302 Works

Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection

Douglas Peters & Robert Garcea
The replication of small DNA viruses requires both host DNA replication and repair factors that are often recruited to subnuclear domains termed viral replication centers (VRCs). Aside from serving as a spatial focus for viral replication, little is known about these dynamic areas in the nucleus. We investigated the organization and function of VRCs during murine polyomavirus (MuPyV) infection using 3D structured illumination microscopy (3D-SIM). We localized MuPyV replication center components, such as the viral...

Fire emissions data before and after peatland restoration, Indonesia, 2004-2015

L. Kiely, D.V. Spracklen & C. Wiedinmyer
This dataset contains fire emissions from Equatorial Asia for the years 2004, 2006, 2009, 2012, 2014 and 2015. The data is based on the Fire Inventory from National Center for Atmospheric Research with the addition of emissions from Indonesian peat fires, which contribute substantially to fire emissions in the region. The files for each year contain daily information on the area burned and emissions of several species, including CO, CO2 and PM2.5. Data is given...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Data from: Parasite infection alters nitrogen cycling at the ecosystem scale

John Mischler, Pieter T. J. Johnson, Valerie J. McKenzie & Alan R. Townsend
Despite growing evidence that parasites often alter nutrient flows through their hosts and can comprise a substantial amount of biomass in many systems, whether endemic parasites influence ecosystem nutrient cycling, and which nutrient pathways may be important, remains conjectural. A framework to evaluate how endemic parasites alter nutrient cycling across varied ecosystems requires an understanding of: (1) parasite effects on host nutrient excretion, (2) ecosystem nutrient limitation, (3) effects of parasite abundance, host density, host...

Data from: Seasonality of soil moisture mediates responses of ecosystem phenology to elevated CO2 and warming in a semi-arid grassland

Tamara J. Zelikova, David G. Williams, Rhonda Hoenigman, Dana M. Blumenthal, Jack A. Morgan & Elise Pendall
Vegetation greenness, detected using digital photography, is useful for monitoring phenology of plant growth, carbon uptake, and water loss at the ecosystem level. Assessing ecosystem phenology by greenness is especially useful in spatially extensive, water-limited ecosystems such as the grasslands of the western United States, where productivity is moisture dependent and may become increasingly vulnerable to future climate change. We used repeat photography and a novel means of quantifying greenness in digital photographs to assess...

Data from: Natural variation, differentiation and genetic tradeoffs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae)

Antonio J. Manzaneda, Pedro José Rey, Jill Theresa Anderson, Evan Raskin, Christopher Weiss-Lehman & Thomas Mitchell-Olds
Differences in tolerance to water stress may underlie ecological divergence of closely-related ploidy lineages. However, the mechanistic basis of physiological variation governing eco-geographical cytotype segregation is not well understood. Here, using Brachypodium distachyon and its derived allotetraploid B. hybridum as model, we test the hypothesis that, for heteroploid annuals, ecological divergence of polyploids in drier environments is based on trait differentiation enabling drought-escape. We demonstrate that under water limitation allotetraploids maintain higher photosynthesis and stomatal...

Data from: Evolution of camouflage drives rapid ecological change in an insect community

Timothy E. Farkas, Tommi Mononen, Aaron A. Comeault, Ilkka Hanski & Patrik Nosil
Evolutionary change in individual species has been hypothesized to have far-reaching consequences for entire ecological communities, and such coupling of ecological and evolutionary dynamics (“eco-evolutionary dynamics”) has been demonstrated for a variety systems. However, the relative importance of evolutionary dynamics for ecological dynamics remains unclear. Here, we investigate how spatial patterns of local adaptation in the stick insect Timema cristinae, driven by natural selection, gene flow and founder effects, structure metapopulations, communities, and multitrophic interactions....

Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic

Lorena Torres-Martínez & Nancy C. Emery
California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction...

Data from: The lichens and allied fungi of Mount Mitchell State Park, North Carolina: a first checklist with comprehensive keys and comparison to historical data

James C. Lendemer, Carly R. Anderson Stewart, Betty Besa, Jim Goldsmith, Haley Griffith, Jordan R. Hoffman, Betsy Kraus, Paula LaPoint, Lin Li, Zachary Muscavitch, Joel Schultz, Rebecca Schultz & Jessica L. Allen
A total of 171 species of lichens and allied fungi are reported from the spruce-fir forests of Mount Mitchell State Park, in the Black Mountains of North Carolina, based on both historical and modern records. Comparison of the modern baseline with the historical macrolichen baseline generated in the 1970s revealed potential losses of high-elevation southern Appalachian endemics (2 species), cyanolichens (5 species), species typical of exposed rock outcrops (1 species), and widespread species typical of...

