404 Works

Data from: Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history

Tim Coulson, Daniel R. MacNulty, Daniel R. Stahler, Bridgett VonHoldt, Robert K. Wayne & Douglas W. Smith
Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected...

Data from: A computational model of flow between the microscale respiratory structures of fish gills

James A. Strother
The gills of most teleost fishes are covered by plate-like structures, the secondary lamellae, that provide the bulk of the respiratory surface area. Water passing over the secondary lamellae exchanges gases with blood passing through the secondary lamellae, forming a system that has served as a classic model of counter-current exchange. In this study, a computational model of flow around the secondary lamellae is used to examine the hydrodynamic consequences of changes to the lamellar...

Data from: The role of inbreeding depression and mating system in the evolution of heterostyly

Jennifer J. Weber, Stephen G. Weller, Ann K. Sakai, Olga V. Tsyusko, Travis C. Glenn, Cesar A. Dominguez, Francisco E. Molina-Freaner, Juan Fornoni, Mike Tran, Nhu Nguyen, Karen Nguyen, Lien-Khuong Tran, Greg Joice & Ellen Harding
We investigated the role of morph-based differences in the expression of inbreeding depression in loss of the mid-styled morph from populations of tristylous Oxalis alpina as proposed by theoretical analyses. The extent of self-compatibility of reproductive morphs, the degree of self-fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous...

Data from: The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples

Emilio Rolan-Alvarez, Antonio Carvajal-Rodriguez, Alicia De Coo, Beatriz Cortés, Daniel Estévez-Barcia, Mar Ferreira, Rubén González & Adriana D. Briscoe
The mode in which sexual organisms choose mates is a key evolutionary process, as it can have a profound impact on fitness and speciation. One way to study mate choice in the wild is by measuring trait correlation between mates. Positive assortative mating is inferred when individuals of a mating pair display traits that are more similar than those expected under random mating while negative assortative mating is the opposite. A recent review of 1134...

Data from: Leaf development and demography explain photosynthetic seasonality in Amazon evergreen forests

Jin Wu, Loren P. Albert, Aline P. Lopes, Natalia Restrepo-Coupe, Matthew Hayek, Kenia T. Wiedemann, Kaiyu Guan, Scott C. Stark, Bradley Christoffersen, Neill Prohaska, Julia V. Tavares, Suelen Marostica, Hideki Kobayashi, Mauricio L. Ferreira, Kleber Silva Campos, Rodrigo Da Silva, Paulo M. Brando, Dennis G. Dye, Travis E. Huxman, Alfredo R. Huete, Bruce W. Nelson & Scott R. Saleska
In evergreen tropical forests, the extent, magnitude, and controls on photosynthetic seasonality are poorly resolved and inadequately represented in Earth system models. Combining camera observations with ecosystem carbon dioxide fluxes at forests across rainfall gradients in Amazônia, we show that aggregate canopy phenology, not seasonality of climate drivers, is the primary cause of photosynthetic seasonality in these forests. Specifically, synchronization of new leaf growth with dry season litterfall shifts canopy composition toward younger, more light-use...

Establishment and management of native functional groups in restoration

Sarah Kimball, Megan E. Lulow & Quinn M. Sorenson
The limiting similarity hypothesis predicts that communities should be more resistant to invasion by non-natives when they include natives with a diversity of traits from more than one functional group. In restoration, planting natives with a diversity of traits may result in competition between natives of different functional groups and may influence the efficacy of different seeding and maintenance methods, potentially impacting native establishment. We compare initial establishment and first-year performance of natives and the...

Data from: Phenotypic constraints and community structure: linking trade-offs within and among species

Amy L. Angert, Sarah Kimball, Megan Peterson, Travis E. Huxman & D. Lawrence Venable
Trade-offs are central to many topics in biology, from the evolution of life histories to ecological mechanisms of species coexistence. Trade-offs observed among species may reflect pervasive constraints on phenotypes that are achievable given biophysical and resource limitations. If so, then among-species trade-offs should be consistent with trade-offs within species. Alternatively, trait variation among co-occurring species may reflect historical contingencies during community assembly rather than within-species constraints. Here, we test whether a key trade-off between...

Data from: Pupil-linked arousal determines variability in perceptual decision making

Peter R. Murphy, Joachim Vandekerckhove & Sander Nieuwenhuis
Decision making between several alternatives is thought to involve the gradual accumulation of evidence in favor of each available choice. This process is profoundly variable even for nominally identical stimuli, yet the neuro-cognitive substrates that determine the magnitude of this variability are poorly understood. Here, we demonstrate that arousal state is a powerful determinant of variability in perceptual decision making. We measured pupil size, a highly sensitive index of arousal, while human subjects performed a...

