56 Works

Value of Curation Survey, January 2021

Lisa R Johnston, Renata Gonçalves Curty, Sophia Lafferty-Hess, Hannah Hadley, Jonathan Petters, Hoa Luong, Susan Braxton, Jake Carlson & Wendy A Kozlowski
This dataset includes the raw and augmented survey results from the January 2021 Value of Curation survey run by the Data Curation Network. Distributed to US data repository staff and directors via email listservs the survey received a total of 120 responses. 22 responses were for non-US repositories and three did not provide a repository of reference. A majority of the participants self-identified as staff members with 52 staff and 34 repository directors. The remaining...

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Andrew Nosal, Daniel Cartamil, Arnold Ammann, Lyall Bellquist, Noah Ben-Aderet, Kayla Blincow, Echelle Burns, Eric Chapman, Ryan Freedman, Peter Klimley, Ryan Logan, Christopher Lowe, Brice Semmens, Connor White & Philip Hastings
Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years...

Protecting the global ocean for biodiversity, food and climate

Enric Sala, Juan Mayorga, Darcy Bradley, Reniel Cabral, Trisha Atwood, Arnaud Auber, William Cheung, Francesco Ferretti, Alan Friedlander, Steven Gaines, Cristina Garilao, Whitney Goodell, Benjamin Halpern, Audra Hinson, Kristin Kaschner, Kathleen Kesner-Reyes, Fabien Leprieur, Jennifer McGowan, Lance Morgan, David Mouillot, Juliano Palacios-Abrantes, Hugh Possingham, Kristin Rechberger, Boris Worm & Jane Lubchenco
The ocean contains unique biodiversity, provides valuable food resources, and is a major sink for anthropogenic carbon. Marine protected areas (MPAs) are an effective tool for restoring ocean biodiversity and ecosystem services but at present only 2.7% of the ocean is highly protected. This low level of ocean protection is due largely to conflicts with fisheries and other extractive uses. To address this issue, here we developed a conservation planning framework to prioritize highly protected...

Using acoustic telemetry to quantify potential contaminant exposure of Vermilion Rockfish (Sebastes miniatus), Hornyhead Turbot (Pleuronichthys verticalis), and White Croaker (Genyonemus lineatus) at wastewater outfalls in southern California

Echelle Burns, Barrett Wolfe, Jeff Armstrong, Danny Tang, Ken Sakamoto & Christopher Lowe
Contaminant Exposure Models (CEMs) were developed to predict population-level tissue contaminant concentrations in fishes by pairing sediment-bound contaminant concentrations (DDTs, PCBs) and fine-scale acoustic telemetry data from a habitat- associated species (Vermilion Rockfish, Sebastes miniatus), nomadic flatfish species (Hornyhead Turbot, Pleuronichthys verticalis), and nomadic benthic/midwater schooling species (White Croaker, Genyonemus lineatus) tagged near wastewater outfalls in southern California. Model results were compared to contaminant concentrations in tissue samples. The CEMs developed require further refinement before...

A distributed circuit for associating environmental context to motor choice in retrosplenial cortex

Luis Franco & Michael Goard
During navigation, animals often use recognition of familiar environmental contexts to guide motor action selection. The retrosplenial cortex (RSC) receives inputs from both visual cortex and subcortical regions required for spatial memory, and projects to motor planning regions. However, it is not known whether RSC is important for associating familiar environmental contexts with specific motor actions. Here, we test this possibility by developing a task in which trajectories are chosen based on the context. We...

El Niño and marine heatwaves: Ecological impacts on Oregon rocky intertidal kelp communities at local to regional scales

Barbara Spiecker & Bruce Menge
El Niños and marine heatwaves are predicted to increase in frequency under greenhouse warming. The impact of climate oscillations like El Niño-Southern Oscillation on coastal environments in the short-term likely mimics those of climate change in the long-term; therefore, El Niños may serve as a short-term proxy for possible long-term ecological responses to an increasingly variable climate. Understanding and prediction of ecosystem responses requires elucidating the mechanisms underlying different organizational scales (organism, space, and time)....

