300 Works

Date from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants

Michael O'Brien, Elisa Carbonell, Gianalberto Losapio, Philipp Schlüter & Christian Schöb
1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. 2) We reciprocally transplanted perennial species (Arenaria armerina and Festuca indigesta) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated...

Trajectories of body landmarks in videos of cerebral palsy patients and corresponding clinical labels

Łukasz Kidziński, Bryan Yang, Jennifer Hicks, Apoorva Rajagopal, Scott Delp & Michael Schwartz
Cerebral Palsy (CP) is a neurological disorder that is usually caused by mechanical damage to the brain at or around birth. One of the main symptoms of CP is impaired motor control and development of walking skills. In clinical practice in the US child’s gait is often recorded with a camera and the recording can be used by a doctor for assessment. In this dataset we provide body landmarks (such as positions of knees, elbow,...

The anthropology of mind: Exploring unusual sensations and spiritual experiences across cultures. An interview with Tanya Luhrmann.

Tanya Luhrmann & Martin Fortier
In this interview, Tanya Luhrmann discusses her position within the field of anthropology as well as her methodological commitments. She also addresses her view about the mechanisms governing the shift from experiential unreality (imagination-like mental representations) to experiential reality (perception-like mental representations) as well as the role of personal proclivity (in particular the trait of absorption) within religious practice and experience. Finally, the interview tackles the question of cognitive penetrability: can folk models of the...

Data from: Discrimination of fast click series produced by tagged Risso’s dolphins (Grampus griseus) for echolocation or communication

Patricia Arranz, Stacy L. DeRuiter, Alison K. Stimpert, Silvana Neves, Ari S. Friedlaender, Jeremy A. Goldbogen, Fleur Visser, John Calambokidis, Brandon L. Southall & Peter L. Tyack
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two...

Data from: Genetic basis of priority effects: insights from nectar yeast

Manpreet K. Dhami, Thomas Hartwig & Tadashi Fukami
Priority effects, in which the order of species arrival dictates community assembly, can have a major influence on species diversity, but the genetic basis of priority effects remains unknown. Here, we suggest that nitrogen scavenging genes previously considered responsible for starvation avoidance may drive priority effects by causing rapid resource depletion. Using single-molecule sequencing, we de novo assembled the genome of the nectar-colonizing yeast, Metschnikowia reukaufii, across eight scaffolds and complete mitochondrion, with gap-free coverage...

Data from: Coralline algae in a naturally acidified ecosystem persist by maintaining control of skeletal mineralogy and size

Nicholas A. Kamenos, Gabriela Perna, Maria Cristina Gambi, Fiorenza Micheli, Kristy J. Kroeker, K. J. Kroeker, F. Micheli, N. A. Kamenos & G. Perna
To understand the effects of ocean acidification (OA) on marine calcifiers, the trade-offs among different sublethal responses within individual species and the emergent effects of these trade-offs must be determined in an ecosystem setting. Crustose coralline algae (CCA) provide a model to test the ecological consequences of such sublethal effects as they are important in ecosystem functioning, service provision, carbon cycling and use dissolved inorganic carbon to calcify and photosynthesize. Settlement tiles were placed in...

Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals

Siobhán B. Cooke, Liliana M. Dávalos, Alexis M. Mychajliw, Samuel T. Turvey & Nathan S. Upham
The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals...

Data from: Dispersal enhances beta diversity in nectar microbes

Rachel L. Vannette & Tadashi Fukami
Dispersal is considered a key driver of beta diversity, the variation in species composition among local communities, but empirical tests remain limited. We manipulated dispersal of nectar-inhabiting bacteria and yeasts via flower-visiting animals to examine how dispersal influenced microbial beta diversity among flowers. Contrary to the prevailing view that dispersal lowers beta diversity, we found beta diversity was highest when dispersal was least limited. Our analysis suggested that this unexpected pattern might have resulted from...