Data from: Fire severity unaffected by spruce beetle outbreak in spruce-fir forests in southwestern Colorado

Robert A. Andrus, Thomas T. Veblen, Brian J. Harvey & Sarah J. Hart
Recent large and severe outbreaks of native bark beetles have raised concern among the general public and land managers about potential for amplified fire activity in western North America. To date, the majority of studies examining bark beetle outbreaks and subsequent fire severity in the U.S. Rocky Mountains have focused on outbreaks of mountain pine beetle (MPB, Dendroctonus ponderosae) in lodgepole pine (Pinus contorta) forests, but few studies, particularly field studies, have addressed the effects...

Data from: Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography

Elizabeth S. C. Scordato & Melissa R. Kardish
1. Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species, and the geographic scale of comparisons. In this study, we asked if these factors also predict diversity and turnover in parasite communities. 2. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked if parasite prevalence and community structure varied with host population, host...

Data from: Convergent evolution of floral shape tied to pollinator shifts in Iochrominae (Solanaceae)

Stacey D. Smith & Ricardo Kriebel
Flower form is one of many floral features thought to be shaped by pollinator-mediated selection. Although the drivers of variation in flower shape have often been examined in microevolutionary studies, relatively few have tested the relationship between shape evolution and shifts in pollination system across clades. In the present study, we use morphometric approaches to quantify shape variation across the Andean clade Iochrominae and estimate the relationship between changes in shape and shifts in pollination...

Data from: The same picture through different lenses: quantifying the effects of two preservation pathways on Green River Formation insects

Evan P. Anderson & Dena M. Smith
Insects in the fossil record are generally preserved in lacustrine shales or in amber. For those in lacustrine shales, preservation is usually via keroginization or mineralization. Given the extended period of microbial decay required to generate ions for mineralization, there is a predicted inherent bias toward lower preservation quality for this pathway by most taphonomic indices compared with keroginization. This study tests this hypothesis by comparing multiple measures of preservation quality between sites with similar...

Data from: Host and parasite thermal acclimation responses depend on the stage of infection

Karie A. Altman, Sara H. Paull, Pieter T. J. Johnson, Michelle N. Golembieski, Jeffrey P. Stephens, Bryan E. LaFonte & Thomas R. Raffel
1. Global climate change is expected to alter patterns of temperature variability, which could influence species interactions including parasitism. Species interactions can be difficult to predict in variable-temperature environments because of thermal acclimation responses, i.e. physiological changes that allow organisms to adjust to a new temperature following a temperature shift. 2. The goal of this study was to determine how thermal acclimation influences host resistance to infection and to test for parasite acclimation responses, which...

Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation

Rebecca J. Safran, Elizabeth S. C. Scordato, Matthew R. Wilkins, Joanna K. Hubbard, Brittany R. Jenkins, Tomas Albrecht, Samuel M. Flaxman, Hakan Karaardic, Yoni Vortman, Arnon Lotem, Patrik Nosil, Péter Pap, Sheng-Feng Shen, Shih-Fan Chan, Thomas L. Parchman, Nolan C. Kane, S.-F. Chan & T.L. Parchman
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘isolation by adaptation’ (IBA). IBA can be complementary to the well-known pattern of ‘isolation by distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies,...

Data from: Why are red flowers so rare? Testing the macroevolutionary causes of tippiness.

Julienne Ng & Stacey D. Smith
Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches, and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short‐term evolutionary advantage, but it ultimately leads species...

Data from: Combining ground‐penetrating radar with terrestrial LiDAR scanning to estimate the spatial distribution of liquid water content in seasonal snowpacks

R. W. Webb, K.S. Jennings, M. Fend, N.P. Molotch, K. S. Jennings & N. P. Molotch
Many communities and ecosystems around the world rely on mountain snowpacks to provide valuable water resources. An important consideration for water resources planning is runoff timing, which can be strongly influenced by the physical process of water storage within and release from seasonal snowpacks. The aim of this study is to present a novel method that combines light detection and ranging with ground‐penetrating radar to nondestructively estimate the spatial distribution of bulk liquid water content...

