33 Works

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...

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...

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...

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...

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...

Age-specific habitat preference, carrying capacity, and landscape structure determine the response of population spatial variability to fishing-driven age truncation

Hsiao-Hang Tao, Gaël Dur, Po-Ju Ke, Sami Souissi & Chih-Hao Hsieh
1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size-selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability respond to age truncation and the underlying mechanisms remain unclear. 2. We hypothesize that age-specific habitat preference, together with environmental carrying...

Ecological and behavioral mechanisms of density-dependent habitat expansion in a recovering African ungulate population

Justine A. Becker, Matthew Hutchinson, Arjun Potter, Shinkyu Park, Jennifer Guyton, Kyler Abernathy, Victor Americo, Ana Gledis Da Conceiçāo, Tyler Kartzinel, Luca Kuziel, Naomi Leonard, Eli Lorenzi, Nuno Martins, Johan Pansu, William Scott, Maria Stahl, Kai Torrens, Marc Stalmans, Ryan Long & Robert Pringle
Major disturbances can temporarily remove factors that otherwise constrain population abundance and distribution. During such windows of relaxed top-down and/or bottom-up control, ungulate populations can grow rapidly, eventually leading to resource depletion and density-dependent expansion into less-preferred habitats. Although many studies have explored the demographic outcomes and ecological impacts of these processes, fewer have examined the individual-level mechanisms by which they occur. We investigated these mechanisms in Gorongosa National Park, where the Mozambican Civil War...

Seasonal variation in community composition and distributional ranges of birds along a subtropical elevation gradient in China

Dan Liang, Xinyuan Pan, Xu Luo, Cheng Wenda, Yanyan Zhao, Yiming Hu, Scott Robinson & Yang Liu
Aim Seasonal variation in community composition and species distributional ranges along elevational gradients remain poorly known but are essential to inform conservation. In this study, we aim to understand how species richness, community composition, and elevational ranges of montane birds change between the breeding and the non-breeding season. Location The east slope of the southern Gaoligong Mountains, Yunnan, southwestern China, elevational range: 700 - 3400 m a.s.l.; latitudinal range: 24°56´- 26°09´ N. Methods We compared...

Cooperative communication with humans evolved to emerge early in domestic dogs

Hannah Salomons, Kyle C.M. Smith, Megan Callahan-Beckel, Margaret Callahan, Kerinne Levy, Brenda S. Kennedy, Emily E. Bray, Gitanjali E. Gnanadesikan, Daniel J. Horschler, Margaret Gruen, Jingzhi Tan, Philip White, Bridgett M. VonHoldt, Evan L. MacLean & Brian Hare
While we know that dogs evolved from wolves, it remains unclear how domestication affected dog cognition. One hypothesis suggests dog domestication altered social maturation by a process of selecting for an attraction to humans. Under this account, dogs became more flexible in using inherited skills to cooperatively-communicate with a new social partner that was previously feared and expressed these unusual social skills early in development. Here we tested dog (N=44) and wolf (N=37) puppies, 5-18...

The temporal dimension of plant-soil microbe interactions: mechanisms promoting feedback between generations

Po-Ju Ke & Jonathan Levine
Soil microbes can influence plant competitive outcomes by stabilizing plant community dynamics or mediating plant competitive hierarchies. Which effect dominates depends on whether microbial effects can extend beyond the focal conditioning individual. While it is well-known that microbial effects can extend to other individuals through space, we lack an explicit theoretical understanding of the factors that regulate their spread to other individuals in subsequent generations. Here, we examine how the commonly-assumed stabilizing effects of host-specific...

Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time

Po-Ju Ke, Peter Zee & Tadashi Fukami
Plant-soil feedbacks (PSF) may change in strength over the life of plant individuals as plants continue to modify the soil microbial community. However, the temporal variation in PSF is rarely quantified and its impacts on plant communities remain unknown. Using a chronosequence reconstructed from annual aerial photos of a coastal dune ecosystem, we characterized >20-year changes in soil microbial communities associated with individuals of the four dominant perennial species, one legume and three non-legume. We...

