45 Works

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
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....

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: 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...

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: 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: Evolution of the exclusively human-pathogen Neisseria gonorrhoeae: human-specific engagement of immunoregulatory Siglecs

Corinna S. Landig, Ashley Hazel, Benjamin P. Kellman, Jerry J. Fong, Flavio Schwarz, Sarika Agarwal, Nissi Varki, Paola Massari, Nathan E. Lewis, Sanjay Ram & Ajit Varki
Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea exclusively in humans and uses multiple strategies to infect, including acquisition of host sialic acids that cap and mask lipooligosaccharide termini, while restricting complement activation. We hypothesized that gonococci selectively target human anti-inflammatory sialic acid-recognizing Siglec receptors on innate immune cells to blunt host responses, and that pro-inflammatory Siglecs and SIGLEC pseudogene polymorphisms represent host evolutionary adaptions to counteract this interaction. N. gonorrhoeae can indeed engage multiple...

Data from: Long-term live imaging of the Drosophila adult midgut reveals real-time dynamics of division, differentiation, and loss

Judy Lisette Martin, Erin Nicole Sanders, Paola Moreno-Roman, Leslie Ann Jaramillo Koyama, Shruthi Balachandra, XinXin Du & Lucy Erin O'Brien
Organ renewal is governed by the dynamics of cell division, differentiation, and loss. To study these dynamics in real time, we present a platform for extended live imaging of the adult Drosophila midgut, a premier genetic model for stem cell-based organs. A window cut into a living animal allows the midgut to be imaged while intact and physiologically functioning. This approach prolongs imaging sessions to 12-16 hours and yields movies that document cell and tissue...

Data from: U-Index, a dataset and an impact metric for informatics tools and databases

Alison Callahan, Rainer Winnenburg & Nigam H. Shah
Measuring the usage of informatics resources such as software tools and databases is essential to quantifying their impact, value and return on investment. We have developed a publicly available dataset of informatics resource publications and their citation network, along with an associated metric (u-Index) to measure informatics resources’ impact over time. Our dataset differentiates the context in which citations occur to distinguish between ‘awareness’ and ‘usage’, and uses a citing universe of open access publications...

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph Frederic Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximillian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & Stephen A. Smith
Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available...

Data from: Temperature explains broad patterns of Ross River virus transmission

Marta Shocket, Sadie Ryan, Erin Mordecai, Marta Strecker Shocket, Erin A Mordecai & Sadie J Ryan
Thermal biology predicts that vector-borne disease transmission peaks at intermediate temperatures and declines at high and low temperatures. However, thermal optima and limits remain unknown for most vector-borne pathogens. We built a mechanistic model for the thermal response of Ross River virus, an important mosquito-borne pathogen in Australia, Pacific Islands, and potentially at risk of emerging worldwide. Transmission peaks at moderate temperatures (26.4{degree sign}C) and declines to zero at thermal limits (17.0{degree sign}C and 31.5{degree...

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,...

Hawaiian forest bird foraging height

Erin Wilson Rankin, Jessie Knowlton, Daniel Gruner, David Flaspohler, Christian Giardina, Devin Leopold, Anna Buckhardt, William Pitt & Tadashi Fukami
Data relevant to study on the foraging height of Hawaiian forest birds collected in kipuka along the Saddle Road, Upper Waiakea Forest Reserve.

Data from: Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences

Soo-Yon Rhee & Robert W. Shafer
Accurate classification of HIV-1 group M lineages, henceforth referred to as subtyping, is essential for understanding global HIV-1 molecular epidemiology. Because most HIV-1 sequencing is done for genotypic resistance testing pol gene, we sought to develop a set of geographically-stratified pol sequences that represent HIV-1 group M sequence diversity. Representative pol sequences differ from representative complete genome sequences because not all CRFs have pol recombination points and because complete genome sequences may not faithfully reflect...

