491 Works

Data from: Temporal scale-dependence of plant-pollinator networks

Benjamin Schwarz, Diego Vázquez, Paul CaraDonna, Tiffany Knight, Gita Benadi, Carsten Dormann, Benoit Gauzens, Elena Motivans, Julian Resasco, Nico Blüthgen, Laura Burkle, Qiang Fang, Christopher Kaiser-Bunbury, Ruben Alarcón, Justin Bain, Natacha Chacoff, Shuang-Quan Huang, Gretchen LeBuhn, Molly MacLeod, Theodora Petanidou, Claus Rasmussen, Michael Simanonok, Amibeth Thompson, Daniel Cariveau, Michael Roswell … & Jochen Fründ
The study of mutualistic interaction networks has led to valuable insights into ecological and evolutionary processes. However, our understanding of network structure may depend upon the temporal scale at which we sample and analyze network data. To date, we lack a comprehensive assessment of the temporal scale-dependence of network structure across a wide range of temporal scales and geographic locations. If network structure is temporally scale-dependent, networks constructed over different temporal scales may provide very...

An exotic herbivore reinforces competition between exotic and native plants

Yuzu Sakata & Timothy Craig
Despite increasing evidence that herbivore-mediated indirect effects play a major role in plant competition, it is unclear how and when they contribute to plant invasiveness. The outcomes of herbivore-mediated indirect effects are primarily dependent on the environment and have complex interactions with the direct interactions between plants. We evaluated the herbivore-mediated indirect effects of Solidago altissima (Asteraceae) on other co-occurring native Asteraceae species at multiple sites in a native range [the United States (US)] and...

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Ryan Campbell, George Tiley, Jelmer Poelstra, Kelsie Hunnicutt, Peter Larsen, Hui-Jie Lee, Jeffrey Thorne, Mario Dos Reis & Anne Yoder
Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage...

Wavenumber-space band clipping in nonlinear periodic structures

Weijian Jiao & Stefano Gonella
In weakly nonlinear systems, the main effect of cubic nonlinearity on wave propagation is an amplitude-dependent correction of the dispersion relation. This phenomenon can manifest either as a frequency shift or as a wavenumber shift depending on whether the excitation is prescribed as a initial condition or as a boundary condition, respectively. Several models have been proposed to capture the frequency shifts observed when the system is subjected to harmonic initial excitations. However, these models...

Sudden Unexpected Death in Epilepsy: A Personalized Prediction Tool

Ashwani Jha, Cheongeun Oh, Dale Hesdorffer, Beate Diehl, Sasha Devore, Martin Brodie, Torbjörn Tomson, Josemir W. Sander, Thaddeus S. Walczak & Orrin Devinsky
Objective: To develop and validate a tool for individualised prediction of Sudden Unexpected Death in Epilepsy (SUDEP) risk, we re-analysed data from one cohort and three case-control studies undertaken 1980-2005. Methods: We entered 1273 epilepsy cases (287 SUDEP, 986 controls) and 22 clinical predictor variables into a Bayesian logistic regression model. Results: Cross-validated individualized model predictions were superior to baseline models developed from only average population risk or from generalised tonic-clonic seizure frequency (pairwise difference...

Exotics are more complementary over time in tree biodiversity-ecosystem functioning experiments

Michael Belluau, Alain Paquette, Dominique Gravel, Peter Reich, Artur Stefanski & Christian Messier
Background and aims The Biodiversity – Ecosystem Functioning (BEF) literature proposes that ecosystem functioning increases with biodiversity because of complementarity in resource use among species, associated with functional diversity. In this study, we challenge the trait-based ecology framework by comparing congeneric exotic (European) and native (North American) tree species showing similar resource-use functional trait values. The trait-based framework suggests that two functionally equivalent species should play similar roles in a community, resulting in similar interactions...

Performance and refinement of nitrogen fertilization tools

Curtis Ransom, Jason Clark, Gregory Bean, Christopher Bandura, Matthew Shafer, Newell Kitchen, James Camberato, Paul Carter, Richard Ferguson, Fabián Fernández, David Franzen, Carrie Laboski, David Myers, Emerson Nafziger & John Sawyer
Improving corn (Zea mays L.) N management is pertinent to economic and environmental objectives. However, there are limited comprehensive data sources to develop and test N fertilizer decision aid tools across a wide geographic range of soil and weather scenarios. Therefore, a public-industry partnership was formed to conduct standardized corn N rate response field studies throughout the U.S. Midwest. This research was conducted using a standardized protocol at 49 site-years across eight states over the...

