355 Works

Data from: Lambda interferon restructures the nasal microbiome and increases susceptibility to Staphylococcus aureus superinfection

Paul J. Planet, Dane Parker, Taylor S. Cohen, Hannah Smith, Justinne D. Leon, Chanelle Ryan, Tobin J. Hammer, Noah Fierer, Emily I. Chen & Alice S. Prince
Much of the morbidity and mortality associated with influenza virus respiratory infection is due to bacterial coinfection with pathogens that colonize the upper respiratory tract such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae. A major component of the immune response to influenza virus is the production of type I and III interferons. Here we show that the immune response to infection with influenza virus causes an increase and restructuring of the upper respiratory microbiota...

Data from: Commensal associations and benthic habitats shape macroevolution of the bivalve clade Galeommatoidea

Jingchun Li, Diarmaid Ó Foighil & Ellen E. Strong
The great diversity of marine life has been shaped by the interplay between abiotic and biotic factors. Among different biotic interactions, symbiosis is an important yet less studied phenomenon. Here, we tested how symbiotic associations affected marine diversification, using the bivalve superfamily Galeommatoidea as a study system. This superfamily contains large numbers of obligate commensal as well as free-living species and is therefore amenable to comparative approaches. We constructed a global molecular phylogeny of Galeommatoidea...

Data from: Performance of Encounternet tags: field tests of miniaturized proximity loggers for use on small animals

Iris I. Levin, David M. Zonana, John M. Burt & Rebecca J. Safran
Proximity logging is a new tool for understanding social behavior as it allows for accurate quantification of social networks. We report results from field calibration and deployment tests of miniaturized proximity tags (Encounternet), digital transceivers that log encounters between tagged individuals. We examined radio signal behavior in relation to tag attachment (tag, tag on bird, tag on saline-filled balloon) to understand how radio signal strength is affected by the tag mounting technique used for calibration...

Data from: A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird

Sara Kaiser, Scott A. Taylor, Nancy Chen, Scott Sillett, Eliana R. Bondra, Michael Webster, Sara A. Kaiser & T. Scott Sillett
Single-nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120 SNP markers from a transcriptome assembled using RNA-sequencing of a songbird with the most common...

Data from: Herbivory mediates the long-term shifts in the relative importance of microsite and propagule limitation

Anu Eskelinen, Patrick Saccone, Marko J. Spasojevic & Risto Virtanen
Microsite and propagule limitation are predicted to jointly influence plant community assembly and diversity, with shifts in their relative contributions under different ecological conditions. Mammalian herbivory can also exhibit strong impact on community assembly and diversity. However, to date few studies have considered how herbivory might interact with propagule and microsite limitation and how herbivory might alter their relative importance. Even fewer studies have examined how these processes manifest over time to influence community assembly....

Data from: Phenotypic differentiation is associated with divergent sexual selection among closely related barn swallow populations

Matthew R. Wilkins, Hakan Karaardıç, Yoni Vortman, Thomas L. Parchman, Tomáš Albrecht, Adéla Petrželková, Leyla Özkan, Peter L. Pap, Joanna K. Hubbard, Amanda K. Hund & Rebecca J. Safran
Sexual selection plays a key role in the diversification of numerous animal clades and may accelerate trait divergence during speciation. However, much of our understanding of this process comes from phylogenetic comparative studies, which rely on surrogate measures such as dimorphism that may not represent selection in wild populations. In this study, we assess sexual selection pressures for multiple male visual signals across four barn swallow (Hirundo rustica) populations. Our sample encompassed 2400 linear km...

Data from: Tempo and mode of flower color evolution

Stacey D. Smith & Emma E. Goldberg
Premise of the study: Flower color is one of the best-studied floral traits in terms of its genetic basis and ecological significance, yet few studies have examined the processes that shape its evolution across deep timescales. Advances in comparative methods along with larger phylogenies for floral radiations offer new opportunities for investigating the macroevolution of flower color. Methods: We examined the tempo and mode of flower color evolution in four clades (Antirrhineae, Iochrominae, Loeselieae, Quamoclit)...

Data from: Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Galápagos archipelago

Sofía Carvajal-Endara, Andrew P. Hendry, Nancy C. Emery & T. Jonathan Davies
Remote locations, such as oceanic islands, typically harbour relatively few species, some of which go on to generate endemic radiations. Species colonising these locations tend to be a non-random subset from source communities, which is thought to reflect dispersal limitation. However, non-random colonisation could also result from habitat filtering, whereby only a few continental species can become established. We evaluate the imprints of these processes on the Galápagos flora by analysing a comprehensive regional phylogeny...

