414 Works

Data from: Pollination mitigates cucumber yield gaps more than pesticide and fertilizer use in tropical smallholder gardens

Iris Motzke, Teja Tscharntke, Thomas C. Wanger & Alexandra-Maria Klein
1. Pollination can be an essential but often neglected ecosystem service to mitigate crop yield gaps. Pollination services are usually studied in isolation and their relative role and possible interactions with other factors, such as major management practices, is little understood. 2. We tested how pollination (insect versus wind- and self-pollination) interacts with weed control, fertilization, and insect herbivore control and how these factors as well as flower-visiting bees influence fruit set and yield of...

Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod

Nina O. Therkildsen, Jakob Hemmer-Hansen, Thomas D. Als, Douglas P. Swain, M. Joanne Morgan, Edward A. Trippel, Stephen R. Palumbi, Dorte Meldrup & Einar E. Nielsen
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an...

Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin

Melissa Helen Pespeni, Bryan T. Barney & Stephen R. Palumbi
Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three...

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: Patterned frequency-modulated oral stimulation in preterm infants: a multicenter randomized controlled trial

Dongli Song, Priya Jegatheesan, Suhas Nafday, Kaashif A. Ahmad, Jonathan Nedrelow, Mary Wearden, Sheri Nemerofsky, Sunshine Pooley, Diane Thompson, Daniel Vail, Tania Cornejo, Zahava Cohen & Balaji Govindaswami
Objective To evaluate the effect of patterned, frequency-modulated oro-somatosensory stimulation on time to full oral feeds in preterm infants born 26 - 30 weeks gestation. Study Design This is a multicenter randomized controlled trial. The experimental group (n = 109) received patterned, frequency-modulated oral stimulation via the NTrainer system through a pulsatile pacifier and the control group (n = 101) received a non-pulsatile pacifier. Intent-to-treat analysis (n = 210) was performed to compare the experimental...

Data from: Applying modern coexistence theory to priority effects

Tess Nahanni Grainger, Andrew D. Letten, Benjamin Gilbert & Tadashi Fukami
Modern coexistence theory is increasingly used to explain how differences between competing species lead to coexistence versus competitive exclusion. Although research testing this theory has focused on deterministic cases of competitive exclusion, in which the same species always wins, mounting evidence suggests that competitive exclusion is often historically contingent, such that whichever species happens to arrive first excludes the other. Coexistence theory predicts that historically contingent exclusion, known as priority effects, will occur when large...

Data from: Empowering conservation practice with efficient and economical genotyping from poor quality samples

Meghana Natesh, Ryan W. Taylor, Nathan Truelove, Elizabeth A. Hadly, Stephen Palumbi, Dmitri Petrov & Uma Ramakrishnan
1. Moderate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations. 2. However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from lab or medical settings. As a result, most genetic data from market or field settings is limited to easily-amplified mitochondrial DNA or a...

Data from: Species richness change across spatial scales

Jonathan M. Chase, Brian J. McGill, Patrick L. Thompson, Laura H. Antão, Amanda E. Bates, Shane A. Blowes, Maria Dornelas, Andrew Gonzalez, Anne E. Magurran, Sarah R. Supp, Marten Winter, Anne D. Bjorkmann, Helge Bruelheide, Jarrett E.K. Byrnes, Juliano Sarmento Cabral, Robin Ehali, Catalina Gomez, Hector M. Guzman, Forest Isbell, Isla H. Myers-Smith, Holly P. Jones, Jessica Hines, Mark Vellend, Conor Waldock & Mary O'Connor
Humans have elevated global extinction rates and thus lowered global-scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in...

Data from: Molecular physiology of chemical defenses in a poison frog

Stephanie N Caty, Aurora Alvarez-Buylla, Gary` D Byrd, Charles Vidoudez, Alexandre B Roland, Elicio E Tapia, Bogdan Bodnik, Sunia A Trauger, Luis A Coloma & Lauren A O'Connell
Poison frogs sequester small molecule lipophilic alkaloids from their diet of leaf litter arthropods for use as chemical defenses against predation. Although the dietary acquisition of chemical defenses in poison frogs is well-documented, the physiological mechanisms of alkaloid sequestration has not been investigated. Here, we used RNA sequencing and proteomics to determine how alkaloids impact mRNA or protein abundance in the Little Devil Frog (Oophaga sylvatica) and compared wild caught chemically defended frogs to laboratory...

