21 Works

PrioritEvac: An Agent-Based Model of Evacuation from Building Fires

Eileen Young
This simulation is of the 2003 Station Nightclub Fire and is part of the Interdependencies in Community Resilience (ICoR) project (http://www-personal.umich.edu/~eltawil/icor.html). The git contains the simulation as well as csvs of data about the fire, smoke, building, and people involved.

Data from: The genomic basis for short-term evolution of environmental adaptation in maize

Randall Wisser
Quality control genotype data (45,718 variant sites) for samples from Hallauer's Tusón. Tab delimited file. A header row is included. The first column ("label") lists sample names, the second column ("popdata") lists the generation to which each sample belongs, and the remaining columns correspond to the genotype data. Unphased diploid genotype calls are recorded in the following format: 1/1. Variant encoding: 1=A, 2=C, 3=G, 4=T, 5=deletion, 6=insertion (5 and 6 are used for the ZmCCT10_CACTA...

Data from: Recalibrating timing behavior via expected covariance between temporal cues

Benjamin J. De Corte, Rebecca R. Della Valle, Matthew S. Matell, Rebecca R Della Valle, Matthew S Matell & Benjamin J De Corte
Individuals must predict future events to proactively guide their behavior. Predicting when events will occur is a critical component of these expectations. Temporal expectations are often generated based on individual cue-duration relationships. However, the durations associated with different environmental cues will often co-vary due to a common cause. We show that timing behavior may be calibrated based on this expected covariance, which we refer to as the 'common cause hypothesis'. In five experiments using rats,...

Data from: Quantifying the importance of geographic replication and representativeness when estimating demographic rates, using a coastal species as a case study

Christopher R. Field, Katharine J. Ruskin, Bri Benvenuti, Alyssa C. Borowske, Jonathan B. Cohen, Laura Garey, Thomas P. Hodgman, Rebecca A. Kern, Erin King, Alison R. Kocek, Adrienne I. Kovach, Kathleen M. O'Brien, Brian J. Olsen, Nancy Pau, Samuel G. Roberts, Emma Shelly, W. Gregory Shriver, Jennifer Walsh, Chris S. Elphick & Rebecca A. Longenecker
Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify...

Data from: Subspecies delineation amid phenotypic, geographic, and genetic discordance in a songbird

Jennifer Walsh, Irby J. Lovette, Virginia Winder, Chris S. Elphick, Brian J. Olsen, W. Gregory Shriver, Adrienne I. Kovach & Gregory Shriver
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to...

Data from: Effects of cell-cycle-dependent expression on random fluctuations in protein levels

Mohammad Soltani & Abhyudai Singh
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We analyse a model where a stable protein is synthesized in random bursts, and the frequency with which bursts occur varies within the cell cycle. Formulae quantifying the extent of fluctuations in the protein copy number are derived and decomposed into...

Data from: Predator-guided sampling reveals biotic structure in the bathypelagic

Kelly J. Benoit-Bird, Brandon L. Southall & Mark A. Moline
We targeted habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey’s distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was...

Data from: Acidification and γ-aminobutyric acid independently alter kairomone-induced behaviour

Corie L. Charpentier & Jonathan H. Cohen
Exposure to high pCO2 or low pH alters sensation and behaviour in many marine animals. We show that crab larvae lose their ability to detect and/or process predator kairomones after exposure to low pH over a time scale relevant to diel pH cycles in coastal environments. Previous work suggests that acidification affects sensation and behaviour through altered neural function, specifically the action of γ-aminobutyric acid (GABA), because a GABA antagonist, gabazine, restores the original behaviour....

Data from: Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins

Daniel J. Thornhill, Yu Xiang, Min Zhong, Scott R. Santos & D. Tye Pettay
The Aiptasia-Symbiodinium symbiosis is a promising model for experimental studies of cnidarian-dinoflagellate associations, yet relatively little is known regarding the genetic diversity of either symbiotic partner. To address this we collected Aiptasia from 17 localities throughout the world and examined the genetic diversity of both anemones and their endosymbionts. Based on newly-developed SCAR markers, Aiptasia consisted of two genetically-distinct populations, one Aiptasia lineage from Florida and a second network of Aiptasia genotypes found at other...