Data from: Whole genome amplification and reduced-representation genome sequencing of Schistosoma japonicum miracidia

Jonathan A. Shortt, Daren C. Card, Drew R. Schield, Yang Liu, Bo Zhong, Todd A. Castoe, Elizabeth J. Carlton & David D. Pollock
Background: In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small...

Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Kira E. Delmore, Sariel Hübner, Nolan C. Kane, Richard Schuster, Rose L. Andrew, Francisco Câmara, Roderic Guigo & Darren E. Irwin
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for...

Data from: Edaphic properties enable facilitative and competitive interactions resulting in fairy circle formation

Michael D. Cramer, Nichole N. Barger & Walter R. Tschinkel
Millions of generally regularly spaced, roughly circular barren patches called fairy circles occur in a narrow band ca. 100 km inland of the south-west African coast. These generally have conspicuously taller peripheral grasses in a shorter grass matrix. The origins of these fairy circles are controversial, but one possibility is that they are self-organizing emergent vegetation patterns that are the consequence of interplay between positive (facilitative) and negative (competitive) interactions between grasses. We hypothesized that...

Data from: Generalist predator's niche shifts reveal ecosystem changes in an experimentally fragmented landscape

Julian Resasco, Kika T. Tuff, Saul A. Cunningham, Brett A. Melbourne, Andrew L. Hicks, Seth D. Newsome & Kendi F. Davies
Habitat fragmentation can alter the trophic structure of communities and environmental conditions, thus driving changes in biodiversity and ecosystem functions. Quantifying niches of generalist predators can reveal how fragmentation alters ecosystems. In a habitat fragmentation experiment, we used stable isotopes of a generalist predator skink to test predictions from spatial theory on trophic structure and to quantify abiotic changes associated with fragmentation among continuous forest, fragments, and matrix habitats. We predicted that in fragments and...

Data from: A comparative approach to cooperative transport in ants: individual persistence correlates with group coordination

Helen F. McCreery
When groups of ants work together to carry large objects—called cooperative transport—they must form consensus on a travel direction. In many species, groups are unsuccessful at this decision, and deadlock. In other collective decisions, including nest-site selection in honeybees, individuals’ enthusiasm or recruitment intensity for a given option affects the selection process. A similar mechanism may be important during cooperative transport in ants and may account for coordination differences among species. Results from theoretical models...

Data from: Noise pollution alters ecological services: enhanced pollination and disrupted seed dispersal

Clinton D. Francis, Nathan J. Kleist, Catherine P. Ortega & Alexander Cruz
Noise pollution is a novel, widespread environmental force that has recently been shown to alter the behavior and distribution of birds and other vertebrates, yet whether noise has cumulative, community-level consequences by changing critical ecological services is unknown. Herein, we examined the effects of noise pollution on pollination and seed dispersal and seedling establishment within a study system that isolated the effects of noise from confounding stimuli common to human-altered landscapes. Using observations, vegetation surveys...

Data from: Extensive phenotypic diversification coexists with little genetic divergence and a lack of population structure in the White Wagtail subspecies complex (Motacilla alba)

Georgy A. Semenov, Evgeniy A. Koblik, Yaroslav A. Red'kin & Alexander V. Badyaev
Geographically clustered phenotypes often demonstrate consistent patterns in molecular markers, particularly mitochondrial DNA (mtDNA) traditionally used in phylogeographic studies. However distinct evolutionary trajectories among traits and markers can lead to their discordance. First, geographic structure in phenotypic traits and nuclear molecular markers can be co-aligned but inconsistent with mtDNA (mito-nuclear discordance). Alternatively, phenotypic variation can have little to do with patterns in neither mtDNA nor nuclear markers. Disentangling between these distinct patterns can provide insight...

Data from: Livestock activity increases exotic plant richness, but wildlife increases native richness, with stronger effects under low productivity

David J. Eldridge, Manuel Delgado-Baquerizo, Samantha K. Travers, James Val, Ian Oliver, Josh W. Dorrough & Santiago Soliveres
1.Grazing by domestic livestock is one of the most widespread land uses worldwide, particularly in rangelands, where it co-occurs with grazing by wild herbivores. Grazing effects on plant diversity are likely to depend on intensity of grazing, herbivore type, coevolution with plants and prevailing environmental conditions. 2.We collected data on climate, plant productivity, soil properties, grazing intensity and herbivore type; and measured their effects on plant species richness from 451 sites across 0.4 M km2...

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