39 Works

Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

Aaron A. Comeault, Mathew Sommers, Tanja Schwander, C. Alex Buerkle, Timothy E. Farkas, Patrik Nosil & Thomas L. Parchman
Adaptation to different ecological environments can promote speciation. Although numerous examples of such ‘ecological speciation’ exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms...

Data from: Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

Noah Fierer, Joshua Ladau, Jose C. Clemente, Jonathan W. Leff, Sarah M. Owens, Katherine S. Pollard, Rob Knight, Jack A. Gilbert & Rebecca L. McCulley
Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum...

Data from: Climatic warming and the future of bison as grazers

Joseph M. Craine, E. Gene Towne, Mary Miller & Noah Fierer
Climatic warming is likely to exacerbate nutritional stress and reduce weight gain in large mammalian herbivores by reducing plant nutritional quality. Yet accurate predictions of the effects of climatic warming on herbivores are limited by a poor understanding of how herbivore diet varies along climate gradients. We utilized DNA metabarcoding to reconstruct seasonal variation in the diet of North American bison (Bison bison) in two grasslands that differ in mean annual temperature by 6 °C....

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: Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Noah Fierer, Jonathan W. Leff, Byron J. Adams, Uffe N. Nielsen, Scott Thomas Bates, Christian L. Lauber, Sarah Owens, Jack A. Gilbert, Diana H. Wall & J. Gregory Caporaso
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts,...

Data from: Collective strategy for obstacle navigation during cooperative transport by ants

Helen F. McCreery, Zachary A. Dix, Michael D. Breed & Radhika Nagpal
Group cohesion and consensus have primarily been studied in the context of discrete decisions, but some group tasks require making serial decisions that build on one another. We examine such collective problem solving by studying obstacle navigation during cooperative transport in ants. In cooperative transport, ants work together to move a large object back to their nest. We blocked cooperative transport groups of Paratrechina longicornis with obstacles of varying complexity, analyzing groups' trajectories to infer...

Data from: Rapid adaptive evolution in novel environments acts as an architect of population range expansion

Marianna Szűcs, Megan L. Vahsen, Brett A. Melbourne, Charlotte Hoover, Christopher Weiss-Lehman & Ruth A. Hufbauer
Colonization and expansion into novel landscapes determine the distribution and abundance of species in our rapidly changing ecosystems worldwide. Colonization events are crucibles for rapid evolution, but it is not known whether evolutionary changes arise mainly after successful colonization has occurred, or if evolution plays an immediate role, governing the growth and expansion speed of colonizing populations. There is evidence that spatial evolutionary processes can speed range expansion within a few generations because dispersal tendencies...

Climate manipulations differentially affect plant population dynamics within versus beyond northern range limits

Paul Reed, Megan Peterson, Laurel Pfeifer-Meister, William Morris, Daniel Doak, Bitty Roy, Bart Johnson, Graham Bailes & Aaron Nelson
Predicting species’ range shifts under future climate is a central goal of conservation ecology. Studying populations within and beyond multiple species’ current ranges can help identify whether demographic responses to climate change exhibit directionality, indicative of range shifts, and whether responses are uniform across a suite of species. We quantified the demographic responses of six native perennial prairie species planted within and, for two species, beyond their northern range limits to a three-year experimental manipulation...

Data from: Dietary resource overlap among three species of frugivorous bat in Costa Rica

Lauren D. Maynard, Ariana Ananda, Maria F. Sides, Hannah Burk & Susan R. Whitehead
The maintenance of biodiversity in tropical forests is thought to be dependent on fine-scale mechanisms of niche partitioning that allow species to coexist. This study examined whether three species of short-tailed fruit bat that co-occur at a lowland tropical forest site in Costa Rica (Carollia castanea, C. perspicillata, C. sowelli) avoid inter- and intraspecific competition through dietary specialization on species in the genus Piper. First, dietary composition was examined using faecal samples (n = 210),...

Social effects on annual fitness in red squirrels

Andrew McAdam, Quinn Webber, Ben Dantzer, Jeff Lane & Stan Boutin
When resources are limited, mean fitness is constrained and competition can cause genes and phenotypes to enhance an individual’s own fitness while reducing the fitness of their competitors. Negative social effects on fitness have the potential to constrain adaptation, but the interplay between ecological opportunity and social constraints on adaptation remains poorly studied in nature. Here, we tested for evidence of phenotypic social effects on annual fitness (survival and reproductive success) in a long-term study...

Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom

Celine Caseys, Gongjun Shi, Nicole Soltis, Raoni Gwinner, Jason Corwin, Susanna Atwell & Daniel Kliebenstein
Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host...

Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. De Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert & Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to...

Data from: Specific membrane capacitance, cytoplasm conductivity and instantaneous Young’s modulus of single tumour cells

Ke Wang, Yang Zhao, Deyong Chen, Beiyuan Fan, Yulan Lu, Lianhong Chen, Rong Long, Junbo Wang & Jian Chen
As label-free biomarkers, biophysical properties of cells are widely used for cell type classification. However, intrinsic biophysical markers, e.g. specific membrane capacitance (Cspecific membrane), cytoplasm conductivity (σconductivity) and instantaneous Young’s modulus (Einstantaneous) measured for hundreds of single cells were not yet reported. In this study, single cells in suspension (adherent cells treated with trypsin) were aspirated through a microfluidic constriction channel at 25°C, and the entry processes and impedance profiles were recorded and translated to...