Data from: Asymmetric competition impacts evolutionary rescue in a changing environment

Courtney L. Van Den Elzen, Elizabeth J. Kleynhans & Sarah P. Otto
Interspecific competition can strongly influence the evolutionary response of a species to a changing environment, impacting the chance that the species survives or goes extinct. Previous work has shown that when two species compete for a temporally shifting resource distribution, the species lagging behind the resource peak is the first to go extinct due to competitive exclusion. However, this work assumed symmetrically distributed resources and competition. Asymmetries can generate differences between species in population sizes,...

Data from: Biological and statistical processes jointly drive population aggregation: using host–parasite interactions to understand Taylor's power law

Pieter T. J. Johnson & Mark Q. Wilber
The macroecological pattern known as Taylor's power law (TPL) represents the pervasive tendency of the variance in population density to increase as a power function of the mean. Despite empirical illustrations in systems ranging from viruses to vertebrates, the biological significance of this relationship continues to be debated. Here we combined collection of a unique dataset involving 11 987 amphibian hosts and 332 684 trematode parasites with experimental measurements of core epidemiological outcomes to explicitly...

Data from: Composition of micro-eukaryotes on the skin of the Cascades frog (Rana cascadae) and patterns of correlation between skin microbes and Batrachochytrium dendrobatidis

Jordan G. Kueneman, Sophie Weiss & Valerie J. McKenzie
Global amphibian decline linked to fungal pathogens has galvanized research on applied amphibian conservation. Skin-associated bacterial communities of amphibians have been shown to mediate fungal skin infections and the development of probiotic treatments with antifungal bacteria has become an emergent area of research. While exploring the role of protective bacteria has been a primary focus for amphibian conservation, we aim to expand and study the other microbes present in amphibian skin communities including fungi and...

Data from: FEATHER: automated analysis of force spectroscopy unbinding and unfolding data via a Bayesian algorithm

Patrick R. Heenan & Thomas T. Perkins
Single-molecule force spectroscopy (SMFS) provides a powerful tool to explore the dynamics and energetics of individual proteins, protein-ligand interactions, and nucleic acid structures. In the canonical assay, a force probe is retracted at constant velocity to induce a mechanical unfolding/unbinding event. Next, two energy landscape parameters, the zero-force dissociation rate constant (ko) and the distance to the transition state (Δx‡), are deduced by analyzing the most probable rupture force as a function of the loading...

Data from: Information-theoretic analysis of realistic odor plumes: what cues are useful for determining location?

Sebastian D. Boie, Erin G. Connor, Margaret McHugh, Katherine I. Nagel, G. Bard Ermentrout, John P. Crimaldi & Jonathan D. Victor
Many species rely on olfaction to navigate towards food sources or mates. Olfactory navigation is a challenging task since odor environments are typically turbulent. While time-averaged odor concentration varies smoothly with the distance to the source, instaneous concentrations are intermittent and obtaining stable averages takes longer than the typical intervals between animals’ navigation decisions. How to effectively sample from the odor distribution to determine sampling location is the focus on this article. To investigate which...

Data from: Explosion-generated infrasound recorded on ground and airborne microbarometers at regional distances

Eliot F. Young, Daniel C. Bowman, Jonathan M. Lees, Viliam Klein, Steven J. Arrowsmith & Courtney Ballard
Recent work in deploying infrasound (low frequency sound) sensors on aerostats and free flying balloons has shown them to be viable alternatives to ground stations. However, no study to date has compared the performance of surface and free floating infrasound microbarometers with respect to acoustic events at regional (100s of kilometers) range. The prospect of enhanced detection of aerial explosions at similar ranges, such as those from bolides, has not been investigated either. We examined...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: Caenorhabditis elegans genes affecting interindividual variation in life-span biomarker gene expression

Alexander Mendenhall, Matthew M. Crane, Patricia M. Tedesco, Thomas E. Johnson & Roger Brent
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior...

Data from: Explaining large mitochondrial sequence differences within a population sample

Mary Morgan-Richards, Mariana Bulgarella, Louisa Sivyer, Edwina J. Dowle, Marie Hale, Rachael Van Heugten, Natasha E. McKean & Steven A. Trewick
Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an...