Spenders versus savers: climate-induced carbon allocation tradeoffs in a recently introduced woody plant

Randall Long, Tom Dudley, Carla D'Antonio, Kevin Grady, Susan Bush & Kevin Hultine
Non-structural carbohydrate(NSC) storage may be under strong selection in woody plant species that occur across strong environmental gradients. We therefore investigated carbon allocation strategies in a widely distributed, introduced woody plant. We predicted genotypes from cold climates with exposure to episodic freeze events, would have elevated NSC concentrations with the tradeoff of reduced growth and reproduction relative to warm-adapted genotypes. We established an experimental common garden using genotypes of Tamarix spp., sourced across a large...

Data from: Dermal denticle shedding rates vary between two captive shark species

Erin Dillon, Anshika Bagla, Kiera Plioplys, Douglas McCauley, Kevin Lafferty & Aaron O'Dea
Shark dermal scale (denticle) accumulation in the fossil record can provide information about the abundance and composition of past shark communities. Denticles are shed continuously, such that a single shark leaves a scattered composite of many isolated denticles in sediments. However, the rate of denticle shedding as well as how these rates vary among shark species with different life modes and their consistency over time are unknown, limiting the interpretation of denticle assemblages. To better...

Experience-dependent plasticity modulates ongoing activity in the antennal lobe and enhances odor representations

Luis Franco & Emre Yaksi
Ongoing neural activity has been observed across several brain regions and is thought to reflect the internal state of the brain. Yet, it is important to understand how ongoing neural activity interacts with sensory experience, and shapes sensory representations. Here, we show that projection neurons of the fruit fly antennal lobe exhibit spatiotemporally organized ongoing activity. After repeated exposure to odors, we observe a gradual and cumulative decrease in the amplitude and number of calcium...

Exposure, hazard and vulnerability all contribute to Schistosoma haematobium re-infection in northern Senegal

Andrea Lund, Susanne Sokolow, Isabel Jones, Chelsea Wood, Sofia Ali, Andrew Chamberlin, Alioune Sy, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Raphael Ndione, Gilles Riveau, Giulio De Leo & David Lopez-Carr
The risk of infectious diseases, including snail-borne schistosomiasis, is determined by three interrelated components: exposure, hazard and vulnerability. For schistosomiasis, exposure occurs through behaviors involving water contact, but not without the environmental hazard of snails and parasites in the water. Socio-economic vulnerability makes it difficult to reduce exposure in the presence of hazard, because it increases reliance on hazardous activities and environments. We aimed to quantify the contributions of exposure, hazard and vulnerability to schistosome...

Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters

Yuning Shen, Abe Pressman, Evan Janzen & Irene Chen
Characterizing genotype-phenotype relationships of biomolecules (e.g., ribozymes) requires accurate ways to measure activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g., k-Seq) is an emerging assay applicable in various domains that potentially scales up measurement throughput to over 106 unique nucleic acid sequences. However, maximizing the return of such assays requires understanding the technical challenges introduced by sequence heterogeneity and DNA sequencing. We characterized the k-Seq method in terms of model...

Long-term change in the parasite burden of shore crabs (Hemigrapsus oregonensis and H. nudus) on the northwestern Pacific coast of North America

Jessica Quinn, Sarah Lee, Duncan Greeley, Alyssa Gehman, Armand Kuris & Chelsea Wood
The abundances of free-living species have changed dramatically in recent decades, but little is known about change in the abundance of parasitic species. We investigated whether populations of several parasites have shifted over time in two shore crab hosts, Hemigrapsus oregonensis and H. nudus, by comparing the prevalence and abundance of three parasite taxa in a historical dataset (1969–1970) to contemporary parasite abundance (2018–2020) for hosts collected from 11 intertidal sites located from Oregon, USA...

