218 Works

Data from: Determinants of elephant foraging behavior in a coupled human-natural system: is brown the new green?

Paola S. Branco, Jerod A. Merkle, Robert M. Pringle, Johan Pansu, Arjun B. Potter, Alana Reynolds, Marc Stalmans & Ryan A. Long
1. Crop raiding by wildlife poses major threats to both wildlife conservation and human wellbeing in agro-ecosystems worldwide. These threats are particularly acute in many parts of Africa, where crop raiders include globally threatened megafauna such as elephants, and where smallholder agriculture is a primary source of human livelihood. One framework for understanding herbivore feeding behavior, the forage-maturation hypothesis, predicts that herbivores should align their movements with intermediate forage biomass (i.e., peak green-up); this phenomenon...

Data from: A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs

Youssef Idaghdour, John D. Storey, Sami J. Jadallah & Greg Gibson
The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism...

Data from: An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences

Molly Schumer, Rongfeng Cui, Bastien Boussau, Ronald Brice Walter, Gil G. Rosenthal & Peter Andolfatto
Once thought rare in animal taxa, hybridization has been increasingly recognized as an important and common force in animal evolution. In the past decade, a number of studies have suggested that hybridization has driven speciation in some animal groups. We investigate the signature of hybridization in the genome of a putative hybrid species, Xiphophorus clemenciae, through whole genome sequencing of this species and its hypothesized progenitors. Based on analysis of this data, we find that...

Data from: Social environment influences the relationship between genotype and gene expression in wild baboons

Daniel E. Runcie, Ralph T. Wiedmann, Elizabeth A. Archie, Jeanne Altmann, Gregory A. Wray, Susan C. Alberts & Jenny Tung
Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression...

Data from: Endocrine phenotype, reproductive success and survival in the great tit, Parus major

Jenny Q. Ouyang, Peter Sharp, Michael Quetting & Michaela Hau
A central goal in evolutionary ecology is to characterize and identify selection patterns on the optimal phenotype in different environments. Physiological traits, such as hormonal responses, provide important mechanisms by which individuals can adapt to fluctuating environmental conditions. It is therefore expected that selection shapes hormonal traits, but the strength and the direction of selection on plastic hormonal signals are still under investigation. Here, we determined whether, and in which way, selection is acting on...

Data from: Water stress strengthens mutualism among ants, trees, and scale insects

Elizabeth G. Pringle, Erol Akçay, Ted K. Raab, Rodolfo Dirzo & Deborah M. Gordon
Abiotic environmental variables strongly affect the outcomes of species interactions. For example, mutualistic interactions between species are often stronger when resources are limited. The effect might be indirect: water stress on plants can lead to carbon stress, which could alter carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses, plants host ant colonies that defend them against herbivores. Here we show that the partners' investments in a widespread ant–plant symbiosis increase with water stress across 26 sites...

LAMMPS simulations scripts for the manuscript \"A granular-physics-based view of fault friction experiments\"

Behrooz Ferdowsi & Allan M. Rubin
Rate- and State-dependent Friction (RSF) equations are commonly used to describe the time-dependent frictional response of fault gouge to perturbations in sliding velocity. Among the better-known versions are the Aging and Slip laws for the evolution of state. Although the Slip law is more successful, neither can predict all the robust features of lab data. RSF laws are also empirical, and their micromechanical origin is a matter of much debate. Here we use a granular-physics-based...

Data from: The role of infectious disease in the evolution of females: evidence from anther-smut disease on a gynodioecious alpine carnation

Emily L. Bruns, Ian Miller, Michael E. Hood, Valentina Carasso & Janis Antonovics
In flowering plants, the evolution of females is widely hypothesized to be the first step in the evolutionary pathway to separate male and female sexes, or dioecy. Natural enemies have the potential to drive this evolution if they preferentially attack hermaphrodites over females. We studied sex-based differences in exposure to anther-smut (Microbotryum), a sterilizing pollinator-transmitted disease, in Dianthus pavonius, a gynodioecious perennial herb. We found that within a heavily diseased population, females consistently had lower...

Data from: Trophic ecology of large herbivores in a reassembling African ecosystem

Johan Pansu, Jennifer A. Guyton, Arjun B. Potter, Justine L. Atkins, Joshua H. Daskin, Bart Wursten, Tyler R. Kartzinel & Robert M. Pringle
1. Diverse megafauna assemblages have declined or disappeared throughout much of the world, and many efforts are underway to restore them. Understanding the trophic ecology of such reassembling systems is necessary for predicting recovery dynamics, guiding management, and testing general theory. Yet there are few studies of recovering large-mammal communities, and fewer still that have characterized food-web structure with high taxonomic resolution. 2. In Gorongosa National Park, large herbivores have rebounded from near-extirpation following the...

