63 Works

Supplementary information for: Using networks to identify structure in phylogenetic tree sets

Jeremy Brown, Melissa Marchand, Wen Huang, Guifang Zhou, Genevieve Mount, Jeremy Ash, Kyle Gallivan & James Wilgenbusch
Modern phylogenomic studies produce large sets of trees that can represent variation in inferred phylogenies across genes, uncertainty in estimated phylogenies for a given gene, or both. Standard practice is to condense this variation down to a small set of point estimates or consensus trees in order to facilitate display and interpretation. However, doing so results in the loss of enormous amounts of information about the structure of the underlying tree set. Here, we propose...

Supplement to: Hippocampal neurochemical profile and glucose transport kinetics in patients with type 1 diabetes

Petr Bednařík, Pierre Gilles Henry, Ameer Khowaja, Nathan Rubin, Anjali Kumar, Dinesh Deelchand, Lynn Eberly, Elizabeth Seaquist, Gülin Öz & Moheet Amir
Context Longstanding type 1 diabetes (T1D) may lead to alterations in hippocampal neurochemical profile. Upregulation of hippocampal glucose transport as a result of recurrent exposure to hypoglycemia may preserve cognitive function during future hypoglycemia in subjects with T1D and impaired awareness of hypoglycemia (IAH). The effect of T1D on hippocampal neurochemical profile and glucose transport is unknown. Objective To test the hypothesis that hippocampal neurochemical composition is altered in T1D and glucose transport is upregulated...

Wolves choose ambushing locations to counter and capitalize on the sensory abilities of their prey

Thomas Gable, Austin Homkes, Sean Johnson-Bice, Steve Windels & Joseph Bump
Wolves (Canis lupus) are primarily cursorial predators, but they use ambush strategies to hunt beavers (Castor canadensis). Terrestrial beaver activity is predictable because beavers use well-defined, conspicuous habitat features repeatedly. Thus, studying where wolves wait-in-ambush for beavers provides a unique opportunity to understand how predators choose ambush locations in relation to prey activity. We searched 11,817 clusters of GPS-locations from wolves in the Greater Voyageurs Ecosystem, Minnesota, USA and documented 748 ambushing sites and 214...

Data from Beyond MAP: A guide to dimensions of rainfall variability for tropical ecology

Naomi Schwartz, Benjamin R. Lintner, Xue Feng & Jennifer S. Powers
Tropical ecologists have long recognized rainfall as the key climate filter shaping tropical ecosystem structure and function across space and time. Still, tropical ecologists have historically had a limited toolkit for characterizing rainfall, largely relying on simple metrics like mean annual precipitation (MAP) and dry season length to characterize rainfall regimes that vary along many more dimensions. Here, we review methods for quantifying dimensions of rainfall variability on multiple time scales, with a focus on...

Data from: Treefrogs exploit temporal coherence to form perceptual objects of communication signals

Saumya Gupta & Mark A. Bee
For many animals, navigating their environment requires an ability to organize continuous streams of sensory input into discrete “perceptual objects” that correspond to physical entities in visual and auditory scenes. The human visual and auditory systems follow several Gestalt laws of perceptual organization to bind constituent features into coherent perceptual objects. A largely unexplored question is whether nonhuman animals follow similar Gestalt laws in perceiving behaviorally relevant stimuli, such as communication signals. We used females...

Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Alexandra Kaye Fraik, Mark Margres, Brendan Epstein, Soraia Barbosa, Menna Jones, Sarah Hendricks, Barbara Schonfeld, Amanda R. Stahlke, Anne Veillet, Rodrigo Hamede, Hamish McCallum, Elisa Lopez-Contreras, Samantha J Kallinen, Paul A Hohenlohe, Joanna Kelley & Andrew Storfer
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species’ extinction, suggesting possible adaptation to...

Data from: Honeybee microbiome is stabilized in the presence of propolis

Perot Saelao, Renata S. Borba, Vincent Ricigliano, Marla Spivak & Michael Simone-Finstrom
Honey bees have developed many unique mechanisms to help ensure the proper maintenance of homeostasis within the hive. One specific method includes the collection of antimicrobial plant resins and wax to form propolis, which is deposited throughout the hive. Propolis is believed to play a significant role in reducing disease load in the colony due to its antimicrobial and antiseptic properties. However, little is known on how propolis may be interacting with the commensal bacteria...

Artificial nightlight alters the predator-prey dynamics of an apex carnivore

Mark Ditmer, David Stoner, Clinton D. Francis, Jesse Barber, James Forester, David Choate, Kirsten Ironside, Kathleen Longshore, Kent Hersey, Randy Larsen, Brock McMillan, Daniel Olson, Alyson Andreasen, Jon Beckmann, Brandon Holton, Terry Messmer & Neil Carter
Artificial nightlight is increasingly recognized as an important environmental disturbance that influences the habitats and fitness of numerous species. However, its effects on wide-ranging vertebrates and their interactions remain unclear. Light pollution has the potential to amplify land-use change, and as such, answering the question of how this sensory stimulant affects behavior and habitat use of species valued for their ecological roles and economic impacts is critical for conservation and land-use planning. Here, we combined...

