307 Works

Data from: Food and habitat provisions jointly determine competitive and facilitative interactions among distantly related herbivores

Duofeng Pan, Xincheng Li, Kejia De, Ling Wang, Deli Wang, Qinfeng Guo, Chao Gao, Zhiwei Zhong, Zhu Hui, Zhongbao Shen & Timothy Seastedt
1. Interactions between distantly related herbivores exert powerful influences on ecosystems, but most studies to date have only considered unidirectional effects. Few have simultaneously examined the mutual effects that vertebrate herbivores and insect herbivores have on one another. 2. We conducted a set of manipulative experiments to evaluate the potential competition and facilitation between two pairs of distantly related herbivore taxa: an insect caterpillar (Gynaephora alpherakii) and two large vertebrate herbivores, yak (Bos grunniens) and...

Bending and Looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid

Patrick Heenan, Anne Gooding, Xueyin Wang, Thomas Perkins & Thomas Cech
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation, and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the...

E. coli aminoglycoside treatment

Joel Kralj & Giancarlo Bruni
Aminoglycosides are broad-spectrum antibiotics whose mechanism of action is under debate. It is widely accepted that membrane voltage potentiates aminoglycoside activity, which is ascribed to voltage-dependent drug uptake. In this paper, we measured the response of Escherichia coli treated with aminoglycosides and discovered that the bactericidal action arises not from the downstream effects of voltage dependent drug uptake, but rather directly from dysregulated membrane potential. In the absence of voltage, aminoglycosides are taken into cells...

Age predicts risky investment better than residual reproductive value

David Delaney, Luke Hoekstra & Fredric Janzen
Life-history theory predicts that investment into reproduction should increase as future reproductive opportunities (i.e., residual reproductive value, RRV) decrease. Researchers have thus intuitively used age as a proxy for RRV and assume RRV decreases with age when interpreting age-specific investment. Yet, age is an imperfect proxy for RRV and may even be a poor correlate in some systems. We used a 30-year study of the nesting ecology of painted turtles ( Chrysemys picta ) to...

Wolves are back: Sociopolitical identity and opinions on management of Canis lupus

Joel Hartter & Lawrence Hamilton
In 2010 an interdisciplinary team of social and natural scientists began a project to study society–environment interactions in northeast Oregon. At first, the Communities and Forests in Oregon (CAFOR) project focused on Baker, Union and Wallowa Counties. Subsequently the project’s scope expanded to cover Crook, Grant, Umatilla and Wheeler Counties. One part of the CAFOR research involved a series of telephone surveys carried out in four stages over 2011 to 2018. The surveys employed consistent...

Weather variation affects the dispersal of grasshoppers beyond their elevational ranges

Cesar Nufio, Andrew Prinster & Julian Resasco
Understanding how abiotic conditions influence dispersal patterns of organisms is important for understanding the degree to which species can track and persist in the face of changing climate. The goal of this study was to understand how weather conditions (temperature, precipitation and wind patterns) influence the dispersal patterns of multiple non-migratory grasshopper species from lower elevation grassland habitats in which they ­­complete their life-cycles to higher elevations that extend beyond their range limits. The study...

Data from: A trait-based approach to assessing resistance and resilience to wildfire in two iconic North American conifers

Kyle Rodman, Thomas Veblen, Robert Andrus, Neil Enright, Joseph Fontaine, Angela Gonzalez, Miranda Redmond & Andreas Wion
Ongoing changes in fire activity have the potential to drive widespread shifts in Earth’s vegetation. Plant traits and vital rates can be indicators of the ability of individuals to survive fire (resistance) and populations to persist (resilience) following fire and provide a method to assess vulnerability to fire-driven vegetation shifts. In 15 study sites spanning climatic gradients in the southern Rocky Mountains, U.S.A., we quantified variation in key traits and vital rates of two co-occurring,...

Data from: A quantitative inventory of yeast P body proteins reveals principles of composition and specificity

Wenmin Xing, Denise Muhlrad, Roy Parker & Michael K. Rosen
P bodies are archetypal biomolecular condensates that concentrate proteins and RNA without a surrounding membrane. While dozens of P body proteins are known, the concentrations of components in the compartment have not been measured. We used live cell imaging to generate a quantitative inventory of the major proteins in yeast P bodies. Only 7 proteins are highly concentrated in P bodies (5.1-15 uM); the 24 others examined are appreciably lower (most ≤ 2.6 uM). P...

