51 Works

Data from: Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Amanda L. Grusz, Carl J. Rothfels & Eric Schuettpelz
Background: Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which...

Data from: Precipitation alters interactions in a grassland ecological community

Nicolas Deguines, Justin S. Brashares & Laura R. Prugh
Climate change is transforming precipitation regimes world-wide. Changes in precipitation regimes are known to have powerful effects on plant productivity, but the consequences of these shifts for the dynamics of ecological communities are poorly understood. This knowledge gap hinders our ability to anticipate and mitigate the impacts of climate change on biodiversity. Precipitation may affect fauna through direct effects on physiology, behaviour or demography, through plant-mediated indirect effects, or by modifying interactions among species. In...

Data from: Inferring the timing of long-distance dispersal between Rail metapopulations using genetic and isotopic assignments

Laurie A. Hall & Steven R. Beissinger
The stochastic and infrequent nature of long-distance dispersal often makes it difficult to detect. We quantified the frequency, distance, and timing of long-distance dispersal in a non-migratory, secretive wetland bird, the California black rail (Laterallus jamaicensis coturniculus), between an inland and a coastal metapopulation separated by greater than 100 km. Using 15 microsatellites in conjunction with stable carbon, nitrogen, and sulfur isotopes, we classified rails as: residents of their capture population, recent migrants that dispersed...

Data from: Survival by genotype: patterns at Mc1r are not black and white at the White Sands ecotone

Simone Des Roches, Rahel Sollmann, Kendall Calhoun, A. P. Rothstein & Erica B. Rosenblum
Measuring links among genotype, phenotype and survival in the wild has long been a focus of studies of adaptation. We conducted a 4-year capture–recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched coloration in S. cowlesi from the heart...

Data from: Social selection parapatry in Afrotropical sunbirds

Jay P. McEntee, Joshua V. Peñalba, Chacha Werema, Elia Mulungu, Maneno Mbilinyi, David Moyer, Louis Hansen, Jon Fjeldså & Rauri C. K. Bowie
The extent of range overlap of incipient and recent species depends on the type and magnitude of phenotypic divergence that separates them, and the consequences of phenotypic divergence on their interactions. Signal divergence by social selection likely initiates many speciation events, but may yield niche-conserved lineages predisposed to limit each others’ ranges via ecological competition. Here we examine this neglected aspect of social selection speciation theory in relation to the discovery of a non-ecotonal species...

Data from: Mutations of the calcium channel gene cacophony suppress seizures in Drosophila

Arunesh Saras & Mark A. Tanouye
Bang sensitive (BS) Drosophila mutants display characteristic seizure-like phenotypes resembling, in some aspects, those of human seizure disorders such as epilepsy. The BS mutant parabss1, caused by a gain-of-function mutation of the voltage-gated Na+ channel gene, is extremely seizure-sensitive with phenotypes that have proven difficult to ameliorate by anti-epileptic drug feeding or by seizure-suppressor mutation. It has been presented as a model for intractable human epilepsy. Here we show that cacophony (cacTS2), a mutation of...

Data from: Mediating water temperature increases due to livestock and global change in high elevation meadow streams of the Golden Trout Wilderness

Sébastien Nusslé, Kathleen R. Matthews & Stephanie M. Carlson
Rising temperatures due to climate change are pushing the thermal limits of many species, but how climate warming interacts with other anthropogenic disturbances such as land use remains poorly understood. To understand the interactive effects of climate warming and livestock grazing on water temperature in three high elevation meadow streams in the Golden Trout Wilderness, California, we measured riparian vegetation and monitored water temperature in three meadow streams between 2008 and 2013, including two “resting”...

Data from: Spatiotemporal rank filtering improves image quality compared to frame averaging in 2-photon laser scanning microscopy

Henry Pinkard, Kaitlin Corbin & Matthew F. Krummel
Live imaging of biological specimens using optical microscopy is limited by tradeoffs between spatial and temporal resolution, depth into intact samples, and phototoxicity. Two-photon laser scanning microscopy (2P-LSM), the gold standard for imaging turbid samples in vivo, has conventionally constructed images with sufficient signal-to-noise ratio (SNR) generated by sequential raster scans of the focal plane and temporal integration of the collected signals. Here, we describe spatiotemporal rank filtering, a nonlinear alternative to temporal integration, which...

Data from: Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata)

Barbara-Anne Battelle, Joseph F. Ryan, Karen E. Kempler, Spencer R. Saraf, Catherine E. Marten, Wesley C. Warren, Patrick Minx, Michael J. Montague, Pamela J. Green, Skye A. Schmidt, Lucinda Fulton, Nipam H. Patel, Merideth E. Protas, Richard K. Wilson & Megan L. Porter
Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of...