Data from: Using greenhouse gas fluxes to define soil functional types

Sandra Petrakis, Josep Barba, Benjamin Bond-Lamberty & Rodrigo Vargas
Aim: Soils provide key ecosystem services and directly control ecosystem functions; thus, there is a need to define the reference state of soil functionality. Most common functional classifications are vegetation-centered, such as plant functional types (PFTs), and neglect soil characteristics and processes. We propose Soil Functional Types (SFTs) as a conceptual approach to represent and describe the functionality of soils based on characteristics of their greenhouse gas (GHG) flux dynamics. Methods: We used automated measurements...

Data from: Animal-mediated organic matter transformation: aquatic insects as a source of microbially bioavailable organic nutrients and energy

Thomas B. Parr, Krista A. Capps, Shreeram P. Inamdar & Kari A. Metcalf
1. Animal communities are essential drivers of energy and elemental flow in ecosystems. However, few studies have investigated the functional role of animals as sources of dissolved organic matter (DOM) and the subsequent utilization of that DOM by the microbial community. 2. In a small forested headwater stream, we tested the effects of taxonomy, feeding traits, and body size on the quality and quantity of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) excreted...

Data from: Biodiverse cities: the nursery industry, homeowners, and neighborhood differences drive urban tree composition

Meghan Avolio, Diane Pataki, Tara Trammell, Joanna Endter-Wada, Meghan L. Avolio, Diane E. Pataki & Tara L. E. Trammell
In arid and semi-arid regions, where few if any trees are native, city trees are largely human-planted. Societal factors such as resident preferences for tree traits, nursery offerings, and neighborhood characteristics are potentially key drivers of urban tree community composition and diversity, however they remain critically understudied. We investigated patterns of urban tree structure in residential neighborhoods of the Salt Lake Valley, Utah, combining biological variables, such as neighborhood and plant nursery tree species and...

Data from: Geographic variation in Megalorchestia californiana allele frequencies may be caused by winter rather than summer temperatures

John H. McDonald & JH McDonald
There are many allozyme polymorphisms with latitudinal clines, for which selection by climate is one obvious explanation. Both warm summer temperatures and cold winter temperatures could plausibly impose selection on enzyme polymorphisms, but because summer and winter temperatures are usually geographically correlated, there has been little attempt to use patterns of geographic variation to discriminate between these possible selective factors. The glucose-6-phosphate isomerase and mannose-6-phosphate isomerase allozyme polymorphisms in the amphipod crustacean Megalorchestia californiana have...

Data from: A connection between colony biomass and death in Caribbean reef-building corals

Daniel J. Thornhill, Randi D. Rotjan, Brian D. Todd, Geoff C. Chilcoat, Roberto Iglesias-Prieto, Todd C. LaJeunesse, Dustin W. Kemp, Jennifer McCabe Reynolds, Gregory W. Schmidt, Thomas Shannon, Mark E. Warner & William K. Fitt
Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994–2007), eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in Puerto Morelos, Mexico (2003–2007). For...

Data from: Post‐independence mortality of juveniles is driven by anthropogenic hazards for two passerines in an urban landscape

Solny A. Adalsteinsson, Jeffrey J. Buler, Jacob L. Bowman, Vincent D'Amico, Zachary S. Ladin & W. Gregory Shriver
Urban environments impose novel selection pressures with varying impacts across species and life history stages. The post‐fledging stage for migratory passerines, defined as the period of time from when hatch‐year birds fledge until their first migration, is a poorly understood component of annual productivity that potentially limits population growth. We studied two migratory passerines with positive and negative population responses to urbanization, respectively: Gray Catbird (Dumetella carolinensis) and Wood Thrush (Hylocichla mustelina). Our goals were...