Supplemental Data for N management paper

Yixin Guo & Denise Mauzerall

Data from: Competitive history shapes rapid evolution in a seasonal climate

Tess Grainger, Seth Rudman, Paul Schmidt & Jonathan Levine
Eco-evolutionary dynamics will play a critical role in determining species’ fates as climatic conditions change. Unfortunately, we have little understanding of how rapid evolutionary responses to climate play out when species are embedded in the competitive communities that they inhabit in nature. We tested the effects of rapid evolution in response to interspecific competition on subsequent ecological and evolutionary trajectories in a seasonally changing climate using a field-based evolution experiment with Drosophila melanogaster. Populations of...

Shakespeare and Company Project Dataset: Lending Library Books

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Paige Allen, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Yun Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Violet Gautreua, Alex Gjaja, Elspeth Green, Isaac Hart, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Elizabeth Macksey, Cate Mahoney … & Clifford E. Wulfman
This dataset includes information about approximately 6,000 books and other items with bibliographic data as well as summary information about when the item circulated in the Shakespeare and Company lending library and the number of times an item was borrowed or purchased.

Shakespeare and Company Project Dataset: Lending Library Members, Books, Events

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Paige Allen, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Yun Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Violet Gautreua, Alex Gjaja, Elspeth Green, Isaac Hart, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Elizabeth Macksey, Cate Mahoney … & Clifford E. Wulfman
The Shakespeare and Company Project makes three datasets available to download in CSV and JSON formats. The datasets provide information about lending library members; the books that circulated in the lending library; and lending library events, including borrows, purchases, memberships, and renewals. The datasets may be used individually or in combination site URLs are consistent identifiers across all three. The DOIs for each dataset are as follows: Members (https://doi.org/10.34770/nsa4-3t76); Books (https://doi.org/10.34770/079z-h206); Events (https://doi.org/10.34770/rtbp-kv40).

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics

Andrew Letten, Michael Baumgartner, Katia Pfrunder-Cardozo, Jonathan Levine & Alex Hall
In light of their adverse impacts on resident microbial communities, it is widely predicted that broad-spectrum antibiotics can promote the spread of resistance by releasing resistant strains from competition with other strains and species. We investigated the competitive suppression of a resistant strain of Escherichia coli inoculated into human-associated communities in the presence and absence of the broad and narrow spectrum antibiotics rifampicin and polymyxin B, respectively. We found strong evidence of community-level suppression of...

Biodiversity data from: The mass extinction debt of the Anthropocene

Christopher Spalding & Pincelli Hull
To make sense of our present biodiversity crises, the modern rate of species extinctions is commonly compared to a benchmark, or “background,” rate derived from the fossil record. These estimates are critical for bounding the scale of modern diversity loss, but have yet to account for the fundamental structure of extinction rates through time. Namely, a substantial fraction of extinctions within the fossil record occur within relatively short-lived extinction pulses, and not during intervals characterized...

Data for: 'Facies control on carbonate δ13C on the Great Bahama Bank'

Emily Geyman & Adam Maloof
The carbon isotopic (δ13C) composition of shallow-water carbonates often is interpreted to reflect the δ13C of the global ocean and is used as a proxy for changes in the global carbon cycle. However, local platform processes, in addition to meteoric and marine diagenesis, may decouple carbonate δ13C from that of the global ocean. To shed light on the extent to which changing sediment grain composition may produce δ13C shifts in the stratigraphic record, we present...

Social media and public perception as core aspect of public health: the cautionary case of @realdonaldtrump and COVID-19

Jeffrey Peterson & Agustin Fuentes
The social media milieu in which we are enmeshed has substantive impacts on our beliefs and perceptions. Recent work has established that this can play a role in influencing understanding of, and reactions to, public health information. Twitter, in particular, appears to play a substantive role in the public health information ecosystem. From July 25th, 2020 to November 15th, 2020, we collected weekly tweets related to COVID-19 keywords and assessed their networks, patterns and properties....

Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Fan Han, Sangeet Lamichhaney, B. Rosemary Grant, Peter R. Grant, Leif Andersson & Matthew T. Webster
Genomic comparisons of closely related species have identified “islands” of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species...

