228 Works

Data from: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

Cheng Sun & Rachel Lockridge Mueller
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 Gb to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative...

Data from: Plasticity of parental care under the risk of predation: how much should parents reduce care?

Cameron K. Ghalambor, Susana I. Peluc & Thomas E. Martin
Predation can be an important agent of natural selection shaping parental care behaviours, and can also favor behavioural plasticity. Parent birds often decrease the rate that they visit the nest to provision offspring when perceived risk is high. Yet the plasticity of such responses may differ among species as a function of either their relative risk of predation, or the mean rate of provisioning. Here, we report parental provisioning responses to experimental increases in the...

Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome

Matthew G. Bakker, Daniel C. Schlatter, Lindsey Otto-Hanson & Linda L. Kinkel
A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and...

Data from: Linking genotype, ecotype, and phenotype in an intensively managed large carnivore

Aaron B. A. Shafer, Scott E. Nielsen, Joseph M. Northrup & Gordon B. Stenhouse
Numerous factors influence fitness of free-ranging animals, yet often these are uncharacterized. We integrated GPS habitat use data and genetic profiling to determine their influence on fitness proxies (mass, length, and body condition) in a threatened population of grizzly bears (Ursus arctos) in Alberta, Canada. We detected distinct genetic and habitat use (ecotype) clusters, with individual cluster assignments, or genotype/ecotype, being correlated (Pearson r = 0.34, P < 0.01). Related individuals showed evidence of similar...

Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes

Bishwo N. Adhikari, John P. Hamilton, Marcelo M. Zerillo, Ned Tisserat, C. André Lévesque & C. Robin Buell
The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison...

Data from: Aridity Modulates N Availability in Arid and Semiarid Mediterranean Grasslands

Manuel Delgado-Baquerizo, Fernando T. Maestre, Antonio Gallardo, José L. Quero, Victoria Ochoa, Miguel García-Gómez, Cristina Escolar, Pablo García-Palacios, Miguel Berdugo, Enrique Valencia, Beatriz Gozalo, Zouhaier Noumi, Mchich Derak, Matthew D. Wallenstein & Matteo Convertino
While much is known about the factors that control each component of the terrestrial nitrogen (N) cycle, it is less clear how these factors affect total N availability, the sum of organic and inorganic forms potentially available to microorganisms and plants. This is particularly true for N-poor ecosystems such as drylands, which are highly sensitive to climate change and desertification processes that can lead to the loss of soil nutrients such as N. We evaluated...

Ensemble model output of North American atmospheric CO2 simulation (full WRF-chem output)

S. Feng, T. Lauvaux, K.J. Davis, K. Keller, R. Rayner, T. Oda, K. Gurney, Y. Zhou, C. Williams, A.E. Schuh, J. Liu & I. Baker
The uncertainty in biospheric carbon dioxide (CO2) flux estimates drives divergent projections of future climate and uncertainty in prescriptions for climate mitigation. The terrestrial carbon sink can be inferred from atmospheric CO2 observations with transport models via inversion methods. Regional CO2 flux estimates remain uncertain due to the mixture of uncertainties caused by transport models, prior estimates of biospheric fluxes, large-scale CO2 boundary inflow, the assumptions in the inversion process, and the limited density of...

Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

Nicholas Mason, Nicholas Fletcher, Brian Gill, Chris Funk & Kelly Zamudio
Species are a fundamental unit of biodiversity that are delimited via genetic data and coalescent-based methods with increasing frequency. Despite the widespread use of coalescent-based species delimitation, we do not fully understand the sensitivity of these methods to potential sources of bias and violations of their underlying assumptions. One implicit assumption of coalescent-based species delimitation is that geographic sampling is adequate and representative of genetic variation among populations within the lineage of interest. Yet exhaustive...

Data from: Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

Devaughn Fraser, Alice Mouton, Laurel E.K. Serieys, Steve Cole, Scott Carver, Sue Vandewoude, Michael Lappin, Seth P.D. Riley, Robert Wayne & Laurel E. K. Serieys
Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten non-target predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR-related effects on genome wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity, and both adaptive and innate immune function. Further, we...

Data from: Prolonged exposure to manure from livestock administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling

Carl Wepking, Brian Badgley, Jeb Barrett, Katharine Knowlton, Jane Lucas, Kevan Minick, Partha Ray, Sarah Shawver & Michael Strickland
Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially-mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: i) changes in microbial community structure; and ii) alterations in elemental cycling throughout the terrestrial system....

Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass

Ava Hoffman, Julie A. Bushey, Troy W. Ocheltree & Melinda D. Smith
Global change forecasts in ecosystems require knowledge of within species diversity, particularly of dominant species within communities. We assessed site-level diversity and capacity for adaptation of the dominant species of the shortgrass steppe biome of the Central US, Bouteloua gracilis. We quantified genetic diversity from 17 sites across regional scales, north-south from New Mexico to South Dakota, and local scales in Northern Colorado. We also quantified phenotype and plasticity within and among sites and determined...

The importance of nighttime length to latitudinal variation in avian incubation attentiveness

Helen Sofaer, Lauren Nagle, Scott Sillett, Jongmin Yoon & Cameron Ghalambor
Avian incubation provides an opportunity to test how parental behavior and ecological conditions interact to shape variation in offspring traits along geographic gradients. In particular, the duration of the incubation period is shorter at higher latitudes, but the degree to which this pattern arises from genetic divergence in rates of growth and development versus from parentally-mediated variation in egg temperatures is controversial. At higher latitudes parents have higher daytime incubation attentiveness, i.e., they spend a...

Data from: Community-based wildlife management area supports similar mammal species richness and densities compared to a national park

Christian Kiffner, Seth Thomas, Talia Speaker, Victoria O’Connor, Paige Schwarz, John Kioko & Bernard Kissui
Community-based conservation models have been widely implemented across Africa to improve wildlife conservation and livelihoods of rural communities. In Tanzania, communities can set aside land and formally register it as Wildlife Management Area (WMA), which allows them to generate revenue via consumptive or non-consumptive utilization of wildlife. The key, yet often untested, assumption of this model is that economic benefits accrued from wildlife motivate sustainable management of wildlife. To test the ecological effectiveness (here defined...

Novel hybrid finds a peri-urban niche: Allen’s Hummingbirds in southern California

Braden L. Godwin, Melanie E. F. LaCava, Beth Mendelsohn, Roderick B. Gagne, Kyle D. Gustafson, Sierra M. Love Stowell, Andrew Engilis, Lisa A. Tell & Holly B. Ernest
Species range expansions and contractions can have ecological and genetic consequences, and thus are important areas of study for conservation. Hybridization and introgression are not uncommon in closely related populations that experience secondary contact during a range expansion. Allen’s Hummingbird (Selasphorus sasin) in California comprises two subspecies: the migratory S. s. sasin, which winters in central Mexico and breeds in central and northern California, and the resident S. s. sedentarius, which lives and breeds year-round...

Data from: The global compendium of Aedes aegypti and Ae. albopictus occurrence

Moritz U. G. Kraemer, Marianne E. Sinka, Kirsten A. Duda, Adrian Mylne, Freya M. Shearer, Oliver J. Brady, Janey P. Messina, Christopher M. Barker, Chester G. Moore, Roberta G. Carvalho, Giovanini E. Coelho, Wim Van Bortel, Guy Hendrickx, Francis Schaffner, G. R. William Wint, Iqbal R. F. Elyazar, Hwa-Jen Teng & Simon I. Hay
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://dx.doi.org/10.7554/eLife.08347. Aedes aegypti and Ae. albopictus are the main vectors transmitting dengue and chikungunya viruses. Despite being pathogens of global public health importance, knowledge of their vectors’ global distribution remains patchy and sparse. A global geographic database of known occurrences of Ae. aegypti and Ae. albopictus between 1960 and 2014 was compiled. Herein we present the database, which comprises occurrence data linked...

Data from: Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies

Sarah W. Fitzpatrick, Jill C. Gerberich, Lisa M. Angeloni, Larissa L. Bailey, Emily Dale Broder, Julian Torres-Dowdall, Corey A. Handelsman, Andrés López-Sepulcre, David N. Reznick, Cameron K. Ghalambor & W. Chris Funk
Genetic rescue, an increase in population growth owing to the infusion of new alleles, can aid the persistence of small populations, but its use as a management tool is limited by a lack of empirical data geared towards predicting effects of gene flow on local adaptation and demography. Experimental translocations provide an ideal opportunity to monitor the demographic consequences of gene flow. In this study we take advantage of two experimental introductions of Trinidadian guppies...

Data from: The effects of agent hybridization on the efficacy of biological control of tansy ragwort at high elevations

Marianna Szucs, Patricia E. Salerno, Brittany J. Teller, Urs Schaffner, Jeffrey L. Littlefield & Ruth A. Hufbauer
The success rate of weed biological control programs is difficult to evaluate and the factors affecting it remain poorly understood. One aspect which is still unclear is whether releases of multiple, genetically distinct populations of a biological control agent increase the likelihood of success, either by independent colonization of different environmental niches or by hybridization that may increase the agent’s fitness and adaptive ability. Since hybridization is often invoked to explain the success of unintentionally...