Data from: Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Jeremy Bono, Andrew Reed, Jon Pigage, Helen Pigage & Cody Glickman
Microbiota inhabiting the gastrointestinal (GI) tract of animals have important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut microorganismal community, few comparative studies have considered how differences in diet influence community composition across the length the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert’s (Sciurus aberti) and fox squirrels (S. niger) living in...

Data from: The Hawaiian freshwater algae biodiversity survey (2009-2014): systematic and biogeographic trends with an emphasis on the macroalgae

Alison R. Sherwood, Amy L. Carlile, Jessica M. Neumann, J. Patrick Kociolek, Jeffrey R. Johansen, Rex L. Lowe, Kimberly Y. Conklin & Gernot G. Presting
Background A remarkable range of environmental conditions is present in the Hawaiian Islands due to their gradients of elevation, rainfall and island age. Despite being well known as a location for the study of evolutionary processes and island biogeography, little is known about the composition of the non-marine algal flora of the archipelago, its degree of endemism, or affinities with other floras. We conducted a biodiversity survey of the non-marine macroalgae of the six largest...

Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome

Jessica L. Metcalf, Se Jin Song, James T. Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie & Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly...

Data from: Quantifying climate sensitivity and climate-driven change in North American amphibian communities

David A. W. Miller, Evan H. Campbell Grant, Erin Muths, Staci M. Amburgey, Michael J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T. J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A. G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers, Thomas A. Gorman, Carola A. Haas, Ward Hughson, David S. Pilliod, Steven J. Price … & Brent H. Sigafus
Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local...

Data from: Increase in crop losses to insect pests in a warming climate

Curtis A. Deutsch, Joshua J. Tewksbury, Michelle Tigchelaar, David S. Battisti, Scott C. Merrill, Raymond B. Huey & Rosamond L. Naylor
Insect pests substantially reduce yields of three staple grains—rice, maize, and wheat—but models assessing the agricultural impacts of global warming rarely consider crop losses to insects. We use established relationships between temperature and the population growth and metabolic rates of insects to estimate how and where climate warming will augment losses of rice, maize, and wheat to insects. Global yield losses of these grains are projected to increase by 10 to 25% per degree of...

Genomic variation data for the wagtail hybrid zone

Georgy Semenov, Ethan Link, Erik Enbody, Rebecca Harris, David Khaydarov, Per Alström, Leif Andersson & Scott Taylor
Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration...

Grasshopper species’ seasonal timing underlies shifts in community phenological overlap in response to climate gradients, variability, and change

César Nufio, Stuart Graham & Lauren Buckley
1. Species with different life histories and communities that vary in their seasonal constraints tend to shift their phenology (seasonal timing) differentially in response to climate warming. 2. We investigate how these variable phenological shifts aggregate to influence phenological overlap within communities. Phenological advancements of later-season species and extended durations of early-season species may increase phenological overlap, with implications for species’ interactions such as resource competition. 3. We leverage extensive historic (1958-1960) and recent (2006-2015)...

Data from: Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop & Donald M. Waller
Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United...

Data from: Is asexual reproduction an evolutionary dead-end in lichens?

Erin A. Tripp
Classical hypotheses in lichenology predict pairs of species in which sexual lineages are ancestral and long-lived evolutionarily and that these give rise to derived, evolutionarily transient asexual lineages. Extensive phylogenetic information generated over the last 20 years regarding relationships within and among various groups of lichens makes possible an investigation of polarity and lability in reproductive mode across diverse clades. To test the long-held hypothesis of asexual reproduction as an evolutionary dead end in lichens,...

Data from: Transcriptional variation associated with cactus host plant adaptation in Drosophila mettleri

Kim Hoang, Luciano M. Matzkin & Jeremy M. Bono
Although the importance of host plant chemistry in plant–insect interactions is widely accepted, the genetic basis of adaptation to host plants is not well understood. Here, we investigate transcriptional changes associated with a host plant shift in Drosophila mettleri. While D. mettleri is distributed mainly throughout the Sonoran Desert where it specializes on columnar cacti (Carnegiea gigantea and Pachycereus pringleii), a population on Santa Catalina Island has shifted to chemically divergent coastal prickly pear cactus...

Pollen limitation of native plant reproduction in an urban landscape

Rebecca Irwin, Adrian Carper, Lynn Adler & Paige Warren
Premise: Evidence suggests that bees may benefit from moderate levels of human development. However, the effects of human development on pollination and reproduction of bee-pollinated plants are less well understood. Studies have measured natural variation in pollination and plant reproduction as a function of urbanization, but few have experimentally measured the magnitude of pollen limitation in urban versus non-urban sites. Doing so is important to unambiguously link changes in pollination to plant reproduction. Previous work...

Data from: Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group

Jeremy M. Bono, Helen K. Pigage, Peter J. Wettstein, Stephanie A. Prosser & Jon C. Pigage
Background: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these...

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  • University of Colorado Colorado Springs
  • Colorado State University
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  • Utah State University
  • University of Notre Dame
  • University of California, San Diego
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  • University of Colorado Boulder
  • United States Geological Survey