Data from: CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing

Faezeh Salehi, Roberta Baronio, Ryan Idrogo-Lam, Huy Vu, Linda V. Hall, Peter Kaiser, Richard Lathrop & Richard H. Lathrop
Next-generation sequencing (NGS) has revolutionized genetics and enabled the accurate identification of many genetic variants across many genomes. However, detection of biologically important low-frequency variants within genetically heterogeneous populations remains challenging, because they are difficult to distinguish from intrinsic NGS sequencing error rates. Approaches to overcome these limitations are essential to detect rare mutations in large cohorts, virus or microbial populations, mitochondria heteroplasmy, and other heterogeneous mixtures such as tumors. Modifications in library preparation can...

Data from: Genomics of parallel experimental evolution in Drosophila

, Kate L. Hertweck, Mark A. Phillips, Mira V. Han, Larry G. Cabral, Thomas T. Barter, Lee F. Greer, Molly K. Burke, Laurence D. Mueller & Michael R. Rose
What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly forty-year laboratory radiation featuring three selection regimes, each shared by ten populations for up to 837 generations, with moderately large effective population sizes. Each of three sets of ten populations that shared a selection regime consist of five populations that have long...

Data from: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

Will J. R. Stone, Joseph J. Campo, André Lin Ouédraogo, Lisette Meerstein-Kessel, Isabelle Morlais, Dari Da, Anna Cohuet, Sandrine Nsango, Colin J. Sutherland, Marga Van De Vegte-Bolmer, Rianne Siebelink-Stoter, Geert-Jan Van Gemert, Wouter Graumans, Kjerstin Lanke, Adam D. Shandling, Jozelyn V. Pablo, Andy A. Teng, Sophie Jones, Roos M. De Jong, Amanda Fabra-García, John Bradley, Will Roeffen, Edwin Lasonder, Giuliana Gremo, Evelin Schwarzer … & Matthijs M. Jore
Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly...

Data from: Evolution of sex-biased gene expression and dosage compensation in the eye and brain of Heliconius butterflies

Ana Catalan, Aide Macias-Munoz & Adriana D. Briscoe
Differences in behavior and life history traits between females and males are the basis of divergent selective pressures between sexes. It has been suggested that a way for the two sexes to deal with different life history requirements is through sex-biased gene expression. In this study, we performed a comparative sex-biased gene expression analysis of the combined eye and brain transcriptome from five Heliconius species, H. charithonia, H. sara, H. erato, H. melpomene and H....

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

Samuel Gill, Nathan Lim, Patrick Grinaway, Ariën Rustenburg, Josh Fass, Gregory Ross, John Chodera & David Mobley
Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This...

Annual Ice Velocity of the Greenland Ice Sheet (1991-2000)

Jeremie Mouginot, Eric Rignot, Bernd Scheuchl, Romain Millan & Michael Wood
We derive surface ice velocity using data from 16 satellite sensors deployed by 6 different space agencies. The list of sensors is given in the Table S1. The SAR data are processed from raw to single look complex using the GAMMA processor (www.gamma-rs.ch). All measurements rely on consecutive images where the ice displacement is estimated from tracking or interferometry (Joughin et al. 1998, Michel and Rignot 1999, Mouginot et al. 2012). Surface ice motion is...

Crystal Cove Marine Conservation Area Citizen Science Monitoring

Crystal Cove Alliance
Crystal Cove Conservancy operates the Crystal Cove Marine Protected Are Citizen Science Cruise in partnership with Newport Landing Sportfishing. Under the supervision of trained Crystal Cove Conservancy staff, junior high school and high school students collect data on fish and plankton biodiversity and nearshore water quality in the Crystal Cove Marine Conservation Area, following protocols designed in partnership with UCI and other researchers. See README file for more detailed information.Data made available in the OC...

Model output from N isotope global inverse model

Taylor Martin, Francois Primeau & Karen Casciotti
Global inverse nitrogen isotope model in MATLAB. Nitrogen cycle tracers include PON, DON, NO3, and NO2 for 14N and 15N. Model output optimized to three different combinations of isotope effects for nitrate reduction (eNAR), nitrite oxidation (eNXR), and nitrite reduction (eNIR) is also available.

Disparities of HIV risk and PrEP use among transgender women of color in South Florida.

Hector R. Perez-Gilbe, Cheryl L. Holder, Francisco J. Fajardo, Stephanie Garcia & Elena Cyrus
Background: The majority of the transgender female population in South Florida are Latina and Black, and are at greatest risk for acquiring HIV, yet there is limited research focused on South Florida transgender women of color. The study objective was to describe the disparities among racial/ethnic minority transgender women regarding HIV screening, pre exposure prophylaxis (PrEP) knowledge and PrEP utilization. Methods: Sixty transgender women, recruited from South Florida community-based organizations, completed a questionnaire on HIV...

Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

Jonas Kuppler, Cécile H. Albert, Gregory M. Ames, W. Scott Armbruster, Gerhard Boenisch, Florian C. Boucher, Diane R. Campbell, Liedson T. Carneiro, Eduardo Chacón-Madrigal, Brian J. Enquist, Carlos R. Fonseca, José M. Gómez, Antoine Guisan, Pedro Higuchi, Dirk N. Karger, Jens Kattge, Michael Kleyer, Nathan J. B. Kraft, Anne-Amélie C. Larue-Kontić, Amparo Lázaro, Martin Lechleitner, Deirdre Loughnan, Vanessa Minden, Ülo Niinemets, Gerhard E. Overbeck … & Robert R. Junker
Aim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation...

