339 Works

Data from: The maintenance of phenotypic divergence through sexual selection: an experimental study in barn swallows Hirundo rustica

Rebecca Safran, Yoni Vortman, Brittany R. Jenkins, Joanna K. Hubbard, Matthew R. Wilkins, Rachel J. Bradley & Arnon Lotem
Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait-associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage-based traits: ventral color and length of the outermost tail feathers (streamers). Here we...

Data from: A migratory divide spanning two continents is associated with genomic and ecological divergence

Sheela Turbek, Drew Schield, Elizabeth Scordato, Andrea Contina, Xin-Wei Da, Yang Liu, Yu Liu, Emilio Pagani-Núñez, Qing-Miao Ren, Chris Smith, Craig Stricker, Michael Wunder, David Zonana & Rebecca Safran
Migratory divides are contact zones between breeding populations with divergent migratory strategies during the non-breeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide...

Data from: Decoding the dynamics of dental distributions: insights from shark demography and dispersal

Sora Kim, Justin Yeakel, Juergen Kriwet, Meghan Balk, Jaelyn Eberle, Sarah Zeichner & Dina Fieman
Shark teeth are the most abundant vertebrate fossil, and because tooth size generally correlates with body size, their accumulations document the size structure of populations. Understanding how ecological and environmental processes influence size structure, and how this extends to influence these dental distributions, may offer a window into the ecological and environmental dynamics of past and present shark populations. Here we examine the dental distributions of sand tigers, including extant Carcharias taurus and extinct Striatolamia...

The impact of urbanization on body size of Barn Swallows Hirundo rustica gutturalis

Yanyan Zhao, Yu Liu, Elizabeth Scordato, Myung-Bok Lee, Xiaoying Xing, Xinyuan Pan, Yang Liu, Rebecca Safran & Emilio Pagani-Núñez
Urbanization implies a dramatic impact on ecosystems, which may lead to drastic phenotypic differences between urban and non-urban individuals. For instance, urbanization is associated with increased metabolic costs, which may constrain body size, but urbanization also leads to habitat fragmentation, which may favour increases in body mass when for instance it correlates with dispersal capacity. However, this apparent contradiction has rarely been studied. This is particularly evident in China where the urbanization process is currently...

Black capped and mountain chickadee nestling fecal samples

Kathryn Grabenstein
Urban and suburban ecosystems are growing in size and number as the human population continues to increase. Not all cities are built the same, however, and it is still unclear how resident organisms are faring in increasingly urban habitats and whether cities are ecological sinks. To investigate how urbanization is affecting breeding success in insectivorous birds, we studied two species of chickadee, the black-capped and mountain chickadee[KG1] , along an urban-rural gradient in Boulder County,...

Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)

Miranda Sinnott-Armstrong, Yu Ogawa, Gea Van De Kerkhof, Silvia Vignolini & Stacey Smith
Research conducted: The majority of plant colors are produced by anthocyanin and carotenoid pigments, but coloration obtained by nanostructured materials (i.e., structural colors) is increasingly reported in plants. Here, we identify a multilayer photonic structure in the fruits of Lantana strigocamara and compare it to a previously described origin in Viburnum tinus. Methods: We used a combination of transmission electron microscopy, serial EM tomography, scanning force microscopy, and optical simulations to characterize the photonic structure...

SORCE-SIM TSIS1-SIM Irradiance Calibration Ratio (STICR) V2.0

Steven Penton
TSIS1-SIM Recalibration of the SORCE-SIM Absolute Irradiance Scale: V02 This is version 2.0 (V02.0) of the SORCE-SIM to TSIS-SIM Irradiance Calibration Ratio (STICR). This data product uses the temporal overlap of the Solar Radiation and Climate Experiment (SORCE) and the Total and Spectral Solar Irradiance Sensor (TSIS-1) Spectral Irradiance Monitor (SIM) instruments to create an alternate SORCE-SIM irradiance calibration. The STICR is the mean TSIS-SIM/SORCE-SIM irradiance ratio during the temporal overlap between the two missions...

Assessing the impact of diffusion model on the turbulent transport and flame structure of premixed lean hydrogen flames: hydrogen data

Aaron Fillo, PETER HAMLINGTON & Kyle Niemeyer
This dataset contains results from direct numerical simulations of premixed, three-dimensional, turbulent hydrogen/air flames, using the multicomponent and mixture-averaged diffusion models. In particular, this dataset contains information about the enstrophy budget and flame structure. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.

