42 Works

Data from: Canopy tree preference by insectivorous birds in shade-coffee farms: implications for migratory bird conservation

Desirée L. Narango, Douglas W. Tallamy, Kerry J. Snyder & Robert A. Rice
Land converted to coffee agriculture occupies >5 million hectares of what was once prime overwintering natural habitat in the American Neotropics for migrating birds. When tree canopy is retained or restored (i.e. shade-grown), coffee farms can serve as habitat refuge for wildlife. Yet few studies have examined whether canopy tree identity impacts habitat quality for biodiversity. Specifically, whether or not certain tree species are disproportionately important for foraging insectivorous birds remains unclear. In this study,...

Invasive grass (Microstegium vimineum) indirectly benefits spider community by subsidizing available prey

Andrew Landsman, Karin Burghardt & Jacob Bowman
1. Invasive plant species cause a suite of direct, negative ecological impacts, but subsequent, indirect effects are more complex and difficult to detect. Where identified, indirect effects to other taxa can be wide-ranging and include ecological benefits in certain habitats or locations. 2. Here, we simultaneously examine the direct and indirect effects of a common, invasive grass species (Microstegium vimineum) on the invertebrate communities of understory deciduous forests in the eastern United States. To do...

A Metric for Differential Chromatic Refraction in the Context of the Legacy Survey of Space and Time

Weixiang Yu, Gordon Richards, Peter Yoachim & Christina Peters
We provide a code repository for computing a metric to investigate how measurements of differential chromatic refraction might influence choices for survey strategy in the Rubin Observatory Legacy Survey of Space and Time.

Improved household living standards can restore dry tropical forests

Ruth DeFries, Meghna Agarwala, Sandra Baquie, Pooja Choksi, Sarika Khanwilkar, Pinki Mondal, Harini Nagendra & Johannes Uperlainen.
Despite multiple approaches over the last several decades to harmonize conservation and development goals in the tropics, forest-depende­­­­­­nt households remain the poorest in the world. Durable housing and alternatives to fuelwood for cooking are critical needs to reduce multi-dimensional poverty. These improvements also potentially reduce pressure on forests and alleviate forest degradation. We test this possibility in dry tropical forests of the Central Indian Highlands where tribal and other marginalized populations rely on forests for...

Evasion of plant innate defense response by Salmonella on Lettuce

Nicholas Johnson, Harsh Bais, Kalmia Kniel & Pushpinder Kaur Litt
To establish host association, the innate immune system, which is one of the first lines of defense against infectious disease, must be circumvented. Plants encounter enteric foodborne bacterial pathogens under both pre- and post-harvest conditions. Human enteric foodborne pathogens can use plants as temporary hosts. This unique interaction may result in recalls and illness outbreaks associated with raw agricultural commodities. The purpose of this study was to determine if Salmonella enterica Typhimurium applied to lettuce...

Data from: Artificial light at night confounds broad-scale habitat use by migrating birds

James D. McLaren, Jeffrey J. Buler, Tim Schreckengost, Jaclyn A. Smolinsky, Matthew Boone, E. Emiel Van Loon, Deanna K. Dawson & Eric L. Walters
With many of the world's migratory bird populations in alarming decline, broad-scale assessments of responses to migratory hazards may prove crucial to successful conservation efforts. Most birds migrate at night through increasingly light-polluted skies. Bright light sources can attract airborne migrants and lead to collisions with structures, but might also influence selection of migratory stopover habitat and thereby acquisition of food resources. We demonstrate, using multi-year weather radar measurements of nocturnal migrants across the northeastern...

Data from: Hallauer's Tusón: a decade of selection for tropical- to-temperate phenological adaptation in maize

Juliana E. C. Teixeira, Teclemariam Weldekidan, Natalia De Leon, Sherry Flint-Garcia, James B. Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, David A. Hessel, Adrienne E. Kleintop, James A. Hawk, Arnel R. Hallauer & Randall J. Wisser
Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single...

Data from: Recalibrating timing behavior via expected covariance between temporal cues

Benjamin J. De Corte, Rebecca R. Della Valle & Matthew S. Matell
Individuals must predict future events to proactively guide their behavior. Predicting when events will occur is a critical component of these expectations. Temporal expectations are often generated based on individual cue-duration relationships. However, the durations associated with different environmental cues will often co-vary due to a common cause. We show that timing behavior may be calibrated based on this expected covariance, which we refer to as the 'common cause hypothesis'. In five experiments using rats,...