Data from: Host species, pathogens, and disease associated with divergent nasal microbial communities in tortoises

Chava L. Weitzman, Franziska C. Sandmeier & C. Richard Tracy
Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with...

Data from: CO-RIP: a riparian vegetation and corridor extent dataset for Colorado River Basin streams and rivers

Brian D. Woodward, Paul H. Evangelista, Nicholas E. Young, Anthony G. Vorster, Amanda M. West, Sarah L. Carroll, Rebecca K. Girma, Emma Zink Hatcher, Ryan Anderson, Megan L. Vahsen, Amandeep Vashisht, Timothy Mayer, Daniel Carver & Catherine Jarnevich
Here we present “CO-RIP”, a novel spatial dataset delineating riparian corridors and riparian vegetation along large streams and rivers in the United States (U.S.) portion of the Colorado River Basin. The consistent delineation of riparian areas across large areas using remote sensing has been a historically complicated process partially due to differing definitions in the scientific and management communities regarding what a “riparian corridor” or “riparian vegetation” represents. We use valley-bottoms to define the riparian...

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Data from: Within-species tradeoffs in plant-stimulated soil enzyme activity and growth, flowering and seed size

Courtney E. Gomola, John K. McKay, Matthew D. Wallenstein, Cameron Wagg & Michael J. O'Brien
1. Soil microbial communities affect species demographic rates of plants. In turn, plants influence the composition and function of the soil microbiome, potentially resulting in beneficial feedbacks that alter their fitness and establishment. For example, differences in the ability to stimulate soil enzyme activity among plant lineages may affect plant growth and reproduction. 2. We used a common garden study to test differences in plant-stimulated soil enzyme activity between lineages of the same species across...

Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research

Nicholas E. Young, William H. Romme, Paul H. Evangelista, Tefera Mengistu & Asrat Worede
The greatest extent of Afromontane environments in the world is found in Ethiopia. These areas support exceptional biodiversity, but forest cover and ecological integrity have declined sharply in recent decades. Conservation and management efforts are hampered in part by an inadequate understanding of the basic ecology of major tree species. We investigated population structure and inferred population dynamics from size frequency distributions of 22 forest tree species encountered in montane forests of Ethiopia. We collected...

Delimitation despite discordance: evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

Thomas Firneno, Justin O'Neill, Michael Itgen, Timothy Kihneman, Josiah Townsend & Matthew Fujita
The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g. cryptic species), differences in criteria of species concepts, and discordance between gene topologies (e.g. mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to...

Pupil and masking responses to light as functional measures of retinal degeneration in mice Mus Musculus

Stewart Thompson, Ethan Contreras, Carley Dearing, Crystal Ashinhurst, Betty Fish, Sajila Hossain, Ariana Rey & Primal Silva
Background: Pre-clinical testing of retinal pathology and treatment efficacy depends on reliable and valid measures of retinal function. The electroretinogram (ERG) and tests of visual acuity are the ideal standard, but can be unmeasurable while useful vision remains. Non-image-forming responses to light such as the pupillary light reflex (PLR) are attractive surrogates. However, it is not clear how accurately such responses reflect changes in visual capability in specific disease models. The purpose of this study...

Data from: Climate change increases predation risk for a keystone species of the boreal forest

Michael Peers, Yasmine Majchrzak, Allyson Menzies, Emily Studd, Guillaume Bastille-Rousseau, Rudy Boonstra, Murray Humphries, Thomas Jung, Alice Kenney, Charles Krebs, Dennis Murray & Stan Boutin
Canada lynx (Lynx canadensis) and snowshoe hares (Lepus americanus) form a keystone predator-prey cycle that has large impacts on the North-American boreal forest vertebrate community. Snowshoe hares and lynx are both well-suited for snowy winters, but climate change associated shifts in snow conditions could lower hare survival and alter cyclic dynamics. Using detailed monitoring of snowshoe hare cause-specific mortality, behaviour, and prevailing weather, we demonstrate that hare mortality risk is strongly influenced by variation in...

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  • Colorado State University
  • University of Wyoming
  • United States Geological Survey
  • University of California, Davis
  • United States Department of Agriculture
  • National Park Service
  • University of Colorado Boulder
  • University of Minnesota
  • University of Tasmania
  • Cornell University