De novo genome assembly of Leptodactylus fuscus

Lu Yang, Peter Andolfatto, Andrew Crawford, Santiago Herrera-Álvarez, Maríadel Pilar Rodríguez-Ordoñez, Julie Peng, Shabnam Mohammadi, Jay Storz, Arbel Harpak & Susanne Dobler
This presents a de novo genome assembly of Leptodactylus fuscus. High molecular weight DNA was extracted from a L. fuscus embryo which had been preserved in ethanol upon collection in Garzón, Huila, Colombia. The library was prepared and sequenced with 10X Genomics Chromium. Linked reads were processed by Long Ranger basic v2.2.2 and assembled with Supernova v2.1.1. The assembled genome is 2.42 Gb with 16,530 scaffolds >=10 kb, and scaffold N50 = 363 kb. The...

Data from: Concerted evolution reveals co-adapted amino acid substitutions in Na+K+ ATPase of frogs that prey on toxic toads

Shabnam Mohammadi, Lu Yang, Arbel Harpak, Santiago Herrera-Álvarez, María Del Pilar Rodríguez-Ordoñez, Julie Peng, Karen Zhang, Jay Storz, Susanne Dobler, Andrew Crawford & Peter Andolfatto
Gene duplication is an important source of evolutionary innovation, but the functional distinction between duplicates can be opposed by ongoing gene conversion between them. Here we document a tandem duplication of Na+,K+-ATPase subunit α1 (ATP1A1) sharedby frogs in the genus Leptodactylus,a group of species that feeds on toxic toads. One ATP1A1 paralog evolved resistance to toad toxins while the other paralog retained ancestral susceptibility. Frequent non-allelic gene conversion homogenized most of the paralog sequences,yet the...

Data for: 'How is sea level change encoded in carbonate stratigraphy?'

Emily Geyman, Adam Maloof & Blake Dyer
The history of organismal evolution, seawater chemistry, and paleoclimate is recorded in layers of carbonate sedimentary rock. Meter-scale cyclic stacking patterns in these carbonates often are interpreted as representing sea level change. A reliable sedimentary proxy for eustasy would be profoundly useful for reconstructing paleoclimate, since sea level responds to changes in temperature and ice volume. However, the translation from water depth to carbonate layering has proven difficult, with recent surveys of modern shallow water...

High social status males experience accelerated epigenetic aging in wild baboons

Jordan Anderson, Rachel Johnston, Amanda Lea, Fernando Campos, Tawni Voyles, Mercy Akinyi, Susan Alberts, Elizabeth Archie & Jenny Tung
Aging, for virtually all life, is inescapable. However, within populations, biological aging rates vary. Understanding sources of variation in this process is central to understanding the biodemography of natural populations. We constructed a DNA methylation-based age predictor for an intensively studied wild baboon population in Kenya. Consistent with findings in humans, the resulting “epigenetic clock” closely tracks chronological age, but individuals are predicted to be somewhat older or younger than their known ages. Surprisingly, these...

Data from: Host population dynamics in the face of an evolving pathogen

Wesley Hochachka, Andrew Dobson, Dana Hawley & André Dhondt
1. Interactions between hosts and pathogens are dynamic at both ecological and evolutionary levels. In the resultant “eco-evolutionary dynamics” ecological and evolutionary processes affect each other. For example, the house finch (Haemorhous mexicanus) and its recently-emerged pathogen, the bacterium Mycoplasma gallisepticum, form a system in which evidence suggests that changes in bacterial virulence through time enhance levels of host immunity in ways that drive the evolution of virulence in an arms race. 2. We use...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Princeton University
  • Duke University
  • University of Florida
  • University of Wyoming
  • Sun Yat-sen University
  • University of Pennsylvania
  • Universität Hamburg
  • The University of Texas at Austin
  • Columbia University
  • University of Notre Dame