Data from: Consequences of aboveground invasion by non-native plants into restored vernal pools do not prompt changes in belowground processes

Amber Churchill & Akasha Faist
Given the frequent overlap between biological plant invasion and ecological restoration efforts it is important to investigate their interactions to sustain desirable plant communities and modify long-term legacies both above and belowground. To address this relationship, we used natural reference, invaded, and constructed vernal pools in the Central Valley of California to examine potential changes in direct and indirect plant effects on soils associated with biological invasion and active restoration ecosystem disturbances. Our results showed...

Aboveground carbon stocks and dynamics in Andean forests

Alvaro Duque, Miguel Peña, Francisco Cuesta, Sebastián González-Caro, Peter Kennedy, Oliver Phillips, Marco Calderón, Cecilia Blundo, Julieta Carilla, Leslie Cayola, William Farfán-Ríos, Alfredo Fuentes, Ricardo Grau, Jürgen Homeier, María I. Loza-Rivera, Jonathan A. Myers, Oriana Osinaga-Acosta, Manuel Peralvo, Esteban Pinto, Sassan Saatchi, Miles Silman, J. Sebastián Tello, Andrea Terán-Valdez & Kenneth J. Feeley
This dataset (Andean_AGB.xlsx) has the data employed in the paper entitled Old-growth Andean forests as globally important carbon sinks and future carbon refuges. The data was compiled as the results of the work of several research teams spread out across the Andean region. The information available here has data about aboveground carbon stocks and dynamics and the main explanatory variables, such as climate and symbiotic root associations.

Differences in bee community composition between restored and remnant prairies are more strongly linked to forb community differences than landscape differences

Ian Lane, Zachary Portman, Christina Herron-Sweet, Gabriella Pardee & Daniel Cariveau
1. Grassland restoration is an important tool for conserving bee biodiversity within agricultural landscapes. Restorations foster increases in local bee abundance and α-diversity, however, these measures are insufficient for understanding if remnant communities are being conserved. We compared native bee α-diversity, β-diversity, and community composition between restored and remnant prairies in Minnesota, USA. We then investigated two potential drivers of bee community dissimilarity between restored and remnant prairies: proportion of agricultural land surrounding a restoration...

Parasite intensity and the evolution of migratory behavior

Laurinne Balstad, Sandra Binning, Meggan Craft, Marlene Zuk & Allison Shaw
Migration can allow individuals to escape parasite infection, which can lead to a lower infection probability (prevalence) in a population and/or fewer parasites per individual (intensity). Since individuals with more parasites often have lower survival and/or fecundity, infection intensity shapes the life-history tradeoffs determining when migration is favored as a strategy to escape infection. Yet, most theory relies on susceptible-infected (SI) modeling frameworks, defining individuals as either healthy or infected, ignoring details of infection intensity....

PacBio sequencing output increased through uniform and directional 5-fold concatenation

Celia Blanco, Nisha Kanwar, Irene A. Chen & Burckhard Seelig
Advances in sequencing technology have allowed researchers to sequence DNA with greater ease and at decreasing costs. Main developments have focused on either sequencing many short sequences or fewer large sequences. Methods for sequencing mid-sized sequences of 600-5,000 bp are currently less efficient. For example, the PacBio Sequel I system yields ~100,000-300,000 reads with an accuracy per base pair of 90-99%. We sought to sequence several DNA populations of ~870 bp in length with a...

Ictal source imaging in epilepsy patients - Supplementary Data

Shuai Ye, Lin Yang, Yunfeng Lu, Michal Kucewicz, Benjamin Brinkmann, Cindy Nelson, Abbas Sohrabpour, Gregory Worrell & Bin He
Objective Localization of seizure onset zone in focal epilepsy patients is a crucial step prior to surgical planning. Noninvasively achieving this goal would have a tremendous impact on clinical management of intractable seizure. Methods In a total of 39 focal epilepsy patients, we recorded and extracted 138 seizures and 1,325 interictal epileptic discharges using high-density EEG. We have investigated a novel approach for directly imaging sources of seizures and interictal spikes from high density EEG...

SAM Filtering Pipeline (SFP): Algorithm for the determination of integration sites from next generation sequencing data

Sofie A O'Brien & Wei-Shou Hu
The locus at which a vector harboring a product transgene integrates into the genome can have a profound effect on the transgene’s transcript level and the stability of the resulting cell line. In order to identify integration site(s) of a transfected vector from next generation genome sequencing data, the SAM filtering pipeline (SFP) was created. It is best suited for targeted sequence data, such as that from sequence capture of probed vector regions. However, it...