Data from: Priority effects can persist across floral generations in nectar microbial metacommunities

Hirokazu Toju, Rachel L. Vannette, Marie-Pierre L. Gauthier, Manpreet K. Dhami & Tadashi Fukami
The order of species arrival can influence how species interact with one another and, consequently, which species may coexist in local communities. This phenomenon, called priority effects, has been observed in various types of communities, but it remains unclear whether priority effects persist over the long term spanning multiple generations of local communities in metacommunities. Focusing on bacteria and yeasts that colonize floral nectar of the sticky monkey flower, Mimulus aurantiacus, via hummingbirds and other...

Data from: Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations

Adam Lu, Christine Lee, Max Kleiman-Weiner, Brian Truong, Megan Wang, John Huguenard & Mark Beenhakker
Absence seizures result from 3-5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens seizures. Here, we show that blocking GABA transporters (GATs) in acute brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations....

A kaleidoscopic view of ovarian genes associated with infertility, subfertility and senescence

Aaron Hsueh
Ovarian infertility and subfertility presenting with premature ovarian insufficiency (POI) and diminished ovarian reserve are major issues facing in the developed world due to the trend of delaying child birth. Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder affecting 6-10% of women in reproductive age. Based on advances in whole exome sequencing, evaluation of gene copy variants, together with family-based and genome-wide association studies (GWAS), we discussed genes responsible for the POI,...

Data from: Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure

Sonya Erlandson, Xiaojing Wei, Jessica Savage, Jeannine Cavender-Bares & Kabir Peay
Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity, and their interactions in shaping soil microbial communities. Using a multi-factor, split-plot field experiment, we tested how...

Data from: A global perspective on the trophic geography of sharks

Christopher Stephen Bird, Ana Veríssimo, Sarah Magozzi, Kátya G. Abrantes, Alex Aguilar, Hassan Al-Reasi, Adam Barnett, Dana M. Bethea, Gérard Biais, Asuncion Borrell, Marc Bouchoucha, Mariah Boyle, Edward J. Brooks, Juerg Brunnschweiler, Paco Bustamante, Aaron Carlisle, Diana Catarino, Stéphane Caut, Yves Cherel, Tiphaine Chouvelon, Diana Churchill, Javier Ciancio, Julien Claes, Ana Colaço, Dean L. Courtney … & Clive N. Trueman
Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits...

Data from: Spatiotemporal dynamics and genome-wide association analysis of desiccation tolerance in Drosophila melanogaster

Subhash Rajpurohit, Eran Gefen, Alan O. Bergland, Dmitri A. Petrov, Allen G. Gibbs & Paul S. Schmidt
Water availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over spatial and temporal scales and is an important physiological determinant of fitness in natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: 1) natural populations sampled across latitudes and seasons; 2) experimental evolution in field mesocosms over seasonal time; 3) genome-wide associations to identify SNPs/genes associated...

Data from: Environmental influence on growth history in marine benthic foraminifera

Caitlin R. Keating-Bitonti & Jonathan L. Payne
Energy availability influences natural selection on the ontogenetic histories of organisms. However, it remains unclear if physiological controls on size remain constant throughout ontogeny or instead shift as organisms grow larger. Benthic foraminifera provide an opportunity to quantify and interpret the physicochemical controls on both initial (proloculus) and adult volumes across broad environmental gradients using first principles of cell physiology. Here, we measured proloculus and adult test dimensions of 129 modern rotaliid species from published...

Data from: Missing the people for the trees: identifying coupled natural-human system feedbacks driving the ecology of Lyme disease

Andrew J. MacDonald, Ashley E. Larsen & Andrew J. Plantinga
1. Infectious diseases are rapidly emerging and many are increasing in incidence across the globe. Processes of land-use change, notably habitat loss and fragmentation, have been widely implicated in emergence and spread of zoonoses such as Lyme disease, yet evidence remains equivocal. 2. Here we discuss and apply an innovative approach from the social sciences, instrumental variables, that seeks to tease out causality from observational data. Using this approach, we revisit the effect of forest...

