40 Works

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: 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: Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies

Georgy A. Semenov, Elizabeth S.C. Scordato, David R. Khaydarov, Chris C.R. Smith, Nolan C. Kane, Rebecca J. Safran & Elizabeth S. C. Scordato
Phenotypic differentiation plays an important role in the formation and maintenance of reproductive barriers. In some cases, variation in a few key aspects of phenotype can promote and maintain divergence; hence the identification of these traits and their associations with patterns of genomic divergence are crucial for understanding the patterns and processes of population differentiation. We studied hybridization between the alba and personata subspecies of the white wagtail (Motacilla alba), and quantified divergence and introgression...

Data from: Microbial richness and composition independently drive soil multifunctionality

Manuel Delgado-Baquerizo, Pankaj Trivedi, Chanda Trivedi, David J. Eldridge, Peter B. Reich, Thomas C. Jeffries & Brajesh K. Singh
Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend. We used two independent approaches (i.e. experimental and observational), and applied statistical modeling to identify the role and relative...

Data from: Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

Jordan G. Kueneman, Douglas C. Woodhams, Reid Harris, Holly M. Archer, Rob Knight & Valerie J. McKenzie
Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas,...

Data from: Natural selection on MHC IIβ in parapatric lake and stream stickleback: balancing, divergent, both or neither?

William E. Stutz & Daniel I. Bolnick
Major histocompatibility (MHC) genes encode proteins that play a central role in vertebrates’ adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates’ genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or...

Data from: Whether larval amphibians school does not affect the parasite aggregation rule: testing the effects of host spatial heterogeneity in field and experimental studies

Janet Koprivnikar, Tawni B. Riepe, Dana M. Calhoun & Pieter T. J. Johnson
Almost all macroparasites show over-dispersed infections within natural host populations such that most parasites are distributed among a few heavily-infected individuals. Despite the importance of parasite aggregation for understanding system stability, the potential for population regulation, and super-spreading events, many questions persist about its underlying drivers. Theoretically, aggregation results from heterogeneity in host exposure, resistance, and tolerance. However, few studies have examined how host spatial arrangement – which likely affects both parasite encounter and density-dependent...

Data from: Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry

Elizabeth S.C. Scordato, Matthew R. Wilkins, Georgy Semenov, Alexander S. Rubtsov, Nolan C. Kane, Rebecca J. Safran & Elizabeth S. C. Scordato
Hybrid zones are geographic regions where isolating barriers between divergent populations are challenged by admixture. Identifying factors that facilitate or inhibit hybridization in sympatry can illuminate the processes that maintain those reproductive barriers. We analyzed patterns of hybridization and phenotypic variation across two newly-discovered hybrid zones between three subspecies of barn swallow (Hirundo rustica). These subspecies differ in ventral coloration and wing length, traits that are targets of sexual and natural selection, respectively, and are...

Data from: Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

Erin Conlisk, Cristina Castanha, Matthew J. Germino, Thomas T. Veblen, Jeremy M. Smith, Andrew B. Moyes & Lara M. Kueppers
Understanding how climate warming will affect the demographic rates of different ecotypes is critical to predicting shifts in species distributions. Here we present results from a common garden, climate change experiment in which we measured seedling recruitment of lodgepole pine, a widespread North American conifer that is also planted globally. Seeds from a low-elevation provenance had greater recruitment to their third year (by 323%) than seeds from a high-elevation provenance across sites within and above...

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: 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: 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: 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: The power of evolutionary rescue is constrained by genetic load

Gavin S. Stewart, Madeline R. Morris, Allison B. Genis, Marianna Szűcs, Brett A. Melbourne, Simon J. Tavener & Ruth A. Hufbauer
Extinction risk of small isolated populations in changing environments can be reduced by rapid adaptation and subsequent growth to larger, less vulnerable sizes. Whether this process, called evolutionary rescue, is able to reduce extinction risk and sustain population growth over multiple generations is largely unknown. To understand the consequences of adaptive evolution as well as maladaptive processes in small isolated populations, we subjected experimental Tribolium castaneum populations founded with 10 or 40 individuals to novel...

Data from: Taxonomic delimitation of the rare, eastern North American endemic lichen Santessoniella crossophylla (Pannariaceae)

James C. Lendemer, Heather B. Stone & Erin A. Tripp
The taxonomic delimitation and generic placement of Santessoniella crossophylla (Old Gray Crosslobes), a cyanolichen endemic to eastern North America, are revisited based on newly generated nrITS and mtSSU sequences. A population from Nova Scotia whose identification as S. crossophylla has been questioned is confirmed as belonging to the species. The monospecific genus Rockefellera is introduced to accommodate lichens ascribable to S. crossophylla in light of molecular results herein presented. The new name honors the Rockefeller...

Data from: Where and how to restore in a changing world: a demographic-based assessment of resilience

Loralee Larios, Lauren M. Hallett & Katharine N. Suding
Managers are increasingly looking to apply concepts of resilience to better anticipate and understand conservation and restoration in a changing environment. In this study, we explore how information on demography (recruitment, growth and survival) and competitive effects in different environments and with different starting species abundances can be used to better understand resilience. We use observational and experimental data to better understand dynamics between native Stipa pulchra and exotic Avena barbata and fatua, grasses characteristic...

Data from: Life cycle size dynamics in Didymosphenia geminata (Bacillariophytceae)

Ian W. Bishop & Sarah A. Spaulding
Didymosphenia geminata has received a great deal of attention in the last 25 years, and considerable effort has gone into determining the origin, ecological impact, and economic consequences of its invasive behavior. While environmental conditions are a controlling influence in distribution, the extreme success of the species may be tied to its basic biology and life history. Little is known, however, about population dynamics, size restoration and reproduction of D. geminata. The objective of this...

Data from: Plastic transcriptomes stabilize immunity to pathogen diversity: the jasmonic acid and salicylic acid networks within the Arabidopsis/Botrytis pathosystem

Wei Zhang, Jason A. Corwin, Daniel Copeland, Julie Feusier, Robert Eshbaugh, Fang Chen, Susanna Atwell & Daniel J. Kliebenstein
To respond to pathogen attack, selection and associated evolution has led to the creation of plant immune system that are a highly effective and inducible defense system. Central to this system are the plant defense hormones jasmonic acid (JA) and salicylic acid (SA) and crosstalk between the two, which may play an important role in defense responses to specific pathogens or even genotypes. Here, we used the Arabidopsis-B. cinerea pathosystem to test how the host's...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Colorado Boulder
  • University of California, Berkeley
  • Colorado State University
  • University of California System
  • Institute of Systematics and Ecology of Animals
  • University of Washington
  • University of California, San Diego
  • University of Minnesota
  • University of Zurich
  • Lawrence Berkeley National Laboratory