Data from: Hemiparasites can transmit indirect effects from their host plants to herbivores

Nathan L. Haan, Jonathan D. Bakker & M. Deane Bowers
Parasitic plants can serve as critical intermediaries between their hosts and other organisms; however these relationships are not well understood. To investigate the relative importance of plant traits in such interactions, we studied the role of the root hemiparasite, Castilleja levisecta (Orobanchaceae), as a mediator of interactions between the host plants it parasitizes and the lepidopteran herbivore Euphydryas editha (Nymphalidae), whose caterpillars feed on Castilleja and sequester iridoid glycosides from it. We tested whether the...

Data from: Using multi-response models to investigate pathogen coinfections across scales: insights from emerging diseases of amphibians

William E. Stutz, Andrew R. Blaustein, Cheryl J. Briggs, Jason T. Hoverman, Jason R. Rhor & Pieter T. J. Johnson
1.Associations among parasites affect many aspects of host-parasite dynamics, but a lack of analytical tools has limited investigations of parasite correlations in observational data that are often nested across spatial and biological scales. 2.Here we illustrate how hierarchical, multiresponse modeling can characterize parasite associations by allowing for hierarchical structuring, offering estimates of uncertainty, and incorporating correlational model structures. After introducing the general approach, we apply this framework to investigate coinfections among four amphibian parasites (the...

Data from: Multiple mechanisms confer stability to isolated populations of a rare endemic plant

Reilly R. Dibner, Megan L. Peterson, Allison M. Louthan & Daniel F. Doak
The persistence of small populations remains a puzzle for ecology and conservation. Especially interesting is how naturally small, isolated populations are able to persist in the face of multiple environmental forces that create fluctuating conditions and should, theory predicts, lead to high probabilities of extirpation. We used a combination of long term census data and a five-year demographic study of a naturally rare, endemic plant, Yermo xanthocephalus, to evaluate the importance of several possible mechanisms...

Data from: Wildfire activity and land use drove 20th-century changes in forest cover in the Colorado front range

Kyle C. Rodman, Thomas T. Veblen, Sara Saraceni & Teresa B. Chapman
Recent shifts in global forest area highlight the importance of understanding the causes and consequences of forest change. To examine the influence of several potential drivers of forest cover change, we used supervised classifications of historical (1938–1940) and contemporary (2015) aerial imagery covering a 2932‐km2 study area in the northern Front Range (NFR) of Colorado and we linked observed changes in forest cover with abiotic factors, land use, and fire history. Forest cover in the...

Data from: Disease and climate effects on individuals drive post-reintroduction population dynamics of an endangered amphibian

Maxwell B. Joseph & Roland A. Knapp
The emergence of novel pathogens often has dramatic negative effects on previously unexposed host populations. Subsequent disease can drive populations and even species to extinction. After establishment in populations, pathogens can continue to affect host dynamics, influencing the success or failure of species recovery efforts. However, quantifying the effect of pathogens on host populations in the wild is challenging because individual hosts and their pathogens are difficult to observe. Here we use long-term mark-recapture data...

Data from: The adaptive potential of plant populations in response to extreme climate events

Lorena Torres-Martinez, Niall McCarten & Nancy C. Emery
The frequency and magnitude of extreme climate events are increasing with global change, yet we lack predictions and empirical evidence for the ability of wild populations to persist and adapt in response to these events. Here, we used Fisher’s Fundamental Theorem of Natural Selection to evaluate the adaptive potential of Lasthenia fremontii, an herbaceous winter annual that is endemic to seasonally flooded wetlands in California, to alternative flooding regimes that occur during El Niño Southern...

Data from: Experimental habitat fragmentation disrupts nematode infections in Australian skinks

Julian Resasco, Matthew E. Bitters, Saul A. Cunningham, Hugh I. Jones, Valerie J. McKenzie & Kendi F. Davies
Habitat conversion and fragmentation threaten biodiversity and disrupt species interactions. While parasites are recognized as ecologically important, the impacts of fragmentation on parasitism are poorly understood relative to other species interactions. This lack of understanding is in part due to confounding landscape factors that accompany fragmentation. Fragmentation experiments provide the opportunity to fill this knowledge gap by mechanistically testing how fragmentation affects parasitism while controlling landscape factors. In a large-scale, long-term experiment, we asked how...

Terminus data for: Multi-decadal retreat of Greenland’s marine-terminating glaciers

Ian M. Howat & Alex Eddy
Many marine-terminating glaciers draining the Greenland ice sheet have retreated over the past decade, yet the extent and magnitude of retreat relative to past variability is unknown. We measure changes in front positions of 210 marine-terminating glaciers using Landsat imagery spanning nearly four decades and compare decadal-scale rates of change with earlier observations. We find that 90% of the observed glaciers retreated between 2000 and 2010, approaching 100% in the northwest, with rapid retreat observed...

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