Minnesota Solvation Database (MNSOL) version 2012

Aleksandr V Marenich, Casey P Kelly, Jason D Thompson, Gregory D Hawkins, Candy C Chambers, David J Giesen, Paul Winget, Christopher J Cramer & Donald G Truhlar
The Minnesota Solvation Database consists of a collection of 3037 experimental free energies of solvation or transfer free energies for 790 unique solutes in 92 solvents (including water) and gas-phase M06-2X/MG3S optimized molecular geometries in Cartesian coordinates for the corresponding solutes. All of the 790 solutes in this database (541 neutrals and 249 singly-charged ions) contain at most the following elements: H, C, N, O, F, Si, P, S, Cl, Br, and I.

R Code and Output Supporting: Resampling-Based Methods for Biologists

John Fieberg, Kelsy Vitense & Douglas H. Johnson

Data from: Zooming in on mechanistic predator-prey ecology: integrating camera traps with experimental methods to reveal the drivers of ecological interactions

Justine Smith, Justin Suraci, Jennifer Hunter, Kaitlyn Gaynor, Carson Keller, Meredith Palmer, Justine Atkins, Irene Castañeda, Michael Cherry, Patrick Garvey, Sarah Huebner, Dana Morin, Lisa Teckentrup, Martijn Weterings & Lydia Beaudrot
1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive...

Data from: Mixed-source reintroductions lead to outbreeding depression in second-generation descendents of a native North American fish

David D Huff, Loren M Miller, Christopher J Chizinski & Bruce Vondracek
Reintroductions are commonly employed to preserve intraspecific biodiversity in fragmented landscapes. However, reintroduced populations are frequently smaller and more geographically isolated than native populations. Mixing genetically divergent sources is often proposed to attenuate potentially low genetic diversity in reintroduced populations that may result from small effective population sizes. However, a possible negative tradeoff for mixing sources is outbreeding depression in hybrid offspring. We examined the consequences of mixed-source reintroductions on several fitness surrogates at nine...

Data from: Role of climate and competitors in limiting fitness across range edges of an annual plant

John Stanton-Geddes, Peter Tiffin & Ruth G. Shaw
It is often assumed that the geographic distributions of species match their climatic tolerances, but this assumption is not frequently tested. Moreover, few studies examine the relative importance of abiotic and biotic factors for limiting species ranges. We combined multiple approaches to assess the extent to which fitness of a widespread native annual legume, Chamaecrista fasciculata decreases at and beyond its northern and western range edges, and how this is influenced by the presence of...

Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)

Bryce A. Richardson, Justin T. Page, Prabin Bajgain, Stewart C. Sanderson & Joshua A. Udall
PREMISE OF THE STUDY: Hybridization has played an important role in the evolution and ecological adaptation in diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata ssp. wyomingensis, or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. METHODS: We used...

Data from: Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

Kabir G. Peay, Max G. Schubert, Nhu H. Nguyen & Thomas D. Bruns
Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts,...

Data from: Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

Lei Yang, M. Arunachalam, Tetsuya Sado, Boris A. Levin, Alexander S. Golubtsov, Jörg Freyhof, John P. Friel, Wei-Jen Chen, M. Vincent Hirt, Raja Manickam, Mary K. Agnew, Andrew M. Simons, Kenji Saitoh, Masaki Miya, Richard L. Mayden & Shunping He
The cyprinid tribe Labeonini (sensu Rainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and...

Data from: Sex determination meltdown upon biological control introduction of the parasitoid Cotesia rubecula?

Jetske G. De Boer, Bram Kuijper, George E. Heimpel & Leo W. Beukeboom
Natural enemies may go through genetic bottlenecks during the process of biological control introductions. Such bottlenecks are expected to be particularly detrimental in parasitoid Hymenoptera that exhibit complementary sex determination (CSD). CSD is associated with a severe form of inbreeding depression because homozygosity at one or multiple sex loci leads to the production of diploid males that are typically unviable or sterile. We observed that diploid males occur at a relatively high rate (8-13% of...

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Data from: The early diversification history of didelphid marsupials: a window into South America’s “Splendid Isolation”

Sharon A. Jansa, F. Keith Barker & Robert S. Voss
The geological record of South American mammals is spatially biased because productive fossil sites are concentrated at high latitudes. As a result, the history of mammalian diversification in Amazonia and other tropical biomes is largely unknown. Here we report diversification analyses based on a time-calibrated molecular phylogeny of opossums (Didelphidae), a species-rich clade of mostly tropical marsupials descended from a Late Oligocene common ancestor. Optimizations of habitat and geography on this phylogeny suggest that (1)...

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