101 Works

High-Resolution Analog of Time-Domain Phonon Spectroscopy in the TEM Experimental Data and Analysis 2019-2020

Elisah J VandenBussche & David J. Flannigan
The behavior of coherent acoustic phonons (CAPs) as they propagate through a material is a function of the material’s optoelectronic and structural properties, making these collective oscillations a multi-faceted characterization tool. While CAPs are usually detected using transient reflectivity measurements, they have also previously been observed directly in real space using ultrafast electron microscopy (UEM). Here, we report use of UEM to measure localized CAP behavior in an amorphized and annealed GaAs specimen, and demonstrate...

Crossing extreme habitat boundaries: Jack-of-all-trades facilitates invasion but is eroded by adaptation to a master-of-one

Terry Ord & Peter Hundt
1. The invasion of new environments can be a key instigator of adaptive diversification, but the likelihood of such invasions succeeding can depend on the attributes of would-be invaders. Chief among these seems to be a generalist or ‘jack-off-all-trades’ phenotype. 2. Yet, despite the obvious link between habitat transitions and adaptation, we know surprisingly little about how phenotypes that might initially allow taxa to transition between habitats subsequently evolve or influence post-invasion differentiation. 3. We...

Experimental alluvial-river and landsliding response to base-level fall

Andrew D. Wickert, Olivia P Beaulieu, Elizabeth D Witte & Stefanie Tofelde
We observed the incisional response of an alluvial river to base-level fall. We conducted the experiment in a 3.9 × 2.4 × 0.4 m box that we filled with uniform 0.140±0.04 mm sand. We dropped base level by lowering the elevation of an "ocean" pool at the river outlet. As the initial condition, we cut a 10±2 cm wide channel to a steadily increasing depth, from 3±0.5 cm at the inlet, where we supplied water...

Fortran code for modeling the propagation of ULF waves in a 3-dimensional dipole magnetosphere

Robert L Lysak, Colin Waters & Murray Sciffer
This code allows for the modeling of Ultra-Low-Frequency (ULF) waves in the Earth's magnetosphere. It has been used in a number of publications and presentations at conferences. It takes a prescribed driver in the form of a compression at the outer boundary and follows the propagation of the waves through the magnetosphere and to the ground. The output consists of files each containing snapshots of one component of the electromagnetic field at all points in...

Isolation of Infectious SARS-CoV-2 from Urine of a COVID-19 Patient

Jing Sun, Airu Zhu, Heying Li, Kui Zheng, Zhen Zhuang, Zhao Chen, Yongxia Shi, Zhaoyong Zhang, Si-bei Chen, Xuesong Liu, Jun Dai, Xiaobo Li, Shuxiang Huang, Xiaofang Huang, Ling Luo, Liyan Wen, Jianfen Zhuo, Yuming Li, Yanqun Wang, Lu Zhang, Yanjun Zhang, Fang Li, Liqiang Feng, Xinwen Chen, Nanshan Zhong … & Yi-min Li
SARS-CoV-2 caused a major outbreak of severe pneumonia (COVID-19) in humans. Viral RNA was detected in multiple organs in COVID-19 patients. However, infectious SARS-CoV-2 was only isolated from respiratory specimens. Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. The virus isolated could infect new susceptible cells and was recognized by its’ own patient sera. Appropriate precautions should be taken to avoid transmission from urine.

Data from: Group density, disease, and season shape territory size and overlap of social carnivores

Ellen Brandell, Nicholas Fountain-Jones, Marie Gilbertson, Paul Cross, Peter Hudson, Douglas Smith, Daniel Stahler, Craig Packer & Meggan Craft
1. The spatial organization of a population can influence the spread of information, behaviour, and pathogens. Territory size and territory overlap, components of spatial organization, provide key information as these metrics may be indicators of habitat quality, resource dispersion, contact rates, and environmental risk (e.g., indirectly transmitted pathogens). Furthermore, sociality and behaviour can also shape space use, and subsequently, how space use and habitat quality together impact demography. 2. Our study aims to identify factors...

Development of an automatic integrated gene detection system for novel severe acute respiratory syndrome-related coronavirus (SARS-CoV2)

Yuchang Li, Jing Li, Ying Zhang, Lizhong Dai, Lin Li, Juan Liu, Sen Zhang, Xiaoyan Wu, Yi Hu, Chenfeng Qin, Tao Jiang & Xiaoping Kang
In December 2019, Wuhan, China suffered a serious outbreak of a novel coronavirus infectious disease (COVID) caused by novel severe acute respiratory syndrome-related coronavirus (SARS-CoV 2). To quickly identify the pathogen, we designed and screened primer sets, and established a sensitive and specific qRT-PCR assay for SARS-CoV 2; the lower limit of detection (LOD) was 14.8 (95% CI: 9.8–21) copies per reaction. We combined this qRT-PCR assay with an automatic integration system for nucleic acid...

