519 Works

Data from: Physiological thermal limits predict differential responses of bees to urban heat-island effects

April L. Hamblin, Elsa Youngsteadt, Margarita M. López-Uribe & Steven D. Frank
Changes in community composition are an important, but hard to predict, effect of climate change. Here, we use a wild-bee study system to test the ability of critical thermal maxima (CTmax, a measure of heat tolerance) to predict community responses to urban heat-island effects in Raleigh, NC, USA. Among 15 focal species, CTmax ranged from 44.6 to 51.3°C, and was strongly predictive of population responses to urban warming across 18 study sites (r2 = 0.44)....

Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes

Brenna R. Forester, Matthew R. Jones, Stéphane Joost, Erin L. Landguth & Jesse R. Lasky
The spatial structure of the environment (e.g., the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multi-scale habitat structure common in nature. Here, we use simulations to pursue two goals: (1) we explore how landscape heterogeneity, dispersal ability, and selection affect the strength of local adaptation, and...

Data from: A phylogenomic analysis of Marek's disease virus (MDV) reveals independent paths to virulence in Eurasia and North America

Jakob Trimpert, Nicole Groenke, Maria Jenckel, Shulin He, Dusan Kunec, Moriah L. Szpara, Stephen J. Spatz, Nikolaus Osterrieder & Dino P. McMahon
Virulence determines the impact a pathogen has on the fitness of its host, yet current understanding of the evolutionary origins and causes of virulence of many pathogens is surprisingly incomplete. Here, we explore the evolution of Marek's disease virus (MDV), a herpesvirus commonly afflicting chickens and rarely other avian species. The history of MDV in the 20th century represents an important case study in the evolution of virulence. The severity of MDV infection in chickens...

Data from: The stratigraphy of mass extinction

Steven M. Holland, Mark E. Patzkowksy & Mark E. Patzkowsky
Patterns of last occurrences of fossil species are often used to infer the tempo and timing of mass extinction, even though last occurrences generally precede the time of extinction. Numerical simulations with constant extinction demonstrate that last occurrences are not randomly distributed, but tend to cluster at subaerial unconformities, surfaces of forced regression, flooding surfaces and intervals of stratigraphical condensation, all of which occur in predictable stratigraphical positions. This clustering arises not only from hiatuses...

Data from: Weed evolution: genetic differentiation among wild, weedy, and crop radish

Amanda Charbonneau, David Tack, Allison Lale, Josh Goldston, Mackenzie Caple, Emma Conner, Oz Barazani, Jotham Ziffer-Berger, Ian Dworkin & Jeffrey K. Conner
Approximately 200 weed species are responsible for more than 90% of crop losses and these comprise less than one percent of all named plant species, suggesting that there are only a few evolutionary routes that lead to weediness. Agricultural weeds can evolve along three main paths: they can be escaped crops, wild species, or crop-wild hybrids. We tested these three hypotheses in weedy radish, a weed of small grains and an emerging model for investigating...

Density, parasitism, and sexual reproduction are strongly correlated in lake Daphnia populations

Meghan A. Duffy, Camden D. Gowler, Mary A. Rogalski, Clara L. Shaw & Katherine K. Hunsberger
Many organisms can reproduce both asexually and sexually. For cyclical parthenogens, periods of asexual reproduction are punctuated by bouts of sexual reproduction, and the shift from asexual to sexual reproduction has large impacts on fitness and population dynamics. We studied populations of Daphnia dentifera to determine the amount of investment in sexual reproduction as well as the factors associated with variation in investment in sex. To do so, we tracked host density, infections by nine...

High Reynolds Number Wind Turbine Wake Data

Alexander Pique
This dataset is affiliated with the publication https://doi.org/10.1007/s00348-022-03455-0. All of the data provided is necessary to reproduce the results with the aforementioned publication. The data in this repository is for the wake of a wind turbine at high Reynolds numbers. The data is mainly used for reproducing the statistics (deficit and variance profiles) and the phase averaged results.

Vibrant Ecologies of Research

Aaron Knochel
What are the elements necessary to create a vibrant ecology of research where art and design inquiry may flourish alongside, within, and out of social and physical science research that is so deeply embedded within the fiber of research-oriented universities? In this special collection of Ground Works, the project work and commentaries explore vibrant ecologies of research deepening our understanding of the institutional, social, and epistemological systems that effectively weave arts-based inquiry into the scholarly...

