235 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...

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...

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).

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...

Large herbivores transform plant-pollinator networks in an African savanna

Matthew C. Hutchinson, Travis J. Guy, Todd M. Palmer, Robert M. Pringle, Katherine C. R. Baldock, Elisha Kayser, Benjamin Baiser, Phillip P. A. Staniczenko, Jacob R. Goheen, Robert M. Pringle & Todd M. Palmer
Pollination by animals is a key ecosystem service1,2 and interactions between plants and their pollinators are a model system for the study of ecological networks3,4, yet plant-pollinator networks are typically studied in isolation from the broader ecosystems in which they are embedded. The plants visited by pollinators also interact with other consumer guilds that eat stems, leaves, fruits, or seeds. One such guild, large mammalian herbivores, are well-known ecosystem engineers5–7 and may have substantial impacts...

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....

Numbers of individuals and endemicity for birds in three study sites of the Himalayas-Hengduan mountains of China

Yiming Hu, Brett Scheffers, Xinyuan Pan, Huijian Hu, Zhixin Zhou, Dan Liang, Cheng Wenda, Zhixin Wen & Luke Gibson
1. Describing the patterns and revealing the underlying mechanisms responsible for variations in community structure remains a central focus in ecology. However, important gaps remain, including our understanding of species abundance. Most studies on abundance-based relationships are from either temperate ecosystems or tropical ecosystems, and few have explicitly tested abundance-based relationships across a temperate to tropical ecotone. 2. Here, we use a comprehensive dataset of breeding birds across elevation spanning a temperate to subtropical gradient...

Collective detection based on visual information in animal groups

Jacob D. Davidson, Matthew M. G. Sosna, Colin R. Twomey, Vivek H. Sridhar, Simon P. Leblanc & Iain D. Couzin
We investigate key principles underlying individual, and collective, visual detection of stimuli, and how this relates to the internal structure of groups. While the individual and collective detection principles are generally applicable, we employ a model experimental system of schooling golden shiner fish ( Notemigonus crysoleucas ) to relate theory directly to empirical data, using computational reconstruction of the visual fields of all individuals. This reveals how the external visual information available to each group...

Data from: Predicting range shifts of pikas (Mammalia, Ochotonidae) in China under scenarios incorporating land-use change, climate change, and dispersal limitations

Liang Ma, Chunrong Mi, Jiapeng Qu, Deyan Ge, Qisen Yang & David Wilcove
Two of the most important forces affecting biodiversity are land-use change (LUC) and global climate change (GCC). Previous studies have modeled their impacts on species separately and together, but few have done so for multiple species with dispersal limitations incorporated into the models. We integrate species distribution models plus a dispersal model to predict LUC and GCC impacts on the ranges of five species of pikas in the Qinghai-Tibet Plateau region of China. Pikas are...

Delivery Gig Worker Interviews on Automation at Work

Diana Enriquez
These data include 39 structured interview transcripts. Each case is someone who worked at the time for Uber, UberEats, Lyft, and/or Amazon Flex (Amazon’s contractor delivery service). These data were collected between July and September 2019. All but one of the interviews occurred over the phone. My questions are focused on the structure of their gig work jobs and the technology they used at work or expected to use at work in the future. I...

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...

Short-term plant-community responses to large mammalian herbivore exclusion in a rewilded Javan savanna

Matthew Hutchinson, Arjun Potter, Muhammad Ali Imron & Satyawan Pudyatmoko
Grassy biomes such as savannas are maintained by a suite of ecosystem processes from herbivory to rainfall and fire. Many studies have examined the impacts of large mammalian herbivores on herbaceous plant communities but few of these studies have been conducted in humid, fertile savannas. We present the findings of a short-term experiment that investigated the effects of herbivory in one such savanna. We erected large-herbivore exclosures in Alas Purwo National Park, Java where rainfall...

Diverse arsenic-containing lipids in the surface ocean

Katherine Heal, Ashley Maloney, Anitra Ingalls & Randelle Bundy
Arsenic is present at nanomolar levels throughout the ocean, and microbes assimilate this toxic element due to its similarity to inorganic phosphorus. Although dissolved arsenic has been a focus of several oceanographic studies, the size and character of the particulate arsenic pool is not known. We measured particulate arsenic in five samples from the open ocean and determined the contribution of arsenic-containing lipids within this pool. Here we show that the accumulation of arsenic into...

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