44 Works

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: 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: 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...

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: 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: 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...

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: 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: 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: 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: 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: 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...

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: 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: Priority effects are weakened by a short, but not long, history of sympatric evolution

Peter C. Zee & Tadashi Fukami
Priority effects, or the effects of species arrival history on local species abundances, have been documented in a range of taxa. However, factors determining the extent to which priority effects affect community assembly remain unclear. Using laboratory populations of the bacterium Pseudomonas fluorescens, we examined whether shared evolutionary history affected the strength of priority effects. We hypothesized that sympatric evolution of populations belonging to the same guild would lead to niche differentiation, resulting in phenotypic...

Data from: Species coexistence through simultaneous fluctuation-dependent mechanisms

Andrew D. Letten, Manpreet K. Dhami, Po-Ju Ke & Tadashi Fukami
Understanding the origins and maintenance of biodiversity remains one of biology's grand challenges. From theory and observational evidence we know that variability in environmental conditions through time is likely critical to the coexistence of competing species. Nevertheless, strong experimental tests of fluctuation-driven coexistence are rare, and have typically focused on just one of two potential mechanisms, the temporal storage effect, to the neglect of the theoretically equally plausible mechanism known as relatively nonlinearity of competition....

Data from: Oxygen, temperature and the deep-marine stenothermal cradle of Ediacaran evolution

Thomas H. Boag, Richard G. Stockey, Leanne E. Elder, Pincelli M. Hull & Erik A. Sperling
Ediacaran fossils document the early evolution of complex megascopic life, contemporaneous with geochemical evidence for widespread marine anoxia. These data suggest early animals experienced frequent hypoxia. Research has thus focused on the concentration of molecular oxygen (O2) required by early animals, while also considering the impacts of climate. One model, the Cold Cradle hypothesis, proposed the Ediacaran biota originated in cold, shallow-water environments due to increased O2 solubility. First, we demonstrate using principles of gas...

Data from: Temperature drives Zika virus transmission: evidence from empirical and mathematical models

Blanka Tesla, Leah Demakovsky, Erin Mordecai, Sadie Ryan, Matthew Bonds, Calistus Ngonghala, Melinda Brindley & Courtney Murdock
Temperature is a strong driver of vector-borne disease transmission. Yet, for emerging arboviruses we lack fundamental knowledge on the relationship between transmission and temperature. Current models rely on the untested assumption that Zika virus responds similarly to dengue virus, potentially limiting our ability to accurately predict the spread of Zika. We conducted experiments to estimate the thermal performance of Zika virus (ZIKV) in field-derived Aedes aegypti across eight constant temperatures. We observed strong, unimodal effects...

Data from: Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy

Philip Lei Tzou, Soo-Yon Rhee, Sergei L. Kosakovsky Pond, Justen Manasa & Robert W. Shafer
Most HIV-1-infected individuals with virological failure (VF) on a pharmacologically-boosted protease inhibitor (PI)-containing regimen do not develop PI-resistance protease mutations. One proposed explanation is that mutations in HIV-1 gag or gp41 cytoplasmic domain might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with VF on a PI-containing regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from...

Data from: Timing of host feeding drives rhythms in parasite replication

Kimberley F. Prior, Daan R. Van Der Veen, Aidan J. O'Donnell, Katherine Cumnock, David Schneider, Arnab Pain, Amit Subudhi, Abhinay Ramaprasad, Samuel S. C. Rund, Nicholas J. Savill, Sarah E. Reece & Aidan J. O’Donnell
Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence...

Data from: Community-wide consequences of sexual dimorphism: evidence from nectar microbes in dioecious plants

Kaoru Tsuji & Tadashi Fukami
Intra-specific trait variation is receiving renewed interest as a factor affecting the structure of multi-species communities within and across trophic levels. One pervasive form of intra-specific trait variation is sexual dimorphism in animals and plants, which might exert large effects particularly on the communities of host-associated organisms, but the extent of these effects is not well understood. We investigated whether host-associated microbial communities developed differently in the floral nectar of female and male individuals of...

Data from: Invasive rat eradication strongly impacts plant recruitment on a tropical atoll

Coral A. Wolf, Hillary S. Young, Kelly M. Zilliacus, Alex S. Wegmann, Matthew McKown, Nick D. Holmes, Bernie R. Tershy, Rodolfo Dirzo, Stefan Kropidlowski, Donald A. Croll & Alexander S. Wegmann
Rat eradication has become a common conservation intervention in island ecosystems and its effectiveness in protecting native vertebrates is increasingly well documented. Yet, the impacts of rat eradication on plant communities remain poorly understood. Here we compare native and non-native tree and palm seedling abundance before and after eradication of invasive rats (Rattus rattus) from Palmyra Atoll, Line Islands, Central Pacific Ocean. Overall, seedling recruitment increased for five of the six native trees species examined....

Data from: Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies

Alison Ravenscraft, Michelle Berry, Tobin Hammer, Kabir Peay & Carol Boggs
The relationship between animals and their gut flora is simultaneously one of the most common and most complex symbioses on Earth. Despite its ubiquity, our understanding of this invisible but often critical relationship is still in its infancy. We employed adult Neotropical butterflies as a study system to ask three questions: First, how does gut microbial community composition vary across host individuals, species and dietary guilds? Second, how do gut microbiota compare to food microbial...

Registration Year

  • 2018
    44

Resource Types

  • Dataset
    44

Affiliations

  • Stanford University
    44
  • University of California, Santa Barbara
    5
  • University of Michigan-Ann Arbor
    3
  • University of Chicago
    3
  • Cornell University
    3
  • Bangor University
    2
  • University of Massachusetts Amherst
    2
  • University of Pennsylvania
    2
  • University of Washington
    2
  • University of California System
    2