Retreat of Humboldt Gletscher, North Greenland, driven by undercutting from a warmer ocean

Eric Rignot, Lu An, Nolwenn Chauché, Mathieu Morlighem, Seongsu Jeong, Michael Wood, Jeremie Mouginot, Joshua Willis, Ingo Klaucke, Wilhelm Weinrebe & Andreas Muenchow
Humboldt Gletscher is a 100-km wide, slow-moving glacier in north Greenland which holds a 19-cm global sea level equivalent. Humboldt has been the fourth largest contributor to sea level rise since 1972 but the cause of its mass loss has not been elucidated. Multi-beam echo sounding data collected in 2019 indicate a seabed 200 m deeper than previously known. Conductivity temperature depth (CTD) data reveal the presence of warm water of Atlantic origin at 0°C...

PrioritEvac: An Agent-Based Model of Evacuation from Building Fires

Eileen Young
This simulation is of the 2003 Station Nightclub Fire and is part of the Interdependencies in Community Resilience (ICoR) project (http://www-personal.umich.edu/~eltawil/icor.html). The git contains the simulation as well as csvs of data about the fire, smoke, building, and people involved.

Additional material associated with the Matters Arising article published in Nature by Munday and colleagues

Philip Munday, Danielle Dixson, Megan Welch, Douglas Chivers, Paolo Domenici, Martin Grosell, Rachel Heuer, Geoffrey Jones, Mark McCormick, Mark Meekan, Göran Nilsson, Timothy Ravasi & Sue-Ann Watson

Data from: The genomic basis for short-term evolution of environmental adaptation in maize

Randall Wisser
Quality control genotype data (45,718 variant sites) for samples from Hallauer's Tusón. Tab delimited file. A header row is included. The first column ("label") lists sample names, the second column ("popdata") lists the generation to which each sample belongs, and the remaining columns correspond to the genotype data. Unphased diploid genotype calls are recorded in the following format: 1/1. Variant encoding: 1=A, 2=C, 3=G, 4=T, 5=deletion, 6=insertion (5 and 6 are used for the ZmCCT10_CACTA...

Data from: Shark movement strategies influence poaching risk and can guide enforcement decisions in a large, remote Marine Protected Area

David Jacoby, Francesco Ferretti, Robin Freeman, Aaron Carlisle, Taylor Chapple, David Curnick, Jonathan Dale, Robert Schallert, David Tickler & Barbara Block
Large, remote marine protected areas (MPAs) containing both reef and pelagic habitats, have been shown to offer considerable refuge to populations of reef-associated sharks. Many large MPAs are, however, impacted by illegal fishing activity conducted by unlicensed vessels. While enforcement of these reserves is often expensive, it would likely benefit from the integration of ecological data on the mobile animals they are designed to protect. Consequently, shark populations in some protected areas continue to decline,...

Data from: Acidification and γ-aminobutyric acid independently alter kairomone-induced behaviour

Corie L. Charpentier & Jonathan H. Cohen
Exposure to high pCO2 or low pH alters sensation and behaviour in many marine animals. We show that crab larvae lose their ability to detect and/or process predator kairomones after exposure to low pH over a time scale relevant to diel pH cycles in coastal environments. Previous work suggests that acidification affects sensation and behaviour through altered neural function, specifically the action of γ-aminobutyric acid (GABA), because a GABA antagonist, gabazine, restores the original behaviour....

Haemosporidian parasites of Neotropical birds: causes and consequences of infection

Vincenzo A. Ellis, Alan Fecchio & Robert E. Ricklefs
Haemosporidian parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon are among the best studied parasites of Neotropical birds. Here, we describe variation in haemosporidian prevalence (i.e., the proportion of infected birds in a sampled population) in Neotropical birds. We review correlates of haemosporidian prevalence (including several avian life-history traits, climate, and season) and the population and evolutionary consequences of infection for Neotropical birds. We find that prevalence varies among avian taxonomic families, genera, and even...

Data from: Post‐independence mortality of juveniles is driven by anthropogenic hazards for two passerines in an urban landscape

Solny A. Adalsteinsson, Jeffrey J. Buler, Jacob L. Bowman, Vincent D'Amico, Zachary S. Ladin & W. Gregory Shriver
Urban environments impose novel selection pressures with varying impacts across species and life history stages. The post‐fledging stage for migratory passerines, defined as the period of time from when hatch‐year birds fledge until their first migration, is a poorly understood component of annual productivity that potentially limits population growth. We studied two migratory passerines with positive and negative population responses to urbanization, respectively: Gray Catbird (Dumetella carolinensis) and Wood Thrush (Hylocichla mustelina). Our goals were...