Code and data from: Evolution of sexual cooperation from sexual conflict

Maria R Servedio, John M Powers, Russell Lande & Trevor D Price
This C code conducts deterministic iterations of the exact recursion equations presented in the Model section of "Evolution of sexual cooperation from sexual conflict" by Servedio, Powers, Lande and Price. The code produces a two-dimensional grid with any parameters of choice on the x and y axis. Examples can be found in Figures 2c, 3c and 4 of the main text as well as many similar figures in the Supplementary Material. A sample parameter file...

Identifying mechanisms for successful ecological restoration with salvaged topsoil in coastal sage scrub communities

Mia Maltz & Katharina Schmid
Although above-ground metrics remain the standard, restoring functional ecosystems should promote both above- and belowground biotic communities. Restoration using salvaged soil — removal and translocation of topsoil from areas planned for development, with subsequent deposition at degraded sites — is an alternative to traditional methods. Salvaged soil contains both seed and spore banks, which may holistically augment restoration. Salvaged soil methods may reduce non-native germination by burying non-native seeds, increase native diversity by adding native...

A compilation of canopy leaf inclination angle measurements across plant species and biome types

César Hinojo-Hinojo & Michael Goulden
The inclination angle of leaves in plant canopies is important for a range of land ecosystem processes, including radiation absorption from vegetation, land surface reflectance, microclimate, and photosynthetic CO2 uptake. While inclination angles of leaves have been measured for decades, such measurements remain scattered in the scientific literature, and the actual variation of leaf inclination angles across land ecosystems remains poorly understood and quantified. We compiled a dataset of previously published field measurements of mean...

Coastal urbanization influences human pathogens and microdebris contamination in seafood

Raechel Littman, Evan Fiorenza, Amelia Wenger, Kathryn Berry, Jeroen Van De Water, Lily Nguyen, Soe Tint Aung, Daniel Parker, Douglas Rader, C. Drew Harvell & Joleah Lamb
Seafood is one of the leading imported products implicated in foodborne outbreaks worldwide. Coastal marine environments are being increasingly subjected to reduced water quality from urbanization and leading to contamination of important fishery species. Given the importance of seafood exchanged as a global protein source, it is imperative to maintain seafood safety worldwide. To illustrate the potential health risks associated with urbanization in a coastal environment, we use next-generation high-throughput amplicon sequencing of the 16S...

Data from: Testing trade-offs and the dominance-impoverishment rule among ant communities

Julie K. Sheard, Annika S. Nelson, Jeppe Berggreen, Raphael Boulay, Robert R. Dunn & Nathan J. Sanders
Aim: Ant communities are believed to be structured by competition, with dominant species competitively excluding subordinates (the dominance-impoverishment rule). However, a high number of seemingly similar species coexist, possibly due to interspecific trade-offs. Here, we examine the evidence for the dominance-impoverishment rule across a broad latitudinal gradient and explore whether trade-offs explain coexistence within and among ant communities. Location: 40 sites in 19 countries across Europe, western North America and northern South America. Taxon: Formicidae....

Data from: Elevational cline in herbivore abundance driven by a monotonic increase in trophic level sensitivity to aridity

Annika S. Nelson, Cole T. Symanski, Matthew J. Hecking & Kailen A. Mooney
1. The abiotic environment drives species abundances and distributions both directly and indirectly through effects on multi-trophic species interactions. However, few studies have documented the individual and combined consequences of these direct and indirect effects. 2. We studied an ant-tended aphid along an elevational gradient, where lower elevations were more arid. Hypotheses of stronger species interactions at lower elevations and a greater sensitivity of higher trophic levels to climate led us to predict increased top-down...

Association of Serum Paraoxonase/Arylesterase Activity With All-Cause Mortality in Maintenance Hemodialysis Patients

Yasunori Suematsu, Masaki Goto, Christina Park, Ane C.F. Nunes, WangHui Jing, Elani Streja, Connie M. Rhee, Siobanth Cruz, Moti L. Kashyap, Nosratola D. Vaziri, Vasanthy Narayanaswami, Kamyar Kalantar-Zadeh & Hamid Moradi
Context: In end-stage renal disease (ESRD), serum high-density lipoprotein cholesterol (HDL-C) level is not an accurate predictor of mortality, partly because it does not necessarily correlate with indices of HDL function. Paraoxonase (PON) is a major enzyme constituent of HDL and key component of HDL antioxidant activity. Apolipoprotein (Apo) A-I is the core HDL structural protein that plays a major role in various aspects of HDL function. Objective: We sought to examine PON activity and...

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  • University of California, Irvine
  • Jilin University
  • Air Force Medical University
  • Soochow University
  • Fudan University
  • Sun Yat-sen University
  • Lanzhou Veterinary Research Institute
  • University of California, San Diego
  • Chinese Academy of Sciences
  • Zunyi Medical University