Data related to: Open-system evolution of a crustal-scale magma column, Klamath Mountains, California

Calvin Barnes, Nolwenn Coint, Melanie Barnes, Ariel Strickland, John Cottle, O. Ramo, Kevin Chamberlain & John Valley
Granitic magmas commonly display evidence for some level of interaction with and/or origins from crustal rocks. There is fundamental debate in the community as to the processes that control the origins of these magmas and the potential for their contamination as they pass through the crust. One approach to addressing these issues involves a combination of detailed field mapping combined with geochemical analysis of bulk-rock samples and their constituent minerals. In particular, resolution of debates...

Imaging the breakdown of ohmic transport in graphene

Alec Jenkins, Susanne Baumann, Haoxin Zhou, Simon Meynell, Daipeng Yang, Kenji Watanabe, Takashi Taniguchi, Andrew Lucas, Andrea Young & Ania Bleszynski Jayich
Ohm's law describes the proportionality of current density and electric field. In solid-state conductors, Ohm's law emerges due to electron scattering processes that relax the electrical current. Here, we use nitrogen-vacancy center magnetometry to directly image the local breakdown of Ohm's law in a narrow constriction fabricated in a high mobility graphene monolayer. Ohmic flow is visible at room temperature as current concentration on the constriction edges, with flow profiles entirely determined by sample geometry....

Data from: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog

Roland Knapp, Maxwell Joseph, Thomas Smith, Ericka Hegeman, Vance Vredenburg, James Erdman, Daniel Boiano, Andrea Jani & Cheryl Briggs
The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity ("load") and in doing so alter frog-Bd dynamics and increase the probability of frog population...

Testing the adaptive value of sporulation in budding yeast using experimental evolution

Kelly Thomasson, Alexander Franks, Henrique Teotonio & Stephen Proulx
Saccharomyces yeast grow through mitotic cell division, converting resources into biomass. When cells experience starvation, sporulation is initiated and meiosis produces haploid cells inside a protective ascus. The protected spore state does not acquire resources and is partially protected from desiccation, heat, and caustic chemicals. Because cells cannot both be protected and acquire resources simultaneously, committing to sporulation represents a trade-off between current and future reproduction. Recent work has suggested that passaging through insect guts...

Datasets associated with: Late Holocene spread of pastoralism coincides with endemic megafaunal extinction on Madagascar

Sean Hixon, Kristina Douglass, Brooke Crowley, Lucien Rakotozafy, Geoffrey Clark, Atholl Anderson, Simon Haberle, Jean Freddy Ranaivoarisoa, Mike Buckley, Salomon Fidiarisoa, Balzac Mbola & Douglas Kennett
Recently expanded estimates for when humans arrived on Madagascar (up to ~10,000 years ago) highlight questions about the causes of the island’s relatively late megafaunal extinctions (~2000-500 years ago). Introduced domesticated animals could have contributed to extinctions, but the arrival times and past diets of exotic animals are poorly known. To conduct the first explicit test of the potential for competition between introduced livestock and extinct endemic megafauna in southern and western Madagascar, we generated...

Behavioral probabilities and sample videos for \"Behavioral evidence for nested central pattern generator control of Drosophila grooming\"

Primoz Ravbar, Neil Zhang & Julie Simpson
Central pattern generators (CPGs) are neurons or neural circuits that produce periodic output without requiring patterned input. More complex behaviors can be assembled from simpler subroutines, and nested CPGs have been proposed to coordinate their repetitive elements, organizing control over different time-scales. Here, we use behavioral experiments to establish that Drosophila grooming may be controlled by nested CPGs. On a short time-scale (5-7 Hz), flies execute periodic leg sweeps and rubs. More surprisingly, transitions between...

Site fidelity and behavioral plasticity regulate an ungulate’s response to extreme disturbance

Samantha Kreling, Kaitlyn Gaynor, Alex McInturff, Kendall Calhoun & Justin Brashares
1. With rapid global change, the frequency and severity of extreme disturbance events are increasing worldwide. The ability of animal populations to survive these stochastic events depends on how individual animals respond to their altered environments, yet our understanding of the immediate and short-term responses of animals to acute disturbances remains poor. 2. We focused on animal responses to the environmental disturbance created by megafire. Specifically, we explored the effects of the 2018 Mendocino Complex...