Himalayan Seismotectonics, Nepal and Tibet

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15-month broadband seismic experiment to study seismicity and velocity structure at edge of creeping thrusts, Himalaya (eastern Nepal & adjoining southern Tibet).

FIRED URUGUAY

Adam L. Mahood, Jennifer K. Balch, Joe McGlinchy, Estelle J. Lindrooth, Lise A. St. Denis, Maxwell C. Cook, Travis Williams & Nathan P. Mietkiewicz
This is event- and daily-level polygons for the Fire event delineation (FIRED) product for Uruguay from November 2001 to May 2021. It is derived from the MODIS MCD64A1 burned area product (see https://lpdaac.usgs.gov/products/mcd64a1v006/ for more details). The MCD64A1 is a monthly raster grid of estimated burned dates. Firedpy (www.github.com/earthlab/firedpy) is an algorithm that converts these rasters into events by stacking the entire time series into a spatial-temporal data cube, then uses an algorithm to assign...

PSP FIELDS Digital Fields Board (DFB) AC-coupled Searchcoil Magnetometer, SCM, Bandpass filtered, Low Frequency, High Gain, u-component, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Alexandros Chasapis, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMulfhg data. The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. DFB AC bandpass data consist of peak and average values of the absolute value of bandpassed time series waveform data over a time interval equal to the reporting cadence. The AC bandpass data have the peak response frequency of each bin reported in the metadata. The...

Subsurface water dominates seasonal hydrologic storage

Thomas Enzminger
Vertical displacements (dz) in permanent GPS station positions enable estimation of water storage changes (DS), which historically have been impossible to measure directly. We use dz from 924 GPS stations in the western United States to estimate daily DS in California’s Sierra Nevada, and compare it to seasonal snow accumulation and melt over water years 2008-2017. Seasonal variations in GPS-based DS are ~1000 mm. Typically, only ~30% of DS is attributable to snow water equivalent...

Repeat Observations by Gliders in the Equatorial Region (ROGER)

Kristopher Karnauskas
ROGER was an NSF-funded project from 2012–2016 (OCE–1233282 and OCE–1232971). This page provides access to the data analyzed in the following publication: Karnauskas, K. B., J. Jakoboski, T. M. S. Johnston, W. B. Owens, D. L. Rudnick, and R. E. Todd (2020) The Pacific Equatorial Undercurrent in Three Generations of Global Climate Models and Glider Observations. J. Geophys. Res.–Oceans, in revision. As described in the paper, all CMIP3, CMIP5 and CMIP6 global climate model outputs...

CMIP5 Zonal Velocity Volumes Near the Equator (3°S–3°N, 160°E–80°W, 0–400 m)

Kristopher Karnauskas
This data set is part of the larger Repeat Observations by Gliders in the Equatorial Region (ROGER) data set available here: https://doi.org/10.25810/pk4z-n050. ROGER was an NSF-funded project from 2012–2016 (OCE–1233282 and OCE–1232971). This page provides access to the data analyzed in the following publication: Karnauskas, K. B., J. Jakoboski, T. M. S. Johnston, W. B. Owens, D. L. Rudnick, and R. E. Todd (2020) The Pacific Equatorial Undercurrent in Three Generations of Global Climate Models...

CMIP3 Zonal Velocity Sections Along 93°W (3°S–3°N, 0–500 m)

Kristopher Karnauskas
This data set is part of the larger Repeat Observations by Gliders in the Equatorial Region (ROGER) data set available here: https://doi.org/10.25810/pk4z-n050. ROGER was an NSF-funded project from 2012–2016 (OCE–1233282 and OCE–1232971). This page provides access to the data analyzed in the following publication: Karnauskas, K. B., J. Jakoboski, T. M. S. Johnston, W. B. Owens, D. L. Rudnick, and R. E. Todd (2020) The Pacific Equatorial Undercurrent in Three Generations of Global Climate Models...

