178 Works

Small shelly fossils and carbon isotopes from the early Cambrian (Stage 3-4) Mural Formation of western Laurentia

Christian B. Skovsted, Uwe Balthasar, Jakob Vinther & Erik Sperling
The extraordinary window of phosphatised and phosphatic Small Shelly Fossils (SSFs) during the early and middle Cambrian is an important testament to the radiation of biomineralising metazoans. While SSF are well known from most Cambrian palaeocontinents during this time interval, western Laurentia has relatively few SSF faunas. Here we describe a diverse SSF fauna from the early Cambrian (Stage 3-4) Mural Formation at three localities in Alberta and British Columbia, Canada, complemented by carbon isotope...

Data from: Seasonal changes in diet and toxicity in the Climbing Mantella frog (Mantella laevigata)

Nora A. Moskowitz, Alexandre B. Roland, Eva K. Fischer, Ndimbintsoa Ranaivorazo, Charles Vidoudez, Marianne T. Aguilar, Sophia M. Caldera, Jackie Chea, Miruna G. Cristus, Jett P. Crowdis, Bluyé DeMessie, Caroline R. Desjardins-Park, Audrey H. Effenberger, Felipe Flores, Michael Giles, Emma Y. He, Nike S. Izmaylov, ChangWon C. Lee, Nicholas A. Pagel, Krystal K. Phu, Leah U. Rosen, Danielle A. Seda, Yong Shen, Santiago Vargas, Hadley S. Weiss … & Lauren A. O’Connell
Poison frogs acquire chemical defenses from the environment for protection against potential predators. These defensive chemicals are lipophilic alkaloid toxins that are sequestered by poison frogs from dietary arthropods and stored in skin glands. Despite decades of research focusing on identifying poison frog toxins, we know relatively little about how environmental variation and subsequent arthropod availability impacts toxicity in poison frogs. We investigated how seasonal environmental variation influences poison frog toxin profiles through changes in...

Variable prediction accuracy of polygenic scores within an ancestry group

Hakhamanesh Mostafavi, Arbel Harpak, Ipsita Agarwal, Dalton Conley, Jonathan Pritchard & Molly Przeworski
Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there...

A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression

Yuan Xue, Terence Theisen, Suchita Rastogi, Abel Ferrel, Stephen Quake & John Boothroyd
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a...

Rethinking megafauna

Marcos Moleón, José Sánchez-Zapata, José Donázar, Eloy Revilla, Berta Martín-López, Cayetano Gutiérrez-Cánovas, Wayne Getz, Zebensui Morales-Reyes, Ahimsa Campos-Arceiz, Larry Crowder, Mauro Galetti, Manuela González-Suárez, Fengzhi He, Pedro Jordano, Rebecca Lewison, Robin Naidoo, Norman Owen-Smith, Nuria Selva, Jens-Christian Svenning, José Tella, Christiane Zarfl, Sonja Jähnig, Matt Hayward, Søren Faurby, Nuria García … & Klement Tochner
Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are “megafauna”? Here we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyze associated terminology in the scientific literature. Second, we conduct a survey among ecologists and paleontologists to assess the species traits...

Repeated fire shifts carbon and nitrogen cycling by changing plant inputs and soil decomposition across ecosystems

Adam Francis Pellegrini, Sarah Hobbie, Peter Reich, Ari Jumpponen, Jack Brookshire, Anthony Caprio, Corli Coetsee & Robert Jackson
Fires shape the biogeochemistry and functioning of many ecosystems, and fire frequencies are changing across much of the globe. Frequent fires can change soil carbon (C) and nitrogen (N) storage by altering the quantity and chemistry of plant inputs through changes in plant biomass and composition as well as altering decomposition of soil organic matter. How decomposition rates change with shifting inputs remains uncertain because most studies focus on the effects of single fires, where...

