ashley C.Bateman
Gene flow may influence the formation of species range limits, yet little is known about the patterns of gene flow with respect to environmental gradients or proximity to range limits. With rapid environmental change it is especially important to understand patterns of gene flow to inform conservation efforts. Here we investigate the species range of the selfing, annual plant, Mimulus laciniatus, in the California Sierra Nevada. We assessed genetic variation, gene flow, and population abundance...

Data from: Experimental tests of the function and flexibility of song consistency in a wild bird

Conor C. Taff & Corey R. Freeman-Gallant
Measures of bird song that capture aspects of motor performance, such as consistency, have become a major focus in understanding sexual selection on song. Despite accumulating evidence that consistency is related to reproductive success in many species, the relative importance of male–male interactions and female–male interactions is still unclear. We studied the function and flexibility of song consistency and song rate in common yellowthroat warblers (Geothlypis trichas). A previous study of this population found that...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of California, Davis
  • University of California System
  • University of California, Berkeley
  • McGill University
  • San Diego State University
  • University of Washington
  • University of Pittsburgh
  • United States Department of Agriculture
  • University of California, Santa Barbara
  • California Polytechnic State University