76 Works

Data from: The global geography of human subsistence

Michael C. Gavin, Patrick H. Kavanagh, Hannah J. Haynie, Claire Bowern, Carol R. Ember, Russell D. Gray, Fiona M. Jordan, Kathryn R. Kirby, Geoff Kushnick, Bobbi S. Low, Bruno Vilela & Carlos A. Botero
How humans obtain food has dramatically reshaped ecosystems and altered both the trajectory of human history and the characteristics of human societies. Our species’ subsistence varies widely, from predominantly foraging strategies, to plant-based agriculture and animal husbandry. The extent to which environmental, social, and historical factors have driven such variation is currently unclear. Prior attempts to resolve long-standing debates on this topic have been hampered by an over-reliance on narrative arguments, small and geographically-narrow samples,...

Data from: Asymmetric oceanographic processes mediate connectivity and population genetic structure as revealed by RADseq in a highly dispersive marine invertebrate (Parastichopus californicus)

Amanda Xuereb, Laura Benestan, Eric Normandeau, Rémi M. Daigle, Janelle M.R. Curtis, Louis Bernatchez, Marie-Josée Fortin & Janelle M. R. Curtis
Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the...

Data from: Persistence of resident and transplanted genotypes of the undomesticated yeast, Saccharomyces paradoxus in forest soil

James B. Anderson, Dahlia Kasimer, Wenjing Xia, Nicolas C. H. Schröder, Patrick Cichowicz, Silvio Lioniello, Rudrakshi Chakrabarti, Eashwar Mohan & Linda M. Kohn
One might expect yeasts in soil to be highly dispersed via water or insects, forming ephemeral, genetically heterogeneous populations subject to competition and environmental stochasticity. Here, we report persistence of genotypes of the yeast Saccharomyces paradoxus in space and time. Within 1 km2 in a mixed hardwood forest on scales from centimeters to tens of meters, we detect persistence over 3 years of native genotypes, identified by SNPs genome-wide, of the wild yeast, Saccharomyces paradoxus...

Data from: Microglia responses to pro-inflammatory stimuli (LPS, IFNγ+TNFα) and reprogramming by resolving cytokines (IL-4, IL-10)

Starlee Lively & Lyanne C. Schlichter
Microglia respond to CNS injuries and diseases with complex reactions, often called “activation.” A pro-inflammatory phenotype (also called classical or M1 activation) lies at one extreme of the reactivity spectrum. There were several motivations for this study. First, bacterial endotoxin (lipopolysaccharide, LPS) is the most commonly used pro-inflammatory stimulus for microglia, both in vitro and in vivo; however, pro-inflammatory cytokines (e.g., IFNγ, TNFα) rather than LPS will be encountered with sterile CNS damage and disease....

Data from: A note on measuring natural selection on principal component scores

Veronica K. Chong, Hannah F. Fung & John R. Stinchcombe
Measuring natural selection through the use of multiple regression has transformed our understanding of selection, although the methods used remain sensitive to the effects of multicollinearity due to highly correlated traits. While measuring selection on principal component scores is an apparent solution to this challenge, this approach has been heavily criticized due to difficulties in interpretation and relating PC axes back to the original traits. We describe and illustrate how to transform selection gradients for...

Data from: Hepatocyte-specific deletion of TIPARP, a negative regulator of the aryl hydrocarbon receptor, is sufficient to increase sensitivity to dioxin-induced wasting syndrome

David Hutin, Laura Tamblyn, Alvin Gomez, Giulia Grimaldi, Helen Soelding, Tiffany Cho, Shaimaa Ahmed, Christin Lucas, Chakravarthi Kanduri, Denis M. Grant, Jason Matthews & Helen Soedling
The aryl hydrocarbon receptor (AHR) mediates the toxic effects of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin; TCDD), which include thymic atrophy, steatohepatitis, and a lethal wasting syndrome in laboratory rodents. Although the mechanisms of dioxin toxicity remain unknown, AHR signaling in hepatocytes is necessary for dioxin-induced liver toxicity. We previously reported that loss of TCDD-inducible poly(ADP-ribose) polymerase (TIPARP/PARP7/ARTD14), an AHR target gene and mono-ADP-ribosyltransferase, increases the sensitivity of mice to dioxin-induced toxicities. To test the hypothesis that TIPARP is...