A global ecological signal of extinction risk in terrestrial vertebrates

Maya Munstermann, Noel Heim, Douglas McCauley, Jonathan Payne, Nathan Upham, Steve Wang & Matthew Knope
To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled a dataset on ecological traits for 18,016 species and tested, using phylogenetic comparative methods, which categories of habitat association, mode of locomotion, and feeding mode best predict extinction risk. We found that cave-dwelling amphibians, brachiating mammals (all of which are primates), aerial and scavenging birds, and pedal squamates are all disproportionately threatened with extinction. Across four vertebrate classes,...

Diet DNA metabarcoding data from spiders (Heteropoda venatoria) from Palmyra Atoll (2015-2017) with both individual samples that have and have not been surface sterilized

Ana Miller-Ter Kuile, Austen Apigo & Hillary Young
These are data and code from a study examining the potential for surface contamination to influence diet DNA metabarcoding datasets when DNA is sequenced from full body parts (in this case, the opisthosomas of spider individuals). These datasets include the raw sequencing data, all downstream datasets, and taxonomic assignments collected from database searches on BOLD and GenBank (accessed 2019). The code includes code to reproduce all bioinformatics (merge, filter, match to taxonomies, rarefy, sort) as...

Analysis Data for \"Identifying and characterizing pesticide use on 9,000 fields of organic agriculture\"

Ashley Larsen, Sofie McComb, Claire Powers & Sofie McComb
We identify the location of ~9,000 organic fields from 2013 — 2019 using field-level crop and pesticide use data, along with state certification data, for Kern County, CA, one of the US’ most valuable crop producing counties. We parse apart how being organic relative to conventional affects decisions to spray pesticides and, if spraying, how much to spray. We show the expected probability of spraying any pesticides is reduced by about 30 percentage points for...

The release of inertial instability near an idealized zonal jet

Callum Thompson & David M. Schultz
Inertial instability is a hydrodynamic instability that occurs in strong anticyclonic flow and is typically diagnosed by negative absolute vorticity in the Northern Hemisphere. As such, inertial instability is often observed on the anticyclonic-shear side of jet streams, yet the release of the instability in this environment is still poorly understood. We simulate the release of inertial instability near an idealized midlatitude zonal jet compared a control simulation with no instability. We find that the...

Variation in salinity tolerance and water use strategies in an introduced woody halophyte (Tamarix spp.)

Randy Long, Carla D'Antonio, Tom Dudley & Kevin Hultine
1. The form and function of terrestrial plants is largely governed by the availability of water, with plants in water limited environments expressing traits minimizing water loss and tissue damage during drought. Areas with high salinity are analogous to those with low water availability, even where water is abundant. We evaluated variation in salinity tolerance and water use strategies in an introduced halophytic shrub, Tamarix spp by measuring gas exchange rates, biomass accumulation, and turgor...

Sex differences in behavioural and anatomical estimates of visual acuity in the green swordtail Xiphophorus helleri

Eleanor M Caves, Fanny De Busserolles & Laura A Kelley
Among fishes in the family Poeciliidae, signals such as colour patterns, ornaments, and courtship displays play important roles in mate choice and male-male competition. Despite this, visual capabilities in Poeciliids are understudied, in particular visual acuity, the ability to resolve detail. We used three methods to quantify visual acuity in male and female green swordtails (Xiphophorus helleri), a species in which body size and the length of the male's extended caudal fin ('sword') serve as...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of California, Santa Barbara
  • Stanford University
  • United States Geological Survey
  • University of British Columbia
  • University of Washington
  • Atomic Energy and Alternative Energies Commission
  • University of Queensland
  • University of Colorado Boulder
  • Federal Institute for Geosciences and Natural Resources
  • California State University, Long Beach