Data for Variations in the Intensity and Spatial Extent of Tropical Cyclone Precipitation

Danielle Touma, Samantha Stevenson, Suzana Camargo, Daniel Horton & Noah Diffenbaugh
The intensity and spatial extent of tropical cyclone precipitation (TCP) often shapes the risk posed by landfalling storms. Here we provide a comprehensive climatology of landfalling TCP characteristics as a function of tropical cyclone strength, using daily precipitation station data and Atlantic US landfalling tropical cyclone tracks from 1900-2017. We analyze the intensity and spatial extent of ≥ 1 mm/day TCP (Z1) and ≥ 50 mm/day TCP (Z50). We show that the highest median intensity...

Respiratory medium and circulatory anatomy constrain size evolution in marine macrofauna

Noel Heim, Saket Bakshi, Loc Buu, Stephanie Chen, Shannon Heh, Ashli Jain, Christopher Noll, Ameya Patkar, Noah Rizk, Sriram Sundararajan, Isabella Villante, Matthew Knope & Jonathan Payne
The typical marine animal has increased in biovolume by more than two orders of magnitude since the beginning of the Cambrian, but the causes of this trend remain unknown. We test the hypothesis that the efficiency of intra-organism oxygen delivery is a major constraint on body size evolution in marine animals. To test this hypothesis, we compiled a dataset comprising 13,723 marine animal genera spanning the Phanerozoic. We coded each genus according to its respiratory...

Frequent burning causes large losses of carbon from deep soil layers in a temperate savanna

Adam Francis Pellegrini, Kendra K. McLauchlan, Sarah E. Hobbie, Michelle C. Mack, Abbey L. Marcotte, David M. Nelson, Steven Perakis, Peter B. Reich & Kyle Whittinghill
1. Fire activity is changing dramatically across the globe, with uncertain effects on ecosystem processes, especially belowground. Fire‐driven losses of soil carbon (C) are often assumed to occur primarily in the upper soil layers because the repeated combustion of aboveground biomass limits organic matter inputs into surface soil. However, C losses from deeper soil may occur if frequent burning reduces root biomass inputs of C into deep soil layers or stimulates losses of C via...

Hormonal and neural correlates of care in active versus observing poison frog parents

Eva K. Fischer & Lauren A. O'Connell
The occasional reversal of sex-typical behavior suggests that many of the neural circuits underlying behavior are conserved between males and females and can be activated in response to the appropriate social condition or stimulus. Most poison frog species (Family Dendrobatidae) exhibit male uniparental care, but flexible compensation has been observed in some species, where females will take over parental care duties when males disappear. We investigated hormonal and neural correlates of sex-typical and sex-reversed parental...

Measuring impostor phenomenon among health sciences librarians

Jill Barr-Walker, Michelle B. Bass, Debra A. Werner & Liz Kellermeyer
This dataset contains Appendices A-J corresponding to the article "Measuring impostor phenomenon among health sciences librarians". Objective: Impostor phenomenon, also known as impostor syndrome, is the inability to internalize accomplishments while experiencing the fear of being exposed as a fraud. Previous work has examined impostor phenomenon among academic college and research librarians, but health sciences librarians, who are often asked to be experts in medical subject areas with minimal training or education in these areas,...

WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction

Meredith Lee, Jesse Raffa, Marzyeh Ghassemi, Tom Pollard, Sharada Kalanidhi, Omar Badawi, Karen Matthys & Leo Anthony Celi
WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction focuses on patient health through data from MIT’s GOSSIS (Global Open Source Severity of Illness Score) initiative. Brought to you by the Global WiDS team, the West Big Data Innovation Hub, and the WiDS Datathon Committee, this year’s datathon is launching on Kaggle: bit.ly/WiDSdatathon2020kaggle.

Inference of nonlinear receptive field subunits with spike-triggered clustering

Nishal Shah, Nora Brackbill, Colleen Rhoades, Alexandra Kling, Georges Goetz, Alan Litke, Alexander Sher, Eero Simoncelli & E.J. Chichilnisky
Responses of sensory neurons are often modeled using a weighted combination of rectified linear subunits. Since these subunits often cannot be measured directly, a flexible method is needed to infer their properties from the responses of downstream neurons. We present a method for maximum likelihood estimation of subunits by soft-clustering spike-triggered stimuli, and demonstrate its effectiveness in visual neurons. Subunits estimated from parasol retinal ganglion cells (RGCs) in macaque retina partitioned the receptive field into...