Data from: Catecholaminergic regulation of learning rate in a dynamic environment

Marieke Jepma, Peter R. Murphy, Matthew R. Nassar, Mauricio Rangel-Gomez, Martijn Meeter & Sander Nieuwenhuis
Adaptive behavior in a changing world requires flexibly adapting one’s rate of learning to the rate of environmental change. Recent studies have examined the computational mechanisms by which various environmental factors determine the impact of new outcomes on existing beliefs (i.e., the ‘learning rate’). However, the brain mechanisms, and in particular the neuromodulators, involved in this process are still largely unknown. The brain-wide neurophysiological effects of the catecholamines norepinephrine and dopamine on stimulus-evoked cortical responses...

Data from: The influence of spatially structured soil properties on tree community assemblages at a landscape scale in the tropical forests of southern Cameroon

Jason Vleminckx, Jean-Louis Doucet, Julie Morin-Rivat, Achille Biwolé, David Bauman, Olivier J. Hardy, Adeline Fayolle, Jean-François Gillet, Kasso Daïnou, Anaïs Gorel & Thomas Drouet
Species distribution within plant communities results from both the influence of deterministic processes, related to environmental conditions, and neutral processes related to dispersal limitation and stochastic events, the relative importance of each factor depending on the observation scale. Assessing the relative contribution of environment necessitates controlling for spatial dependences among data points. Recent methods, combining multiple regression and Moran's eigenvectors maps (MEM), have been proved successful in disentangling the influence of pure spatial processes related...

Data from: Changes in spatial variance during a grassland to shrubland state transition

Zak Ratajczak, Paolo D'Odorico, Jesse B. Nippert, Scott L. Collins, Nathaniel A. Brunsell & Sujith Ravi
State transitions are changes in ecosystem structure and self-reinforcing feedbacks that are initiated when an exogenous driver variable crosses a threshold. Reversing state transitions is difficult and costly. While some state transitions are relatively rapid, many take years to decades. Outside of theoretical models, very little is known about slower state transitions and how they unfold in time and space. We quantified changes in spatial variance as a mesic grassland ecosystem shifts to a shrub-dominated...

Data from: Modeling effects of nonbreeders on population growth estimates

Aline M. Lee, Jane M. Reid & Steven R. Beissinger
Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates. We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms...

Data from: Does wildlife resource selection accurately inform corridor conservation?

Briana Abrahms, Sarah C. Sawyer, Neil R. Jordan, J. Weldon McNutt, Alan M. Wilson & Justin S. Brashares
Evaluating landscape connectivity and identifying and protecting corridors for animal movement have become central challenges in applied ecology and conservation. Currently, resource selection analyses are widely used to focus corridor planning where animal movement is predicted to occur. An animal's behavioural state (e.g. foraging, dispersing) is a significant determinant of resource selection patterns, yet has largely been ignored in connectivity assessments. We review 16 years of connectivity studies employing resource selection analysis to evaluate how...

Data from: Description of a new microphthalmous species of Pterostichus Bonelli, 1810 (Coleoptera: Carabidae) from southwestern Oregon and key to species of the subgenus Leptoferonia Casey, 1918

Kipling Will
Pterostichus (Leptoferonia) hackerae sp. nov. is described based on a single male specimen with its type locality No Name Cave, Josephine Co., Oregon. This is the seventh species of microphthalmous Leptoferonia Casey, 1918 to be described, and based on the analysis of DNA data, it is found to be most closely related to another microphthalmous species, P. rothi (Hatch, 1951). A second specimen and location for P. (Leptoferonia) enyo Will, 2007, also a microphthalmous species,...

Data from: Estimating resource preferences of a native bumblebee: the effects of availability and use-availability models on preference estimatess

Alexandra N. Harmon-Threatt, Perry De Valpine & Claire Kremen
Identifying resource preference is considered essential for developing targeted conservation plans but, for many species, questions remain about the best way to estimate preference. Resource preferences for bees are particularly difficult to determine as the resources they collect, nectar and pollen, are challenging to estimate availability and collection. Resources are traditionally measured at the flower or inflorescence level, but these measures of availability do not correspond to the resources actually used by bees. Additionally, it...

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: Global population structure of a worldwide pest and virus vector: genetic diversity and population history of the Bemisia tabaci sibling species group

Margarita Hadjistylli, George K. Roderick & Judith K. Brown
The whitefly Bemisia tabaci sibling species (sibsp.) group comprises morphologically indiscernible lineages of well-known exemplars referred to as biotypes. It is distributed throughout tropical and subtropical latitudes, and includes the contemporary invasive haplotypes, termed B and Q. Several well-studied B. tabaci biotypes exhibit ecological and biological diversity, however, most members are poorly studied or completely uncharacterized. Genetic studies have revealed substantial diversity within the group based on a fragment of the mitochondrial cytochrome oxidase I...

