321 Works

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: 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: Tritrophic interactions at a community level: effects of host-plant species quality on bird predation of caterpillars

Michael S. Singer, Timothy E. Farkas, Christian M. Skorik & Kailen A. Mooney
Effects of plant traits on herbivore-carnivore interactions are well documented in component communities, but are not well understood at the level of large, complex communities. We report on a two-year field experiment testing mechanisms by which variation in food quality among eight temperate forest tree species alters avian suppression of an assemblage of dietary generalist caterpillars. Plant quality and bird effects varied dramatically among tree species; high quality plants yielded herbivores of 50% greater mass...

Data from: Marine protected areas enhance structural complexity but do not buffer the consequences of ocean warming for an overexploited precious coral

Ignasi Montero-Serra, Joaquim Garrabou, Daniel F. Doak, Jean-Baptiste Ledoux & Cristina Linares
1. Global warming and overexploitation both threaten the integrity and resilience of marine ecosystems. Many calls have been made to at least partially offset climate change impacts through local conservation management. However, a mechanistic understanding of the interactions of multiple stressors is generally lacking for habitat-forming species; preventing the development of sound conservation strategies. 2. We examined the effectiveness of no-take marine protected areas (MPAs) at enhancing structural complexity and resilience to climate change on...

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: 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: Elementary sensory-motor transformations underlying olfactory navigation in walking fruit flies

Efrén Álvarez-Salvado, Angela M. Licata, Erin G. Connor, Margaret K. McHugh, Benjamin M.N. King, Nicholas Stavropoulos, Jonathan D. Victor, John P. Crimaldi, Katherine I. Nagel & Benjamin MN King
Odor attraction in walking Drosophila melanogaster is commonly used to relate neural function to behavior, but the algorithms underlying attraction are unclear. Here we develop a high-throughput assay to measure olfactory behavior in response to well-controlled sensory stimuli. We show that odor evokes two behaviors: an upwind run during odor (ON response), and a local search at odor offset (OFF response). Wind orientation requires antennal mechanoreceptors, but search is driven solely by odor. Using dynamic...

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: 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: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Kathryn A. Hodgins, Zhao Lai, Luiz O. Oliveira, David W. Still, Moira Scascitelli, Michael S. Barker, Nolan C. Kane, Hannes Dempewolf, Alex Kozik, Richard V. Kesseli, John M. Burke, Richard W. Michelmore & Loren H. Rieseberg
Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium...

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: 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: 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...

Data from: Environmental gradients determine the potential for ecosystem engineering effects

Joshua B. Grinath, Loralee Larios, Laura R. Prugh, Justin S. Brashares & Katharine N. Suding
Understanding processes that determine biodiversity is a fundamental challenge in ecology. At the landscape scale, physical alteration of ecosystems by organisms, called ecosystem engineering, enhances biodiversity worldwide by increasing heterogeneity in resource conditions and enhancing species coexistence across engineered and non-engineered habitats. Engineering-diversity relationships can vary along environmental gradients due to changes in the amount of physical structuring created by ecosystem engineering, but it is unclear how this variation is influenced by the responsiveness of...

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: Generalized movement strategies for constrained consumers: ignoring fitness can be adaptive

Theodore E. Galanthay & Samuel M. Flaxman
Movements made by real organisms---such as movements involved in dispersal, migration, and habitat selection---are expected to be suboptimal occasionally due to realistic constraints imposed by incomplete information, perceptual limitations, and stochasticity. Previous theory considering such constraints has shown that movements appropriately conditioned upon habitat or resource characteristics can balance out suboptimal components of movement and thereby lead organisms to ideal free distributions and fitness maxima, whereas movements conditioned upon fitness differentials cannot. These findings suggest...

Data from: Noise pollution filters bird communities based on vocal frequency

Clinton D. Francis, Catherine P. Ortega & Alexander Cruz
BACKGROUND: Human-generated noise pollution now permeates natural habitats worldwide, presenting evolutionarily novel acoustic conditions unprecedented to most landscapes. These acoustics are not only harmful to humans, but threaten wildlife, and especially birds, via changes to species densities, foraging behavior, reproductive success, and predator-prey interactions. Explanations for the negative effects of noise on birds include the disruption of acoustic communication through energetic masking, potentially forcing species that rely upon acoustic communication to abandon otherwise suitable areas....

Data from: Host associated bacterial community succession during amphibian development

Tiffany L. Prest, Abigail K. Kimball, Jordan G. Kueneman & Valerie J. Mckenzie
Amphibians undergo significant developmental changes during their life cycle, as they typically move from a primarily aquatic environment to a more terrestrial one. Amphibian skin is a mucosal tissue that assembles communities of symbiotic microbiota. However, it is currently not well understood as to where amphibians acquire their skin symbionts, and whether the sources of microbial symbionts change throughout development. In this study, we utilized data collected from four wild boreal toad populations (Anaxyrus boreas);...

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: 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: 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: 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: Risky business: linking Toxoplasma gondii infection and entrepreneurship behaviours across individuals and countries

Stefanie K. Johnson, Fitza A. Markus, Daniel A. Lerher, Dana M. Calhoun, Marissa A. Beldon, Elsa T. Chan & Pieter T. J. Johnson
Disciplines such as business and economics often rely on the assumption of rationality when explaining complex human behaviours. However, growing evidence suggests that behaviour may concurrently be influenced by infec- tious microorganisms. The protozoan, Toxoplasma gondii, infects an estimated 2 billion people worldwide and has been linked to behavioural alterations in humans and other vertebrates. Here we integrate primary data from college students and business professionals with national-level information on cultural attitudes toward business to...

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...

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