Fluorescence Reconstruction Microscopy: Complete Testing Dataset

& Daniel Cohen
We provide all the test data and corresponding predictions for our paper, “Practical Fluorescence Reconstruction Microscopy for High-Content Imaging”. Please refer to the Methods section in this paper for experimental details. For each experimental condition, we provide the input transmitted-light images (either phase contrast or DIC), the ground truth fluorescence images, and the output predicted fluorescence images which should reconstruct the ground truth fluorescence images.

Dust and Starlight Maps for Galaxies in the KINGFISH Sample

B.T. Draine, G. Aniano, L.K. Hunt, K. Sandstrom, D. Calzetti, R.C. Kennicutt, D.A. Dale, M. Galametz, K.D. Gordon, A.K. Leroy, J.-D.T. Smith, H. Roussel, M. Sauvage, F. Walter, L. Armus, A.D. Bolatto, M. Boquien, A. Crocker, I. De Looze, J. Donovan Meyer, G. Helou, J. Hinz, B.D. Johnson, J. Koda, A. Miller … & C.W. Engelbracht
Dust and starlight have been modeled for the KINGFISH project galaxies. For each pixel in each galaxy, we estimate: (1) dust surface density; (2) q_PAH, the dust mass fraction in PAHs; (3) distribution of starlight intensities heating the dust; (4) luminosity emitted by the dust; and (5) dust luminosity from regions with high starlight intensity.

Shakespeare and Company Project Dataset: Lending Library Members

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Elspeth Green, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Cate Mahoney, Jesse D. McCarthy, Mary Naydan, Isabel Ruehl, Sylvie Thode, Camey VanSant … & Clifford E. Wulfman
The Shakespeare and Company Project: Lending Library Members dataset includes information about approximately 5,700 members of Sylvia Beach's Shakespeare and Company lending library.

A dual-mechanism antibiotic kills Gram-negative bacteria and avoids drug resistance

James K. Martin, Joseph P. Sheehan, Benjamin Bratton, Gabriel M. Moore, André Mateus, Sophia Hsin-Jung Li, Hahn Kim, Joshua D. Rabinowitz, Athanasios Typas, Mikhail M. Savitski, Maxwell Z. Wilson & Zemer Gitai
The rise of antibiotic resistance and declining discovery of new antibiotics have created a global health crisis. Of particular concern, no new antibiotic classes have been approved for treating Gram-negative pathogens in decades. Here, we characterize a compound, SCH-79797, that kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism of action (MoA) with undetectably-low resistance frequencies. To characterize its MoA, we combined quantitative imaging, proteomic, genetic, metabolomic, and cell-based assays. This pipeline demonstrates...

Eagle Ford Shale: Synchrotron-Based Element and Mineral Maps

Catherine Peters & Julie Kim
This project provides 2D synchrotron micro X-ray fluorescence (µXRF) and micro X-ray diffraction (µXRD) data, as well as generated mineral maps for a shale rock from the Eagle Ford formation. The Eagle Ford shale is an organic-rich laminate shale in southern Texas that is actively drilled for unconventional oil and gas operations. The Eagle Ford shale sample in this study is a calcareous mudstone consisting of ultra-fine-grained calcite and silicate minerals arranged in a foliated...

Deep Potential training data for crystalline and disordered TiO2 phases

Marcos Felipe Calegari Andrade & Annabella Selloni
Data set used to train a Deep Potential (DP) model for crystalline and disordered TiO2 phases. Training data contain atomic forces, potential energy, atomic coordinates and cell tensor. Energy and forces were evaluated with the density functional SCAN, as implemented in Quantum-ESPRESSO. Atomic configurations of crystalline systems were generated by random perturbation of atomic positions (0-0.3 A) and cell tensor (1-10%). Amorphous TiO2 was explored by DP molecular dynamics (DPMD) at temperatures in the range...

Chinese overseas development financing of electric power generation: A comparative analysis

Xu Chen, Kevin P. Gallagher & Denise Mauzerall
Global power generation must rapidly decarbonize by mid-century to meet the goal of stabilizing global warming below 2 degree Celsius. To meet this objective, multilateral development banks (MDBs) have gradually reduced fossil fuel and increased renewable energy financing. Meanwhile, globally active national development finance institutions (DFIs) from Japan and South Korea have continued to finance overseas coal plants. Less is known about the increasingly active Chinese DFIs. Here we construct a new dataset of China’s...

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