Data and code from: Vector demography, dispersal, and the spread of disease: Experimental epidemics under elevated resource supply

Alexander Strauss, Jeremiah Henning, Anita Porath-Krause, Ashley Asmus, Allison Shaw, Elizabeth Borer & Eric Seabloom
1. The spread of many diseases depends on the demography and dispersal of arthropod vectors. Classic epidemiological theory typically ignores vector dynamics and instead makes the simplifying assumption of frequency-dependent transmission. Yet vector ecology may be critical for understanding the spread of disease over space and time and how disease dynamics respond to environmental change. 2. Here, we ask how environmental change shapes vector demography and dispersal, and how these traits of vectors govern the...

Biogeographic differences in plant-soil biota relationships contribute to the invasion exotic range expansion of Verbascum thapsus

Julia Dieskau, Helge Bruelheide, Alexandra Erfmeier & Jessica Gutknecht
Exotic plant species can evolve adaptations to environmental conditions in the exotic range. Furthermore, soil biota can foster exotic spread in the absence of negative soil pathogen-plant interactions or because of increased positive soil biota-plant feedbacks in the exotic range. Little is known, however, about the evolutionary dimension of plant-soil biota interactions when comparing native and introduced ranges. To assess the role of soil microbes for rapid evolution in plant invasion, we subjected Verbascum thapsus,...

Infection state can affect host migratory decisions

Naven Narayanan Venkatanarayanan, Allison K. Shaw & Sandra Ann Binning
Organisms across a wide range of taxa use migration as a strategy to avoid, reduce or recover from parasitic infection. Previous work has identified three different processes by which migration can help reduce infection risk and/or costs: migratory escape from infection, migratory culling of infected individuals, and migratory recovery from infection. However, most theoretical modelling of host migration in response to infection assumes that individuals have a single strategy during both infected and susceptible states,...

An effect size statistical framework for investigating sexual dimorphism in non-avian dinosaurs and other extinct taxa

Evan Saitta, Maximilian Stockdale, Nicholas Longrich, Vincent Bonhomme, Michael Benton, Innes Cuthill & Peter Makovicky
Despite reports of sexual dimorphism in extinct taxa, such claims in non-avian dinosaurs have been underrepresented recently (~the last decade) and often criticized. Since dimorphism is widespread in sexually reproducing organisms today, underrepresentation might suggest either methodological shortcomings or that this diverse group exhibited highly unusual reproductive biology. Univariate significance testing, especially for bimodality, is ineffective and prone to false negatives. Species recognition and mutual sexual selection hypotheses, therefore, may not be required to explain...

Data for: Lava crickets (Caconemobius spp.) on Hawai´i Island: first colonizers or persisters in extreme habitats?

Justa Heinen-Kay, John Rotenberry, Adam Kay & Marlene Zuk
1. Primary succession after a volcanic eruption is a major ecological process, but relatively little is known about insects that colonize barren lava before plants become established. 2. On Hawai´i Island, the endemic cricket, Caconemobius fori Gurney & Rentz, 1978, is known as the first multicellular life form to colonize lava after an eruption from Kīlauea Volcano. In the Kona region, a congener, Caconemobius anahulu Otte,1994 inhabits unvegetated lava flows from Hualālai Volcano, but little...

Data from: Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

Brendan Epstein & Peter Tiffin
Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit, and symbiont fitness), we conducted comparative genomic and selection analyses of the full genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among...

PMC Turbo image and lidar data taken in July 2018, supplement to Geach et al. (2020) \"Gravity Wave and Vortex Ring Formation Observed by PMC Turbo\"

Christopher P Geach
These datasets are published in accordance with AGU requirements for journal submission.

Data from: Using large-scale tropical dry forest restoration to test successional theory

Leland Werden, Erick Calderón-Morales, Pedro Alvarado J., Derek Nedveck, Jennifer Powers & Milena Gutiérrez L.
Microclimatic conditions change dramatically as forests age and impose strong filters on community assembly during succession. Light availability is the most limiting environmental factor in tropical wet forest succession; by contrast, water availability is predicted to strongly influence tropical dry forest (TDF) successional dynamics. While mechanisms underlying TDF successional trajectories are not well understood, observational studies have demonstrated that TDF communities transition from being dominated by species with conservative traits to species with acquisitive traits,...

Repeated fire shifts carbon and nitrogen cycling by changing plant inputs and soil decomposition across ecosystems

Adam Francis Pellegrini, Sarah Hobbie, Peter Reich, Ari Jumpponen, Jack Brookshire, Anthony Caprio, Corli Coetsee & Robert Jackson
Fires shape the biogeochemistry and functioning of many ecosystems, and fire frequencies are changing across much of the globe. Frequent fires can change soil carbon (C) and nitrogen (N) storage by altering the quantity and chemistry of plant inputs through changes in plant biomass and composition as well as altering decomposition of soil organic matter. How decomposition rates change with shifting inputs remains uncertain because most studies focus on the effects of single fires, where...