Crosslinguistic Word Orders Enable an Efficient Tradeoff of Memory and Surprisal

Michael Hahn & Richard Futrell

Equiprobable Mappings in Weighted Constraint Grammars

Arto Topani Anttila, Scott Borgeson & Giorgio Magri

DialectGram: Detecting Dialectal Variation at Multiple Geographic Resolutions

Hang Jiang, Haoshen Hong, Yuxing Chen & Vivek Kulkarni

Modeling Behavior in Truth Value Judgment Task Experiments

Brandon Waldon & Judith Degen

Ectomycorrhizal fungal diversity predicted to substantially decline due to climate changes in North American Pinaceae forests.

Brian Steidinger
AIM: Ectomycorrhizal fungi (ECMF) are partners in a globally distributed tree symbiosis implicated in most major ecosystem functions. However, resilience of ECMF to future climates is uncertain. We forecast these changes over the extent of North American Pinaceae forests. LOCATION: 68 sites from North American Pinaceae forests ranging from Florida to Ontario in the east and southern California to Alaska in the west. TAXON: Ectomycorrhizal fungi (Asco- and Basidiomycetes). METHODS: We characterized ECMF communities at...

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

Beth Morrison, Berry Brosi & Rodolfo Dirzo
Within ecological communities, species engage in myriad interaction types, yet empirical examples of hybrid species interaction networks composed of multiple types of interactions are still scarce. A key knowledge gap is understanding how the structure and stability of such hybrid networks are affected by anthropogenic disturbance. Using 15,169 interaction observations, we constructed 16 hybrid herbivore-plant-pollinator networks along an agricultural intensification gradient to explore changes in network structure and robustness to local extinctions. We found that...

Body size, sampling completeness, and extinction risk in the marine fossil record

Jonathan Payne & Noel Heim
Larger body size has long been assumed to correlate with greater risk of extinction, helping to shape body size distributions across the tree of life, but lack of comprehensive size data for fossil taxa have left this hypothesis untested for most higher taxa across the vast majority of evolutionary time. Here we assess the relationship between body size and extinction using a dataset comprising the body sizes, stratigraphic ranges, and occurrence patterns of 9,408 genera...

Data from: Early plant development depends on embryo damage location: the role of seed size in partial seed predation

Ramón Perea García-Calvo, Geraldo Fernandes & Rodolfo Dirzo
Data on 1) Observed weevil-infested acorns in the field; 2) Germination rates and times, and seedling emergence of control and embryo-damaged acorns; 3) Seedling performance and physiology of seedlings

Data from: Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance

Shane Blowes, Jonathan Chase, Antonio Di Franco, Ori Frid, Nicholas Gotelli, Paolo Guidetti, Tiffany Knight, Felix May, Daniel McGlinn, Fiorenza Micheli, Enric Sala & Jonathan Belmaker
1. Protected areas are central to biodiversity conservation. For marine fish, marine protected areas (MPAs) often harbour more individuals, especially of species targeted by fisheries. But precise pathways of biodiversity change remain unclear. For example, how local-scale responses combine to affect regional biodiversity, important for managing spatial networks of MPAs, is not well known. Protection potentially influences three components of fish assemblages that determine how species accumulate with sampling effort and spatial scale: the total...

Top-down forcing of an apex predator (Puma concolor) on a suburban ecosystem

Kevin Leempoel, Jordana Meyer, Trevor Hébert, Nicole Nova & Elizabeth Hadly
Absence of apex predators simplifies food chains, leading to degradation of ecosystems and diminution of the services they provide (Estes et al. 2011). However, large predators do not coexist well with humans, which has resulted in a worldwide decline of carnivores and thus, their roles in ecosystem function (Ripple et al. 2014). With diminution of habitat, carnivores are more likely to move into urban landscapes causing conflict with humans and their domesticated animals. In a...

A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity

Kevin Leempoel, Elizabeth Hadly & Trevor Hebert
Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed...

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