Data from: Rapid divergence of mussel populations despite incomplete barriers to dispersal

Diede L. Maas, Stefan Prost, Ke Bi, Lydia L. Smith, Ellie E. Armstrong, Ludi P. Aji, Abdul H.A. Toha, Rosemary G. Gillespie & Leontine E. Becking
Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to...

Data from: Determining the genetic basis of anthracycline-cardiotoxicity by response QTL mapping in induced cardiomyocytes

David A. Knowles, Courtney K. Burrows, John D. Blischak, Kristen M. Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard & Yoav Gilad
Anthracycline-induced cardiotoxicity (ACT) is a key limiting factor in setting optimal chemotherapy regimes, with almost half of patients expected to develop congestive heart failure given high doses. However, the genetic basis of sensitivity to anthracyclines remains unclear. We created a panel of iPSC-derived cardiomyocytes from 45 individuals and performed RNA-seq after 24h exposure to varying doxorubicin dosages. The transcriptomic response is substantial: the majority of genes are differentially expressed and over 6000 genes show evidence...

Data from: Adaptive developmental plasticity in rhesus macaques: the serotonin transporter gene interacts with maternal care to affect juvenile social behaviour

Jesus E. Madrid, Tara M. Mandalaywala, Sean P. Coyne, Jamie Ahloy-Dallaire, Joseph P. Garner, Christina S. Barr, Dario Maestripieri & Karen J. Parker
Research has increasingly highlighted the role that developmental plasticity-the ability of a particular genotype to produce variable phenotypes in response to different early environments-plays as an adaptive mechanism. One of the most widely studied genetic contributors to developmental plasticity in humans and rhesus macaques is a serotonin transporter gene-linked polymorphic region (5-HTTLPR), which determines transcriptional efficiency of the serotonin transporter gene in-vitro and modifies the availability of synaptic serotonin in these species. A majority of...

Data from: Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages

Manpreet K. Dhami, Thomas Hartwig, Andrew D. Letten, Michael Banf & Tadashi Fukami
Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability, and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M....

Data from: Evaluating tools for the spatial management of fisheries

Steven W.J. Canty, Nathan K. Truelove, Richard F. Preziosi, Simon Chenery, Matthew A.S. Horstwood, Stephen J. Box, Matthew A. S. Horstwood & Steven W. J. Canty
1. The ability to define the spatial dynamics of fish stocks is critical to fisheries management. Combating illegal, unreported and unregulated (IUU) fishing and the implementation of area based management through physical patrols and port side controls are growing areas of management attention. Augmenting the existing approaches to fisheries management with forensic techniques has the potential to increase compliance and enforcement success rates. 2. We tested the accuracy of three techniques that can be used...

Data from: Validation of an algorithm for identifying MS cases in administrative health claims datasets

William J. Culpepper, Ruth Anne Marrie, Annette Langer-Gould, Mitchell T. Wallin, Jonathan D. Campbell, Lorene M. Nelson, Wendy E. Kaye, Laurie Wagner, Helen Tremlett, Lie H. Chen, Stella Leung, Charity Evans, Shenzhen Yao & Nicholas G. LaRocca
Objective: To develop a valid algorithm for identifying multiple sclerosis (MS) cases in administrative health claims (AHC) datasets. Methods: We used 4 AHC datasets from the Veterans Administration (VA), Kaiser Permanente Southern California (KPSC), Manitoba (Canada), and Saskatchewan (Canada). In the VA, KPSC, and Manitoba, we tested the performance of candidate algorithms based on inpatient, outpatient, and disease-modifying therapy (DMT) claims compared to medical records review using sensitivity, specificity, positive and negative predictive values, and...

Data from: Catechol-O-Methyltransferase moderates effect of stress mindset on affect and cognition

Alia J. Crum, Modupe Akinola, Bradley P. Turnwald, Ted J. Kaptchuk & Kathryn T. Hall
There is evidence that altering stress mindset— the belief that stress is enhancing vs. debilitating —can change cognitive, affective and physiological responses to stress. However individual differences in responsiveness to stress mindset manipulations have not been explored. Given the previously established role of catecholamines in both placebo effects and stress, we hypothesized that genetic variation in catechol-O-methyltransferase (COMT), an enzyme that metabolizes catecholamines, would moderate responses to an intervention intended to alter participants’ mindsets about...