Dominant native and non-native graminoids differ in key leaf traits irrespective of nutrient availability

Arthur Broadbent, Jennifer Firn, James McGree, Elizabeth Borer, Yvonne Buckley, W. Stanley Harpole, Kimberly Komatsu, Andrew MacDougall, Kate Orwin, Nicholas Ostle, Eric Seabloom, Jonathan Bakker, Lori Biedermann, Maria Caldeira, Nico Eisenhauer, Nicole Hagenah, Yann Hautier, Joslin Moore, Carla Nogueira, Pablo Peri, Anita Risch, Christiane Roscher, Martin Schuetz & Carly Stevens
Aim Nutrient enrichment is associated with plant invasions and biodiversity loss. Functional trait advantages may predict the ascendancy of invasive plants following nutrient enrichment but this is rarely tested. Here, we investigate 1) whether dominant native and non-native plants differ in important morphological and physiological leaf traits, 2) how their traits respond to nutrient addition, and 3) whether responses are consistent across functional groups. Location Australia, Europe, North America and South Africa Time period 2007...

Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

Diego F. Morales-Briones, Gudrun Kadereit, Delphine Tefarikis, Michael Moore, Stephen Smith, Samuel Brockington, Alfonso Timoneda, Won Yim, John Cushman & Ya Yang
Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we...

The evolution of sex is tempered by costly hybridization in Boechera (rock cress)

Catherine Rushworth & Tom Mitchell-Olds
Despite decades of research, the evolution of sex remains an enigma in evolutionary biology. Typically, research addresses the costs of sex and asexuality to characterize the circumstances favoring one reproductive mode. Surprisingly few studies address the influence of common traits that are, in many organisms, obligately correlated with asexuality, including hybridization and polyploidy. These traits have substantial impacts on traits under selection. In particular, the fitness consequences of hybridization (that is, reduced fitness due to...

Supporting data for: Numerical Study of Near-Surface Jet in the Atmospheric Surface Layer over Oceanic Fronts

Bingqing Deng, Ming-Xiang Zhao, Qing Wang & Lian Shen
Simulation data used for figures in "Numerical study of near-surface jet in the atmospheric surface layer over oceanic fronts" including the mean velocity profiles, the turbulent variance profiles, the vortex structures, the streamwise momentum flux, the surface shear stress, and the local gradient Richardson number, etc. The data was generated and written by our in-house codes. Its format matches the requirement of the software Tecplot, and hence users can open the data using Tecplot.

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation

Donald Shepard, Samuel Weaver & Kenneth Kozak
Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification and the accumulation of species diversity among clades. However, why the climatic niche evolves more rapidly in some lineages than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in...

Data from: Trait plasticity alters the range of possible coexistence conditions in a competition-colonization trade-off

Ranjan Muthukrishnan, Lauren L. Sullivan, Allison Shaw & James Forester
Most of the classical theory on species coexistence has been based on species-level competitive trade-offs. However, it is becoming apparent that plant species display high levels of trait plasticity. The implications of this plasticity are almost completely unknown for most coexistence theory. Here, we model a competition-colonization trade-off and incorporate trait plasticity to evaluate its effects on coexistence. Our simulations show that the classic competition-colonization trade-off is highly sensitive to environmental circumstances and coexistence only...

Data from: Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19

Allison Shaw, Lauren White, Matthew Michalska-Smith, Elizabeth Borer, Meggan Craft, Eric Seabloom, Emilie Snell-Rood & Michael Travisano
Human behavior (movement, social contacts) plays a central role in the spread of pathogens like SARS-CoV-2. The rapid spread of SARS-CoV-2 was driven by global human movement, and initial lockdown measures aimed to localize movement and contact in order to slow spread. Thus, movement and contact patterns need to be explicitly considered when making reopening decisions, especially regarding return to work. Here, as a case study, we consider the initial stages of resuming research at...

Data from: Evolutionary patterns in the geographic range size of Atlantic Forest plants

Tarciso Leão, Eimear Nic Lughadha & Peter Reich
Species’ geographic range size is arguably the single most important predictor of vulnerability to extinction and a key metric in ecology. Despite this, patterns of specific variation in range size and their underlying reasons are still poorly understood. For example, hypotheses on how evolutionary history affects range size have scarcely been tested. To address these questions, we focused on Brazil’s Atlantic Forest flora, one of the most species-rich in the world, relatively well-known and highly...

Data from: Montane regions shape patterns of diversification in small mammals and reptiles from Madagascar’s moist evergreen forest

Kathryn Everson, Sharon Jansa, Steven Goodman & Link Olson
Aim Madagascar is renowned for its exceptional species diversity and endemism. The island’s mountainous regions are thought to have played a role in lineage and species diversification, but this has yet to be explored across taxonomic groups and a temporal context has not yet been identified. We tested whether montane regions have promoted population divergence in Madagascar’s vertebrate fauna and, if so, whether these divergence events were contemporaneous. Location Moist evergreen forests of Madagascar. Taxa...

Registration Year

  • 2020

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  • University of Minnesota
  • Zhejiang University
  • Fudan University
  • Sichuan University
  • Southern Medical University
  • Shanghai Jiao Tong University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Chinese Academy of Sciences
  • West China Hospital of Sichuan University
  • Jiangxi Agricultural University