Grazing and climate change have site-dependent interactive effects on vegetation in Asian montane rangelands

Mayank Kohli, Tserennadmid Mijidorj, Kulbhushansingh Suryawanshi, Charudutt Mishra, Bazartseren Boldgiv & Mahesh Sankaran
1. Climate over Asian montane rangelands is changing faster than the global average, posing serious threats to the future of the region’s livestock-based economies and cultures. Effects of climate change on rangeland vegetation likely depend on grazing by herbivores but the potential responses of vegetation to such changes in climate and grazing regimes remains unclear. 2. We examined vegetation responses to experimentally simulated climate change (warming, drought and increased rainfall) and grazing (clipping vegetation) between...

Nitrate removal and N2O production from upflow and downflow column woodchip bioreactors

Gary Feyereisen, Kurt Spokas, Jeffrey Strock, David Mulla, Andry Ranaivoson & Jeffrey Coulter
Woodchip denitrifying bioreactors (WDBR) reduce off-field tile drainage nitrogen (N) losses from agricultural fields. Limited evaluation exists regarding the influence of flow direction through WDBRs. Changing flow direction could reduce short circuiting. This study evaluated the dependency of nitrate-nitrogen removal and dissolved nitrous oxide (dN2O) production rates on vertical flow direction in triplicate column bioreactors at 12-h (without carbon dosing) and 2-h (with carbon dosing) hydraulic residence times. Results presented demonstrate that there was no...

A catastrophic tropical drought kills hydraulically vulnerable tree species

Jennifer Powers, German Vargas-G, Timothy Brodribb, Naomi Schwartz, Daniel Perez-Aviles, Chris Smith-Martin, Justin Becknell, Filippo Aureli, Roger Blanco, Erick Calderón-Morales, Julio César Calvo-Alvarado, Ana Julieta Calvo-Obando, María Marta Chavarría, Dorian Carvajal-Vanegas, César Dionisio Jiménez-Rodríguez, Evin Murillo Chacon, Colleen Schaffner, Leland Werden, Xiangtao Xu & David Medvigy
Drought-related tree mortality is now a widespread phenomenon predicted to increase in magnitude with climate change. However, the patterns of which species and trees are most vulnerable to drought, and the underlying mechanisms have remained elusive, in part due to the lack of relevant data and difficulty of predicting the location of catastrophic drought years in advance. We used long‐term demographic records and extensive databases of functional traits and distribution patterns to understand the responses...

Weights of gaur (Bos gaurus) and banteng (Bos javanicus) killed by tigers in Thailand

Supawat Khaewphakdee, Achara Simcharoen, Somphot Duangchantrasiri, Vijak Chimchome, Saksit Simcharoen & James Smith
The primary prey of tigers across much of Southeast Asia has been depleted, reducing the ability of already limited habitat to support tigers. To better understand the extent to which two of the largest prey species, gaur (Bos gaurus) and banteng (Bos javanicus), contribute to the tiger’s diet, we estimated the average size of these species killed by tigers. This information is needed to more accurately calculate biomass of these species in the tiger’s diet...

Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chlorophonia finches (Passeriformes: Fringillidae)

Tyler Imfeld, Keith Barker & Robb Brumfield
Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to...

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...

Enhancing crop domestication through genomic selection, a case study of intermediate wheatgrass

Jared Crain, Prabin Bajgain, James Anderson, Xiaofei Zhang, Lee DeHaan & Jesse Poland
Perennial grains could simultaneously provide food for humans and a host of ecosystem services, including reduced erosion, minimized nitrate leaching, and increased carbon capture. Yet most of the world’s food and feed is supplied by annual grains. Efforts to domesticate intermediate wheatgrass (Thinopyrumn intermedium, IWG) as a perennial grain crop have been ongoing since the 1980’s. Currently, there are several breeding programs within North America and Europe working toward developing IWG into a viable crop....

Recovery from infection is more likely to favor the evolution of migration than social escape from infection

Allison Shaw & Sandra Binning
1. Pathogen and parasite infections are increasingly recognized as powerful drivers of animal movement, including migration. Yet, infection-related migration benefits can result from a combination of environmental and/or social conditions, which can be difficult to disentangle. 2. Here, we focus on two infection-related mechanisms that can favor migration: moving to escape versus recover from infection. By directly comparing the evolution of migration in response to each mechanism, we can evaluate the likely importance of changing...

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,...

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...

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...

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 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,...

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: Climate and local environment structure asynchrony and the stability of primary production in grasslands

Benjamin Gilbert, Andrew MacDougall, Taku Kadoya, Munemitsu Akasaka, Joseph Bennett, Eric Lind, Habacuc Flores-Moreno, Jennifer Firn, Yann Hautier, Elizabeth Borer, Eric Seabloom, Peter Adler, Elsa Cleland, James Grace, W. Harpole, Ellen Esch, Joslin Moore, Jean Knops, Rebecca McCulley, B. Mortensen, J. Bakker & Philip Fay
Aim: Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when decreased performance by some species is offset by increased performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species, reducing buffering. Local conditions, such as soil nutrients, can further alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling...

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...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Minnesota
  • University of Michigan-Ann Arbor
  • Field Museum of Natural History
  • University of Guelph
  • Agricultural Research Service
  • Harvard University
  • University of Washington
  • Stanford University
  • University of Pretoria
  • Utah State University