Data from: Asynchrony between ant seed dispersal activity and fruit dehiscence of myrmecochorous plants

Susan C. C. Gordon, Shannon A. Meadley-Dunphy, Kirsten M. Prior & Megan E. Frederickson
Phenological mismatch has received attention in plant-pollinator interactions, but less so in seed dispersal mutualisms. We investigated whether the seasonal availability of myrmecochorous seeds is well matched to the seasonal activity patterns of seed-dispersing ants. Methods We compared seasonal timing of seed removal by a keystone seed-dispersing ant, Aphaenogaster rudis, and fruit dehiscence of several species of plants whose seeds it disperses in a deciduous forest in southern Ontario, Canada. We examined the timing of...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: The spatial ecology of sex ratios in a dioecious plant: relations between ramet and genet sex ratios

David Timerman, Spencer C. H. Barrett & Spencer C.H. Barrett
1. In clonal dioecious plants, the frequency and spatial distribution of flowering ramets contains information on the underlying genet sex ratio. These measures can also provide insight on potential ecological mechanisms causing variation and bias in sex ratios among populations. 2. We used a novel likelihood-based approach and spatial clustering model to estimate the genet sex ratios from flowering ramet data collected from 32 populations of dioecious Thalictrum pubescens, a clonal species from eastern N....

Data from: Cognitive approach to rehabilitation in children with hyperkinetic movement disorders post-DBS

Hortensia Gimeno, Richard G. Brown, Jean-Pierre Lin, Victoria Cornelius & Helene J. Polatajko
Objective: This proof-of-concept feasibility trial examined the potential of the Cognitive Orientation to daily Occupational Performance (CO-OP) ApproachTM to augment deep brain stimulation (DBS) outcomes in childhood-onset hyperkinetic movement disorders (HMD) including dystonia and dyskinetic cerebral palsy. Methods: Single case experimental design using multiple baseline as N-of-1 trial comprised of 10 intervention sessions, with replications across participants (n=10). Treatment focused on three participant-selected goals. Transfer was assessed on two additional untreated goals. Individuals enrolled were...

Data from: Mutation accumulation in selfing populations under fluctuating selection

Eddie Ka Ho Ho & Aneil F. Agrawal
Selfing species are prone to extinction, possibly because highly selfing populations can suffer from a continuous accumulation of deleterious mutations, a process analogous to Muller’s ratchet in asexual populations. However, current theory provides little insight into which types of genes are most likely to accumulate deleterious alleles and what environmental circumstances may accelerate genomic degradation. Here we investigate temporal changes in the environment that cause fluctuations in the strength of purifying selection. We simulate selfing...

Data from: Predator macroevolution drives trophic cascades and ecosystem functioning

Denon Start
Biologists now recognize that ecology can drive evolution, and that evolution in turn produces ecological patterns. I extend this thinking to include longer time-scales, suggesting that macroevolutionary transitions can create phenotypic differences among species, which then have predictable impacts on species interactions, community assembly, and ecosystem functioning. Repeated speciation can exacerbate these patterns by creating communities with similar phenotypes and hence ecological impacts. Here, I use several experiments to test these ideas in dragonfly larvae...

Data from: Systematic analysis of complex genetic interactions

Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Elizabeth N. Koch, Carles Pons, Andrius Jonas Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo … & Chad L. Myers
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended...

Data from: Prevalence of vancomycin-variable Enterococcus faecium (VVE) among vanA-positive sterile site isolates and patient factors associated with VVE bacteremia

Philipp Kohler, Alireza Eshaghi, Hyunjin C. Kim, Agron Plevneshi, Karen Green, Barbara M. Willey, Allison McGeer & Samir N. Patel
Vancomycin-variable enterococci (VVE) are vanA-positive, vancomycin-susceptible enterococci with the ability to revert to a vancomycin-resistant phenotype on exposure to vancomycin. We sought to assess the prevalence of VVE and to determine clinical characteristics of patients infected with VVE. We prospectively collected Enterococcus faecium sterile site isolates from Toronto Invasive Bacterial Diseases Network hospitals from January 2015 to June 2016 and calculated VVE (defined as vanA-positive, vancomycin-susceptible isolates) prevalence among vanA-containing isolates. We performed chart reviews...

Data from: Two decades of evolutionary changes in Brassica rapa in response to fluctuations in precipitation and severe drought

Elena Hamann, Arthur E. Weis & Steven J. Franks
As climate changes at unprecedented rates, understanding population responses is a major challenge. Resurrection studies can provide crucial insights into the contemporary evolution of species to climate change. We used a seed collection of two Californian populations of the annual plant Brassica rapa made over two decades of dramatic precipitation fluctuations, including increasingly severe droughts. We compared flowering phenology, other drought response traits, and seed production among four generations, grown under drought and control conditions,...

Data from: Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Alicia Dalongeville, Marco Andrello, David Mouillot, Stephane Lobreaux, Marie-Josée Fortin, Frida Lasram, Jonathan Belmaker, Delphine Rocklin & Stéphanie Manel
Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea....

Data from: Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling

David Benoit, Donald A. Jackson & Mark S. Ridgway
Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult‐to‐detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management. In this study, we set out to determine the impacts of...