GEOS-Chem output for \"Lightning NOx Emissions: Reconciling measured and modeled emissions estimates with updated NOx chemistry\"

Joshua Laughner, Ronald Cohen & Benjamin Nault
These GEOS-Chem simulations examine the effect of recent advances to our understanding of upper tropospheric chemistry on our ability to constrain lightning NOx emissions. These simulations examine the effect of the addition of methyl peroxy nitrate chemistry, as well as better constraints on the formation of pernitric acid, dinitrogen pentoxide, and nitric acid at the temperatures and pressures of the upper troposphere. These simulations include a base case, simulations implementing each change individually, all four...

Supporting Information: Toward learned chemical perception of force field typing rules

Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael K. Gilson, Michael R. Shirts, John D. Chodera & David L. Mobley
The Open Force Field Initiative seeks to to automate force field development in order to advance force fields and improve accuracy (openforcefield.org). An important part of this effort includes automating the determination of chemical perception --- that is, the way force field parameters are assigned to a molecule based on chemical environment. We developed a novel technology for this purpose, termed SMARTY. It generalizes atom typing by using direct chemical perception with SMARTS strings adopting...

Data from: An effective method for ecosystem-scale manipulation of bird abundance and species richness

Chelsea Wood, Margaret Summerside & Pieter Johnson
Manipulation experiments are a cornerstone of ecological research, but can be logistically challenging to execute – particularly when they are intended to isolate the ecological role of large, vagile species, like birds. Despite indirect evidence that birds are influential in many ecosystems, large-scale, multi-year bird manipulation experiments are rare. When these studies are conducted, they are typically realized with caged or netted exclosures, an approach that can be expensive, risky for wildlife, and difficult to...

A mathematical model of flow-mediated coagulation identifies factor V as a modifier of thrombin generation in hemophilia A

Michael Stobb, Kathryn Link, Matthew Sorrells, Maria Bortot, Katherine Ruegg, Marilyn Manco-Johnson, Jorge DiPaola, Suzanne Sindi, Aaron Fogelson, Karin Leiderman & Keith Neeves
Hemophilia A is a bleeding disorder categorized as severe, mild, and moderate deficiencies in factor VIII (FVIII). Within these categories the variance in bleeding severity is significant and the origins unknown. The number of parameters that could modify bleeding are so numerous that experimental approaches are not feasible for considering all possible combinations. Consequently, we turn to a mathematical model of coagulation under flow to act as a screening tool to identify parameters that are...

Vegetation Change in the Natural Reserve of Orange County

Katherine Suding, Sara Jo Dickens & Samuel Bedgood
This data set describes vegetation change in 109 areas in the Nature Reserve of Orange County. The authors of this data were mainly interested in the success of artichoke thistle (Cynara cardunculus) control, but it could be approached in many different ways. Surveyors identified and recorded more than 375 plant species from the years 1998, 2008, and 2013.

Data from: Declines in pinyon pine cone production associated with regional warming

Miranda D. Redmond, Frank Forcella & Nichole N. Barger
Global climate change is expected to produce large shifts in vegetation distribution and has already increased tree mortality, altering forest structure. However, long-term shifts will be partly dependent on the ability of species to reproduce under a novel climate. Few studies have examined the impact of climate change on the reproductive output of long-lived ‘masting' species, or species characterized by episodic reproductive events. Here, we show that seed cone production among pinyon pine (Pinus edulis),...

Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology

William E. Stutz & Daniel I. Bolnick
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a “gray zone” where low frequency alleles...

Interspecific competition slows range expansion and shapes range boundaries

Geoffrey Legault, Matthew Bitters, Alan Hastings & Brett Melbourne
Species expanding into new habitats as a result of climate change or human introductions will frequently encounter resident competitors. Theoretical models suggest that such interspecific competition can alter the speed of expansion and the shape of expanding range boundaries. However, competitive interactions are rarely considered when forecasting the success or speed of expansion, in part because there has been no direct experimental evidence that competition affects either expansion speed or boundary shape. Here we demonstrate...

Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection

Douglas Peters & Robert Garcea
The replication of small DNA viruses requires both host DNA replication and repair factors that are often recruited to subnuclear domains termed viral replication centers (VRCs). Aside from serving as a spatial focus for viral replication, little is known about these dynamic areas in the nucleus. We investigated the organization and function of VRCs during murine polyomavirus (MuPyV) infection using 3D structured illumination microscopy (3D-SIM). We localized MuPyV replication center components, such as the viral...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

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