Data from: Elevational differences in developmental plasticity determine phenological responses of grasshoppers to recent climate warming

Lauren B. Buckley, César R. Nufio, Evan M. Kirk & Joel G. Kingsolver
Annual species may increase reproduction by increasing adult body size through extended development, but risk being unable to complete development in seasonally limited environments. Synthetic reviews indicate that most, but not all, species have responded to recent climate warming by advancing the seasonal timing of adult emergence or reproduction. Here, we show that 50 years of climate change have delayed development in high-elevation, season-limited grasshopper populations, but advanced development in populations at lower elevations. Developmental...

Data from: Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

Daniel Bolnick, Lisa Snowberg, William Stutz, Greg Caporaso, Christian Lauber, Rob Knight, Daniel I. Bolnick, Chris Lauber, J. Gregory Caporaso, William E. Stutz & Lisa K. Snowberg
Individuals harbor diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge of distinguishing between mutualistic and pathogenic members of diverse and host-specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus MHC polymorphism contributes to microbial variation among hosts. Here, we confirm that, within a single wild vertebrate population of threespine stickleback, different MHC II...

Data from: The roles of demography and genetics in the early stages of colonization

Marianna Szűcs, Brett A. Melbourne, Ty Tuff & Ruth A. Hufbauer
Colonization success increases with the size of the founding group. Both demographic and genetic factors underlie this relationship, yet because genetic diversity normally increases with numbers of individuals, their relative importance remains unclear. Furthermore, their influence may depend on the environment and may change as colonization progresses from establishment through population growth and then dispersal. We tested the roles of genetics, demography and environment in the founding of Tribolium castaneum populations. Using three genetic backgrounds...

Data from: Quantitative genetics of plumage color: lifetime effects of early nest environment on a colorful sexual signal

Joanna K. Hubbard, Brittany R. Jenkins & Rebecca J. Safran
Phenotypic differences among individuals are often linked to differential survival and mating success. Quantifying the relative influence of genetic and environmental variation on phenotype allows evolutionary biologists to make predictions about the potential for a given trait to respond to selection and various aspects of environmental variation. In particular, the environment individuals experience during early development can have lasting effects on phenotype later in life. Here, we used a natural full-sib/half-sib design as well as...

Data from: Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins

Hao Yu, Matthew G. W. Siewny, Devin T. Edwards, Aric W. Sanders & Thomas T. Perkins
Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution. Using force spectroscopy optimized for 1-microsecond resolution, we reexamined the unfolding of individual bacteriorhodopsin molecules in native lipid bilayers. The experimental data reveal the unfolding pathway in unprecedented detail. Numerous newly detected intermediates—many separated by as few as two or three...

Data from: Parasite metacommunities: evaluating the roles of host community composition and environmental gradients in structuring symbiont communities within amphibians

Joseph R. Mihaljevic, Bethany J. Hoye & Pieter T. J. Johnson
1. Ecologists increasingly report the structures of metacommunities for free-living species, yet far less is known about the composition of symbiont communities through space and time. Understanding the drivers of symbiont community patterns has implications ranging from emerging infectious disease to managing host microbiomes. 2. Using symbiont communities from amphibian hosts sampled from wetlands of California, USA, we quantified the effects of spatial, habitat filtering, and host community components on symbiont occupancy and overall metacommunity...

Data from: Chronic anthropogenic noise disrupts glucocorticoid signaling and has multiple effects on fitness in an avian community

Nathan J. Kleist, Robert P. Guralnick, Alexander Cruz, Christopher A. Lowry & Clinton D. Francis
Anthropogenic noise is a pervasive pollutant that decreases environmental quality by disrupting a suite of behaviors vital to perception and communication. However, even within populations of noise-sensitive species, individuals still select breeding sites located within areas exposed to high noise levels, with largely unknown physiological and fitness consequences. We use a study system in the natural gas fields of northern New Mexico to test the prediction that exposure to noise causes glucocorticoid-signaling dysfunction and decreases...

Data from: Inconsistent reproductive isolation revealed by interactions between Catostomus fish species

Elizabeth Mandeville, Thomas Parchman, Kevin Thompson, Robert Compton, Kevin Gelwicks, Se Jin Song, C. Alex Buerkle, Thomas L. Parchman & Elizabeth G. Mandeville
Interactions between species are central to evolution and ecology, but we do not know enough about how outcomes of interactions between species vary across geographic locations, in heterogeneous environments, or over time. Ecological interactions between species are known to vary, but evolutionary interactions such as reproductive isolation are often assumed to be consistent. Hybridization among Catostomus fish species occurs over a large and heterogeneous geographic area and across taxa with distinct evolutionary histories, and allows...