Just-in-time Ecology of Interdisciplinarity

Lauren Stetz, Karen Keifer-Boyd & Michele Mekel
The Pennsylvania State University Viral Imaginations: COVID-19 project is a curated, online, publicly-accessible gallery and archive of Pennsylvanians’ creative expressions in response to their first-person, lived coronavirus pandemic realities. Constructing a safe and empowering space for sharing experiences across strata of race, ethnicity, language, age, socioeconomic status, education, and ability, the archive provides a platform for the preservation of unique and diverse narratives. Designed as a highly interdisciplinary endeavor, Viral Imaginations brings together specialists from...

Data from: Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

Spencer Katz, Maksim Yakovlev, Daniel Vanselow, Yifu Ding, Alex Lin, Dilworth Parkinson, Yuxin Wang, Victor Canfield, Khai Ang & Keith Cheng
Melanin-rich zebrafish melanophores are used to study pigment development, human skin color, and as a large-scale screening phenotype. To facilitate more detailed whole-body, computational analyses of melanin content and morphology, we have combined X-ray microtomography (micro-CT), a non-destructive, full-volume imaging modality, with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and allowed direct quantitative...

Data from: Ecological genetics of Juglans nigra: differences in early growth patterns of natural populations

Laura Leites, Lauren Onofrio & Gary Hawley
Many boreal and temperate forest tree species distributed across large geographic ranges are composed of populations adapted to the climate they inhabit. Forestry provenance studies and common gardens provide evidence of local adaptation to climate when associations between fitness traits and the populations’ home climates are observed. Most studies that evaluate tree height as a fitness trait do so at a specific point in time. In this study, we elucidate differences in early growth patterns...

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris

Sarthok Rasique Rahman, Jonathan Cnaani, Lisa N. Kinch, Nick V. Grishin & Heather M. Hines
Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab-generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and first metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD-Seq and whole-genome re-sequencing,...

Eastern bluebird and tree swallow response to noise from natural gas compressor stations

Margaret Brittingham, Danielle Williams, Julian Avery & Thomas Gabrielson
Natural gas compressor stations emit loud, low-frequency noise that travels hundreds of meters into undisturbed habitat. We used experimental playback of natural gas compressor noise to determine whether and how noise influenced settlement decisions and reproductive output as well as when in the nesting cycle birds were most affected by compressor noise. We established 80 nest boxes to attract Eastern Bluebirds (Sialia sialis) and Tree Swallows (Tachycineta bicolor) to locations where they had not previously...

Changes in arthropod community but not plant quality benefit a specialist herbivore on plants under reduced water availability

Po-An Lin, Chia-Ming Liu, Jia-Ang Ou, Cheng-Han Sun, Wen-Po Chuang, Chuan-Kai Ho, Natsuko Kinoshita & Gary Felton
Plants growing under reduced water availability can affect insect herbivores differently, in some instances benefitting them. However, the forces mediating these positive impacts remain mostly unclear. To identify how water availability impacts plant quality and multitrophic interactions, we conducted manipulative field studies with two populations of the specialist herbivore Pieris rapae, and its host plant, Rorippa indica. We found that P. rapae larvae experienced higher survival on R. indica growing under low water availability compared...

Data from: Archaeological Central American maize genomes suggest ancient gene flow from South America

Logan Kistler, Heather B. Thakar, Amber M. VanDerwarker, Alejandra Domic, Anders Bergström, Richard J. George, Thomas K. Harper, Robin G. Allaby, Kenneth Hirth & Douglas J. Kennett
Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ~9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but...

Geochemical composition of lithic raw materials in the Olduvai Basin, Tanzania

Charles Egeland, Cynthia Fadem, Ryan Byerly, Cory Henderson, Curran Fitzgerald, Audax Mabulla, Enrique Baquedano & Agniss Gidna
The invention and proliferation of stone tool technology in the Early Stone Age (ESA) marks a watershed in human evolution. Patterns of lithic procurement, manufacture, use, and discard have much to tell us about ESA hominin cognition and land use. However, these issues cannot be fully explored outside the context of the physical attributes and spatio-temporal availability of the lithic raw materials themselves. The Olduvai Basin of northern Tanzania, which is home to both a...