Data from: The effects of male harm vary with female quality and environmental complexity in Drosophila melanogaster

Alison MacPherson, Li Yun, Tania S. Barrera, Aneil F. Agrawal & Howard D. Rundle
Mate competition provides the opportunity for sexual selection which often acts strongly on males, but also the opportunity for sexual conflict that can alter natural selection on females. Recent attention has focused on the potential of sexual conflict to weaken selection on females if male sexual attention, and hence harm, is disproportionately directed toward high over low quality females, thereby reducing the fitness difference between these females. However, sexual conflict could instead strengthen selection on...

Data from: Abiotic heterogeneity underlies trait-based competition and assembly

Isabela L. Borges, Leila Z. Forsyth, Denon Start & Benjamin Gilbert
1. The fitness of individual species depends on their ability to persist and establish at low densities, just as the diversity of ecological communities depends on the establishment and persistence of low-density, ‘invader’ species. Theory predicts that abiotic conditions and the competitive make-up of resident communities jointly shape invader fitness, limiting the phenotypic identity of successful invaders. 2. We use an invasion experiment to ask how competitive traits of 20 introduced plant species alter their...

Data from: Herbivores and plant defenses affect selection on plant reproductive traits more strongly than pollinators

James S. Santangelo, Ken A. Thompson & Marc T. J. Johnson
Pollinators and herbivores can both affect the evolutionary diversification of plant reproductive traits. However, plant defenses frequently alter antagonistic and mutualistic interactions and therefore variation in plant defenses may alter patterns of herbivore- and pollinator-mediated selection on plant traits. We tested this hypothesis by conducting a common garden field experiment using 50 clonal genotypes of white clover (Trifolium repens) that varied in a Mendelian inherited chemical antiherbivore defense—the production of hydrogen cyanide (HCN). To evaluate...

Data from: Three new naraoiid species from the Burgess Shale, with a morphometric and phylogenetic reinvestigation of Naraoiidae

Benjamin Mayers, Cédric Aria & Jean-Bernard Caron
Naraoiids are non‐biomineralized euarthropods characterized by the complete fusion of post‐cephalic tergo‐pleurae into a single shield, as well as an extensively ramified digestive tract. Ranging from the early Cambrian to the late Silurian (Pridoli), these arthropods of simple appearance have traditionally been associated with the early diversification of trilobites and their close relatives, but the interrelationships and affinities of naraoiids within Artiopoda remain poorly characterized. Three new species from the Burgess Shale (middle Cambrian, Stage...

Data from: Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover (Trifolium repens)

Marc T.J. Johnson, Cindy M. Prashad, Mélanie Lavoignat & Hargurdeep S. Saini
Urbanization is a global phenomenon with profound effects on the ecology and evolution of organisms. We examined the relative roles of natural selection, genetic drift and gene flow in influencing the evolution of white clover (Trifolium repens), which thrives in urban and rural areas. Trifolium repens exhibits a Mendelian polymorphism for the production of hydrogen cyanide (HCN), a potent antiherbivore defence. We quantified the relative frequency of HCN in 490 populations sampled along urban-rural transects...

Data from: Linking sex differences to the evolution of infectious disease life-histories

Matthew D. Hall & Nicole Mideo
Sex differences in the prevalence, course and severity of infection are widespread, yet the evolutionary consequences of these differences remain unclear. Understanding how male–female differences affect the trajectory of infectious disease requires connecting the contrasting dynamics that pathogens might experience within each sex, to the number of susceptible and infected individuals that are circulating in a population. In this study, we build on theory using genetic covariance functions to link the growth of a pathogen...

Data from: Fine scale waterbody data improve prediction of waterbird occurrence despite coarse species data

Petra Šímová, Vítězslav Moudrý, Jan Komárek, Karel Hrach & Marie-Josée Fortin
While modelling habitat suitability and species distribution, ecologists must deal with issues related to the spatial resolution of species occurrence and environmental data. Indeed, given that the spatial resolution of species and environmental datasets range from centimeters to hundreds of kilometers, it underlines the importance of choosing the optimal combination of resolutions to achieve the highest possible modelling prediction accuracy. We evaluated how the spatial resolution of land cover/waterbody datasets (meters to 1 km) affect...

Data from: Examining community stability in the face of mass extinction in communities of digital organisms

Tian-Tong Luo, Lise Heier, Zaki Ahmad Khan, Faraz Hasan, Trond Reitan, , Zi-Xuan Xie, Jian-Long Zhu & Gabriel Yedid
Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Toronto
  • University of British Columbia
  • University of Washington
  • University of Minnesota
  • Fisheries and Oceans Canada
  • Duke University
  • University of Queensland
  • University of California, San Diego
  • Carleton University
  • Colorado State University