Presentation Panel on Metadata Standards

Andrea d'Andrea, Christina Harlow, Julie Hardesty & Jon Blundell
Examples of topics of interest- Why do we need metadata standards development? How are standards developed? Given the lack of agreed upon standards for 3D data, what solutions are institutions currently using? What are users’ needs regarding metadata? Who are the targeted users? What constitutes the minimal metadata for inclusion in a repository? How can linked metadata be developed for improved workflows. What would be required for data clean up or migration for previously unstandardized...

Data from: No evidence that gut microbiota impose a net cost on their butterfly host

Alison Ravenscraft, Nicole Kish, Kabir Peay & Carol Boggs
Gut microbes are believed to play a critical role in most animal life, yet fitness effects and cost benefit-tradeoffs incurred by the host are poorly understood. Unlike most hosts studied to date, butterflies largely acquire their nutrients from larval feeding, leaving relatively little opportunity for nutritive contributions by the adult’s microbiota. This provides an opportunity to measure whether hosting gut microbiota comes at a net nutritional price. Since host and bacteria may compete for sugars,...

Data from: Direct measurement of swimming and diving kinematics of giant Atlantic bluefin tuna (Thunnus thynnus)

Adrian C. Gleiss, Robert S. Schallert, Jonathan J. Dale, Steven G. Wilson & Barbara A. Block
Tunas possess a range of physiological and mechanical adaptations geared towards high performance swimming that are of considerable interest to physiologists, ecologists and engineers. Advances in biologging have provided significant improvements in understanding tuna migrations and vertical movement patterns, yet our understanding of the locomotion and swimming mechanics of these fish under natural conditions is limited. We equipped Atlantic bluefin tuna (Thunnus thynnus) with motion sensitive tags and video cameras to quantify the gaits and...

Data for: Emergent ferromagnetism near three-quarters filling in twisted bilayer graphene

Aaron Sharpe, Eli Fox, Arthur Barnard, Joe Finney, Kenji Watanabe, Takashi Taniguchi, Marc Kastner & David Goldhaber-Gordon
This archive contains the data and Python code generating figures for the article "Emergent ferromagnetism near three-quarters filling in twisted bilayer graphene" by Aaron L. Sharpe, Eli J. Fox, Arthur W. Barnard, Joe Finney, Kenji Watanabe, Takashi Taniguchi, M. A. Kastner, and David Goldhaber-Gordon and available at https://arxiv.org/abs/1901.03520. This archive contains the following: 1) TBG_ferromagnetism_figures.ipynb, a Jupyter notebook loading data and generating figures. The notebook has been tested with Python version 3.6.7 and Jupyter notebook...

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...

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...

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...

Ecosystem Scale Measurements of Methyl Halide Fluxes from a Brackish Tidal Marsh Invaded with Perennial Pepperweed (Lepidium latifolium)

Malte Julian Deventer, Yi Jiao, Sarah Knox, Frank Anderson, Matthew Ferner, Jared Lewis, Robert Rhew & Robert Rhew
Natural methyl chloride (CH3Cl) and methyl bromide (CH3Br) emissions from coastal marsh ecosystems may constitute a significant proportion of stratospheric chlorine and bromine, which catalyze ozone depletion. Current inventories involve substantial uncertainties associated with up-scaling plot-scale footprints (i.e., ≤ 1m2). Here we present net ecosystem flux measurements of methyl halides from a brackish tidal marsh on the west coast of the United States between April 2016 and June 2017 using the relaxed eddy accumulation method....

Software and Calibration for Photothermal Threshold Quantum Yield

David Hanifi
This is code used to process and apply calibrations to photothermal threshold quantum yields taken, with our specific spectrometer. The calibrations included will not work for any other optics path or components, but this serves as a guide to calibrate one built in any other lab. This code is written in Matlab2018b.

Registration Year

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Resource Types

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Affiliations

  • Stanford University
    289
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