Data and numerical methods for determining the dynamics and kinematics of Newark Bay, NJ

W. Bryce Corlett, W. Rockwell Geyer, Robert Chant, David Ralston & Christopher K. Sommerfield
These observational data and numerical methods were used to investigate the subtidal salt balance of Newark Bay, a sub-estuarine network connected to the Hudson River estuary through New York Harbor. The moored data were collected in 2008 by Chant and Sommerfield, and in 2016 by Corlett, Geyer, and Ralston. Corlett devised the included numerical methods. Shipboard measurements of the vertical salinity profile near each mooring were used to reconstruct the tidally-varying vertical salinity profile from...

Data from: A connection between colony biomass and death in Caribbean reef-building corals

Daniel J. Thornhill, Randi D. Rotjan, Brian D. Todd, Geoff C. Chilcoat, Roberto Iglesias-Prieto, Todd C. LaJeunesse, Dustin W. Kemp, Jennifer McCabe Reynolds, Gregory W. Schmidt, Thomas Shannon, Mark E. Warner & William K. Fitt
Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994–2007), eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in Puerto Morelos, Mexico (2003–2007). For...

Data from: Geographic variation in Megalorchestia californiana allele frequencies may be caused by winter rather than summer temperatures

John H. McDonald & JH McDonald
There are many allozyme polymorphisms with latitudinal clines, for which selection by climate is one obvious explanation. Both warm summer temperatures and cold winter temperatures could plausibly impose selection on enzyme polymorphisms, but because summer and winter temperatures are usually geographically correlated, there has been little attempt to use patterns of geographic variation to discriminate between these possible selective factors. The glucose-6-phosphate isomerase and mannose-6-phosphate isomerase allozyme polymorphisms in the amphipod crustacean Megalorchestia californiana have...

Data from: Predator-guided sampling reveals biotic structure in the bathypelagic

Kelly J. Benoit-Bird, Brandon L. Southall & Mark A. Moline
We targeted habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey’s distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was...

Data from: Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata)

Barbara-Anne Battelle, Joseph F. Ryan, Karen E. Kempler, Spencer R. Saraf, Catherine E. Marten, Wesley C. Warren, Patrick Minx, Michael J. Montague, Pamela J. Green, Skye A. Schmidt, Lucinda Fulton, Nipam H. Patel, Merideth E. Protas, Richard K. Wilson & Megan L. Porter
Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of...

Data from: Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Jennifer Walsh, W. Gregory Shriver, Brian J. Olsen & Adrienne I. Kovach
Background: Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of...

Data from: Soaring across continents: decision-making of a soaring migrant under changing atmospheric conditions along an entire flyway

Wouter Vansteelant, Judy Shamoun-Baranes, James D. McLaren, Jan Van Diermen, Willem Bouten, Wouter M. G. Vansteelant & James McLaren
(1) Thermal soaring birds reduce flight-energy costs by alternatingly gaining altitude in thermals and gliding across the earth’s surface. To find out how soaring migrants adjust their flight behaviour to dynamic atmospheric conditions across entire migration routes, we combined optimal soaring migration theory with high-resolution GPS tracking data of migrating Honey Buzzards Pernis apivorus and wind data from a global numerical atmospheric model. (2) We compared measurements of gliding air speeds to predictions based on...

Data from: Effects of cell-cycle-dependent expression on random fluctuations in protein levels

Mohammad Soltani & Abhyudai Singh
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We analyse a model where a stable protein is synthesized in random bursts, and the frequency with which bursts occur varies within the cell cycle. Formulae quantifying the extent of fluctuations in the protein copy number are derived and decomposed into...

Data from: Biodiverse cities: the nursery industry, homeowners, and neighborhood differences drive urban tree composition

Meghan Avolio, Diane Pataki, Tara Trammell, Joanna Endter-Wada, Meghan L. Avolio, Diane E. Pataki & Tara L. E. Trammell
In arid and semi-arid regions, where few if any trees are native, city trees are largely human-planted. Societal factors such as resident preferences for tree traits, nursery offerings, and neighborhood characteristics are potentially key drivers of urban tree community composition and diversity, however they remain critically understudied. We investigated patterns of urban tree structure in residential neighborhoods of the Salt Lake Valley, Utah, combining biological variables, such as neighborhood and plant nursery tree species and...

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