Data from: An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina

Jasper J. Visser, Yolanda Cheng, Steven C. Perry, Andrew Benjamin Chastain, Bayan Parsa, Shatha S. Masri, Ray Thomas A., Jeremy N. Kay, Woj M. Wojtowicz & Thomas A Ray
In the inner plexiform layer of the mouse retina, ~70 neuronal subtypes form a stereotyped circuit that underlies visual processing. During development, subtypes organize into an intricate laminar structure. This organization is choreographed by extracellular interactions that mediate cell recognition events. To identify recognition proteins involved in lamination, we utilized microarray data from 13 subtypes to identify differentially-expressed cell surface and secreted proteins. Using these candidates, we performed a biochemical screen and identified ~50 previously-unknown...

Data from: Cold adaptation increases rates of nutrient flow and metabolic plasticity during cold exposure in Drosophila melanogaster

Caroline M. Williams, Marshall D. McCue, Nishanth E. Sunny, Andre Szejner-Sigal, Theodore J. Morgan, David B. Allison & Daniel A. Hahn
Metabolic flexibility is an important component of adaptation to stressful environments, including thermal stress and latitudinal adaptation. A long history of population genetic studies suggest that selection on core metabolic enzymes may shape life histories by altering metabolic flux. However, the direct relationship between selection on thermal stress hardiness and metabolic flux has not previously been tested. We investigated flexibility of nutrient catabolism during cold stress in Drosophila melanogaster artificially selected for fast or slow...

Data from: Separating sources of density-dependent and density-independent establishment limitation in invading species

Erica N. Spotswood, Pierre Mariotte, Emily C. Farrer, Liana Nichols, Katherine N. Suding & Katharine N. Suding
Successful colonization by invasive species depends on both the ability to disperse seeds to a site and an ability to establish once seeds have arrived. While seed and establishment limitation are known to jointly influence colonization, decomposing establishment limitation into density-dependent and density-independent components has remained challenging. Here, we couple theoretical models of recruitment with a multispecies invasion experiment conducted within a natural gradient of soil moisture and productivity to assess how variation in establishment...

Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Helene Badouin, Chris E. Ellison, Nhu H. Nguyen, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Christopher E. Ellison
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and...

Data from: Mosquito saliva increases endothelial permeability in the skin, immune cell migration, and dengue pathogenesis during antibody-dependent enhancement

Michael A. Schmid, Dustin R. Glasner, Sanjana Shah, Daniela Michlmayr, Laura D. Kramer, & Eva Harris
Dengue remains the most prevalent arthropod-borne viral disease in humans. While probing for blood vessels, Aedes aegypti and Ae. albopictus mosquitoes transmit the four serotypes of dengue virus (DENV1-4) by injecting virus-containing saliva into the skin. Even though arthropod saliva is known to facilitate transmission and modulate host responses to other pathogens, the full impact of mosquito saliva on dengue pathogenesis is still not well understood. Inoculating mice lacking the interferon-α/β receptor intradermally with DENV...

Data from: Agricultural practices for food safety threaten pest control services for fresh produce

Daniel S. Karp, Rebekah Moses, Sasha Gennet, Matthew S. Jones, Shimat Joseph, Leithen K. M'Gonigle, Lauren C. Ponisio, William E. Snyder & Claire Kremen
Over the past decade, several foodborne disease outbreaks provoked widespread reforms to the fresh produce industry. Subsequent concerns about wildlife vectors and contaminated manures created pressure on growers to discontinue use of manure-based composts and remove nearby semi-natural vegetation. Despite widespread adoption, impacts of these practices on ecosystem services such as pest control have not been assessed. We used a landscape-scale field experiment to quantify associations between compost applications, semi-natural vegetation, pest control services and...

Data from: The secret life of ground squirrels: accelerometry reveals sex-dependent plasticity in above-ground activity

Cory T. Williams, Kathryn Wilsterman, Victor Zhang, Jeanette Moore, Brian M. Barnes & C. Loren Buck
The sexes differ in how and when they allocate energy towards reproduction, but how this influences phenotypic plasticity in daily activity patterns is unclear. Here, we use collar-mounted light loggers and triaxial accelerometers to examine factors that affect time spent above ground and overall dynamic body acceleration (ODBA), an index of activity-specific energy expenditure, across the active season of free-living, semi-fossorial arctic ground squirrels (Urocitellus parryii). We found high day-to-day variability in time spent above...

Registration Year

  • 2016
    51

Resource Types

  • Dataset
    51

Affiliations

  • University of California, Berkeley
    51
  • University of California System
    7
  • University of Florida
    5
  • Duke University
    4
  • United States Department of Agriculture
    3
  • University of California, Davis
    3
  • Helmholtz Centre for Environmental Research
    2
  • University of Washington
    2
  • University of North Carolina
    2
  • University of Virginia
    2