Light and thermal niches of ground-foraging Amazonian insectivorous birds

Vitek Jirinec, Patricia Rodrigues, Bruna Amaral & Philip Stouffer
Insectivores of the tropical rainforest floor are consistently among the most vulnerable birds to forest clearing and fragmentation. Several hypotheses attempt to explain this pattern, including sensitivity to extreme microclimates found near forest borders—particularly brighter and warmer conditions. Importantly, this “microclimate hypothesis” has additional implications for intact forest under global climate change that could be evaluated through direct assessment of the light and temperature environment of terrestrial insectivores. In this study, we harness novel technology...

Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations

Mark Phillips, Kenneth R. Arnold, Zer Vue, Heather K. Beasley, Edgar Garza-Lopez, Andrea G. Marshall, Derrick J. Morton, Melanie R. McReynolds, Thomas T. Barter & Antentor Hinton
Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups...

The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets

Kathryn Stankiewicz, Kate Vasquez Kuntz, Jean-Baptiste Ledoux, Didier Aurelle, Joaquim Garrabou, Yuichi Nakajima, Mikael Dahl, Yuna Zayasu, Sabri Jaziri, Federica Costantini & Iliana Baums
The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical datasets, conclusions about the scale of gene flow may have...

Supplemental information for: An early burst in brachiopod evolution corresponding with significant climatic shifts during the great Ordovician biodiversification event

Curtis Congreve, Mark Patzkowsky & Peter Wagner
We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million-years and rapid divergences shortly before...

Eddy Covariance 30 min flux data at Shale Hills Susquehanna Shale Hills Critical Zone Observatory CZO (SSHCZO)

Y. Smeglin, Y. Shi, K.J. Davis, B. Forsythe & J. Horne
LI-COR LI 7500 measures CO2 and water vapor concentration at 10Hz time resolution. Campbell Scientific CSAT3 gives 3D wind speed and air temperature at 10Hz rate. CO2, sensible heat, latent heat fluxes were calculated every 30min based on the above measurements (time stamp shows the end of the 30min window). • Wind speed and air temperature measured with a Campbell Scientific CSAT3 Three-Dimensional Sonic Anemometer, http://www.campbellsci.com. • CO2 and water vapor concentration measured with a...

Scale Model Equations and Optimization for Annular Flow of Non-Newtonian Fluids Between Eccentric and Rotating Cylinders

Wei Zhang, Pooya Khodaparast, Amin Mehrabian & Amir Shojaei
A broad range of engineering applications involves helical flow of non-Newtonian fluids between two eccentric cylinders. These applications often require estimation of the frictional pressure losses along the axes of the cylinders. Laboratory flow loops are commonly used to study the flow characteristics at smaller scales of investigation. This study uses the laws of similarity and dimensional analysis to obtain a set of scaling equations between the laboratory and prototype scales of the described annular...

Idealized atmospheric boundary layer and tornado simulations for Wang et al. (2022) two-layer-model study.

A. Wang, Y. Pan, G. Bryan & P. Markowski
This dataset contains the numerical simulations used in the Wang et al. (2022) study of two-layer-model in an idealized atmospheric boundary layer and an idealized tornado. That work modifies a wall model from the engineering community known as two-layer model (TLM) to a widely used atmospheric LES mode, Cloud Model 1 (CM1). LES of an idealized, neutral atmospheric boundary layer are performed first, in order to validate the implementation of the TLM in CM1. Next,...

Model Input, Analysis Code, and Select Model Output for the Murdzek et al. (2022) Ordinary Convection Sensitivity Study

S. Murdzek, P. Markowski, Y.P. Richardson & M.R. Kumjian
This dataset contains all relevant Cloud Model 1 (CM1) input files, python analysis code, and select CM1 output for the Murdzek et al. (2022, MWR) study that explores how the sensitivity of simulated ordinary convection changes in environments with different lifting condensation levels (LCLs). Enough CM1 output is provided to recreate most of the figures from Murdzek et al. (2022), and the rest of the output can be recreated using the supplied input files.

Supplementary data, code, and information for ‘On long range dependence in global surface temperature series: An editorial comment’ (Climatic Change, Mann 2011)

M. Mann
Long Range Dependence (LRD) scaling behavior has been argued to characterize long-term surface temperature time series. LRD is typically measured by the so-called “Hurst” coefficient, “H”. Using synthetic temperature time series generated by a simple climate model with known physics, I demonstrate that the values of H obtained for observational temperature time series can be understood in terms of the linear response to past estimated natural and anthropogenic external radiative forcing combined with the effects...

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