Data from: The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development

Archana D. Siddam, Carole Gautier-Courteille, Linette Perez-Campos, Deepti Anand, Atul Kakrana, Christine A. Dang, Vincent Legagneux, Agnès Méreau, Justine Viet, Jeffrey M. Gross, Luc Paillard & Salil A. Lachke
Opacification of the ocular lens, termed cataract, is a common cause of blindness. To become transparent, lens fiber cells undergo degradation of their organelles, including their nuclei, presenting a fundamental question: does signaling/transcription sufficiently explain differentiation of cells progressing toward compromised transcriptional potential? We report that a conserved RNA-binding protein Celf1 post-transcriptionally controls key genes to regulate lens fiber cell differentiation. Celf1-targeted knockout mice and celf1-knockdown zebrafish and Xenopus morphants have severe eye defects/cataract. Celf1...

Data from: Using terrestrial haematophagous leeches to enhance tropical biodiversity monitoring programmes in Bangladesh

Sarah R. Weiskopf, Kyle P. McCarthy, Michael Tessler, Hasan A. Rahman, Jennifer L. McCarthy, Rebecca Hersch, Mohammad M. Faisal & Mark E. Siddall
1. Measuring mammal biodiversity in tropical rainforests is challenging, and methods which reduce effort while maximizing success are crucial for long-term monitoring programmes. Commonly used methods to assess mammal biodiversity may require substantial sampling effort to be effective. Genetic methods are a new and important sampling tool on the horizon, but obtaining sufficient DNA samples can be a challenge. 2. We evaluated the efficacy of using parasitic leeches Haemadipsa spp., as compared to camera trapping,...

Data from: Soaring across continents: decision-making of a soaring migrant under changing atmospheric conditions along an entire flyway

Wouter Vansteelant, Judy Shamoun-Baranes, James D. McLaren, Jan Van Diermen, Willem Bouten, Wouter M. G. Vansteelant & James McLaren
(1) Thermal soaring birds reduce flight-energy costs by alternatingly gaining altitude in thermals and gliding across the earth’s surface. To find out how soaring migrants adjust their flight behaviour to dynamic atmospheric conditions across entire migration routes, we combined optimal soaring migration theory with high-resolution GPS tracking data of migrating Honey Buzzards Pernis apivorus and wind data from a global numerical atmospheric model. (2) We compared measurements of gliding air speeds to predictions based on...

Data from: Artificial light at night confounds broad-scale habitat use by migrating birds

James D. McLaren, Jeffrey J. Buler, Tim Schreckengost, Jaclyn A. Smolinsky, Matthew Boone, E. Emiel Van Loon, Deanna K. Dawson, Eric L. Walters & E. Emiel Van Loon
With many of the world's migratory bird populations in alarming decline, broad-scale assessments of responses to migratory hazards may prove crucial to successful conservation efforts. Most birds migrate at night through increasingly light-polluted skies. Bright light sources can attract airborne migrants and lead to collisions with structures, but might also influence selection of migratory stopover habitat and thereby acquisition of food resources. We demonstrate, using multi-year weather radar measurements of nocturnal migrants across the northeastern...

Data from: Bidirectional adaptive introgression between two ecologically divergent sparrow species

Jennifer Walsh, Adrienne I. Kovach, Brian Justin Olsen, W. Gregory Shriver, Irby J. Lovette & Brian J. Olsen
Natural hybrid zones can be used to dissect the mechanisms driving key evolutionary processes by allowing us to identify genomic regions important for establishing reproductive isolation and that allow for transfer of adaptive variation. We leverage whole-genome data in a system where two bird species, the saltmarsh (Ammospiza caudacutus) and Nelson’s (A. nelsoni) sparrow, hybridize despite their relatively high background genetic differentiation and past ecological divergence. Adaptive introgression is plausible in this system because Nelson’s...

Data from: Neural control of balance during walking

Hendrik Reimann, Tyler Fettrow, Elizabeth D. Thompson & John J. Jeka
Neural control of standing balance has been extensively studied. However, most falls occur during walking rather than standing, and findings from standing balance research do not necessarily carry over to walking. This is primarily due to the constraints of the gait cycle: Body configuration changes dramatically over the gait cycle, necessitating different responses as this configuration changes. Notably, certain responses can only be initiated at specific points in the gait cycle, leading to onset times...

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