Data from: Spatial variation of the rain-snow temperature threshold across the Northern Hemisphere

Keith S. Jennings, Taylor S. Winchell, Ben Livneh & Noah P. Molotch
We present the first continuous map of rain-snow air temperature thresholds over the Northern Hemisphere land surface, underlining the spatial variability of precipitation phase partitioning. Land surface models typically discriminate between rain and snow using a simple, spatially uniform air temperature threshold, but observations indicate the threshold is not static. Our analysis of a 29-year observational dataset (n = 17.8 million) shows the threshold varies significantly, averaging 1.0°C and ranging from -0.4°C to 2.4°C for...

Data from: Trace fossils of possible parasites inside the gut contents of a hadrosaurid dinosaur, Upper Cretaceous Judith River Formation, Montana

Justin S. Tweet, Karen Chin & Allan A. Ekdale
Tiny sinuous trace fossils have been found within probable gut contents of an exceptionally preserved specimen of a hadrosaurid dinosaur, Brachylophosaurus canadensis, from the Judith River Formation of Montana. Approximately 280 examples of the trace fossils were observed in 19 samples of gut region material. The tubular structures typically are about 0.3 mm across. Many have thin calcareous linings or layers, and some exhibit fine surficial striae. At least two dozen of these trace fossils...

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Julia Dupin, Nicholas J. Matzke, Tiina Särkinen, Sandra Knapp, Richard G. Olmstead, Lynn Bohs & Stacey D. Smith
Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location:...

Data from: Genetic and demographic founder effects have long-term fitness consequences for colonising populations

Marianna Szűcs, Brett A. Melbourne, Ty Tuff, Christopher Weiss-Lehman & Ruth A. Hufbauer
Colonisation is a fundamental ecological and evolutionary process that drives the distribution and abundance of organisms. The initial ability of colonists to establish is determined largely by the number of founders and their genetic background. We explore the importance of these demographic and genetic properties for longer term persistence and adaptation of populations colonising a novel habitat using experimental populations of Tribolium castaneum. We introduced individuals from three genetic backgrounds (inbred – outbred) into a...

Data from: Integrating remotely sensed fires for predicting deforestation for REDD+

Dolors Armenteras, Cerian Gibbes, Jesús A. Anaya & Liliana M. Dávalos
Fire is an important tool in tropical forest management, as it alters forest composition, structure, and the carbon budget. The United Nations program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) aims to sustainably manage forests, as well as conserve and enhance their carbon stocks. Despite the crucial role of fire management, decision-making on REDD+ interventions fails to systematically include fires. Here, we address this critical knowledge gap in two ways. First, we review...

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles

Tobin J. Hammer, Noah Fierer, Bess Hardwick, Asko Simojoki, Eleanor Slade, Juhani Taponen, Heidi Viljanen & Tomas Roslin
Antibiotics are routinely used to improve livestock health and growth. However, this practice may have unintended environmental impacts mediated by interactions among the wide range of micro- and macroorganisms found in agroecosystems. For example, antibiotics may alter microbial emissions of greenhouse gases by affecting livestock gut microbiota. Furthermore, antibiotics may affect the microbiota of non-target animals that rely on dung, such as dung beetles, and the ecosystem services they provide. To examine these interactions, we...

Data from: Effects of sea ice cover on satellite-detected primary production in the Arctic Ocean

Mati Kahru, Zhongping Lee, Brian Greg Mitchell & Cynthia D. Nevison
The influence of decreasing Arctic sea ice on net primary production (NPP) in the Arctic Ocean has been considered in multiple publications but is not well constrained owing to the potentially large errors in satellite algorithms. In particular, the Arctic Ocean is rich in coloured dissolved organic matter (CDOM) that interferes in the detection of chlorophyll a concentration of the standard algorithm, which is the primary input to NPP models. We used the quasi-analytic algorithm...

Data from: Convergence of gut microbiomes in myrmecophagous mammals

Frédéric Delsuc, Jessica L. Metcalf, Laura Wegener Parfrey, Se Jin Song, Antonio González & Rob Knight
Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition...

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