Data from: Phytochemical changes in milkweed induced by elevated CO2 alter wing morphology but not toxin sequestration in monarch butterflies

Leslie E. Decker, Abrianna J. Soule, Jacobus C. De Roode & Mark D. Hunter
1. Environmental change has the potential to influence trophic interactions by altering the defensive phenotype of prey. 2. Here, we examine the effects of a pervasive environmental change driver, elevated atmospheric concentrations of CO2 (eCO2), on toxin sequestration and flight morphology of a specialist herbivore. 3. We fed monarch butterfly larvae, Danaus plexippus, foliage from four milkweed, Asclepias, species of varying chemical defense profiles grown under either ambient or eCO2. We also infected a subset...

Data from: Biodiversity monitoring, earth observations, and the ecology of scale

Christopher B. Anderson
Human activity and land use change are dramatically altering the sizes, geographic distributions, and functioning of biological populations worldwide, with tremendous consequences for human well-being. Yet our ability to measure, monitor, and forecast biodiversity change – crucial to addressing it – remains limited. Biodiversity monitoring systems are being developed to improve this capacity by deriving metrics of change from an array of in situ data (e.g., field plots or species occurrence records) and Earth observations...

Data from: Increase in crop losses to insect pests in a warming climate

Curtis A. Deutsch, Joshua J. Tewksbury, Michelle Tigchelaar, David S. Battisti, Scott C. Merrill, Raymond B. Huey & Rosamond L. Naylor
Insect pests substantially reduce yields of three staple grains—rice, maize, and wheat—but models assessing the agricultural impacts of global warming rarely consider crop losses to insects. We use established relationships between temperature and the population growth and metabolic rates of insects to estimate how and where climate warming will augment losses of rice, maize, and wheat to insects. Global yield losses of these grains are projected to increase by 10 to 25% per degree of...

Data from: Potential limitations of behavioral plasticity and the role of egg relocation in climate change mitigation for a thermally-sensitive endangered species

Michael J. Liles, Tarla Rai Peterson, Jeffrey A. Seminoff, Alexander R. Gaos, Eduardo Altamirano, Ana V. Henríquez, Velkiss Gadea, Sofía Chavarría, José Urteaga, Bryan P. Wallace & Markus J. Peterson
Anthropogenic climate change is widely considered a major threat to global biodiversity, such that the ability of a species to adapt will determine its likelihood of survival. Egg-burying reptiles that exhibit temperature-dependent sex determination, such as critically endangered hawksbill turtles (Eretmochelys imbricata), are particularly vulnerable to changes in thermal regimes because nest temperatures affect offspring sex, fitness, and survival. It is unclear whether hawksbills possess sufficient behavioral plasticity of nesting traits (i.e., redistribution of nesting...

Data from: Combining fish and benthic communities into multiple regimes reveals complex reef dynamics

Mary K. Donovan, Alan M. Friedlander, Joey Lecky, Jean-Baptiste Jouffray, Gareth J. Williams, Lisa M. Wedding, Larry B. Crowder, Ashley L. Erickson, Nick A. J. Graham, Jamison M. Gove, Carrie V. Kappel, Kendra Karr, John N. Kittinger, Albert V. Norström, Magnus Nyström, Kirsten L. L. Oleson, Kostantinos A. Stamoulis, Crow White, Ivor D. Williams & Kimberly A. Selkoe
Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai‘i to...

Registration Year

  • 2018

Resource Types

  • Dataset
  • Text


  • Stanford University
  • University of California, Santa Barbara
  • University of Michigan-Ann Arbor
  • University of Chicago
  • Cornell University
  • Bangor University
  • University of Massachusetts Amherst
  • University of Pennsylvania
  • University of Washington
  • University of California System