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: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task

Krista K. Ingram, Deborah M. Gordon, Daniel A. Friedman, Michael Greene, John Kahler & Swetha Peteru
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure...

Data from: Patterns of variation during adaptation in functionally linked loci

Diamantis Sellis & Mark D. Longo
An understanding of the distribution of natural patterns of genetic variation is relevant to such fundamental biological fields as evolution and development. One recent approach to understanding such patterns has been to focus on the constraints which may arise as a function of the network or pathway context in which genes are embedded. Despite theoretical expectations of higher evolutionary constraint for genes encoding upstream versus downstream enzymes in metabolic pathways, empirical results have varied. Here...

Data from: Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic

Melissa H. Pespeni & Stephen R. Palumbi
Local adaptation reflects a balance between natural selection and gene flow and is classically thought to require the retention of locally adapted alleles. However, organisms with high dispersal potential across a spatially or temporally heterogeneous landscape pose an interesting challenge to this view requiring local selection every generation or when environmental conditions change to generate adaptation in adults. Here, we test for geographical and sequence-based signals of selection in five putatively adaptive and two putatively...

Data from: Rapid adaptation in large populations with very rare sex: scalings and spontaneous oscillations

Michael T. Pearce & Daniel S. Fisher
Genetic exchange in microbes and other facultative sexuals can be rare enough that evolution is almost entirely asexual and populations almost clonal. But the benefits of genetic exchange depend crucially on the diversity of genotypes in a population. How very rare recombination together with the accumulation of new mutations shapes the diversity of large populations and gives rise to faster adaptation is still poorly understood. This paper analyzes a particularly simple model: organisms with two...

Data from: Pinus ponderosa alters nitrogen dynamics and diminishes the climate footprint in natural ecosystems of Patagonia

Laura J. T. Hess & Amy T. Austin
1. Evaluating climate effects on plant-soil interactions in terrestrial ecosystems remains challenging due to the fact that floristic composition co-varies with climate, particularly along rainfall gradients. It is difficult to separate effects of precipitation per se from those mediated indirectly through changes in species composition. As such, afforestation (the intentional planting of woody species) in terrestrial ecosystems provides an ecological opportunity to assess the relative importance of climate and vegetation controls on ecosystem processes. 2....

Data from: A curated and standardized adverse drug event resource to accelerate drug safety research

Juan M. Banda, Lee Evans, Rami S. Vanguri, Nicholas P. Tatonetti, Patrick B. Ryan & Nigam H. Shah
Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for...

Data from: In an age of open access to research policies: physician and public health NGO staff research use and policy awareness

Laura L. Moorhead, Cheryl Holzmeyer, Lauren A. Maggio, Ryan M. Steinberg, John M. Willinsky & John Willinsky
Introduction: Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. Methods: A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the...

Data from: Forage species in predator diets: synthesis of data from the California Current

Amber I. Szoboszlai, Julie A. Thayer, Spencer A. Wood, William J. Sydeman & Laura E. Koehn
Characterization of the diets of upper-trophic pelagic predators that consume forage species is a key ingredient in the development of ecosystem-based fishery management plans, conservation of marine predators, and ecological and economic modeling of trophic interactions. Here we present the California Current Predator Diet Database (CCPDD) for the California Current region of the Pacific Ocean over the past century, assimilating over 190 published records of predator food habits for over 100 predator species and 32...

Data from: Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population

Jessika Adrian, Jessica Chang, Catherine E. Ballenger, Bastiaan O. R. Bargmann, Julien Alassimone, Kelli A. Davies, On Sun Lau, Juliana L. Matos, Charles Hachez, Amy Lanctot, Anne Vatén, Kenneth D. Birnbaum & Dominique C. Bergmann
Developmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell lineage in the Arabidopsis leaf. We show that regulatory...

Data from: Muscle-tendon mechanics explain unexpected effects of exoskeleton assistance on metabolic rate during walking

Rachel W. Jackson, Christopher L. Dembia, Scott L. Delp & Steve H. Collins
The goal of this study was to gain insight into how ankle exoskeletons affect the behavior of the plantarflexor muscles during walking. Using data from previous experiments, we performed electromyography-driven simulations of musculoskeletal dynamics to explore how changes in exoskeleton assistance affected plantarflexor muscle–tendon mechanics, particularly for the soleus. We used a model of muscle energy consumption to estimate individual muscle metabolic rate. As average exoskeleton torque was increased, while no net exoskeleton work was...

Data from: Adaptive dynamics of cuticular hydrocarbons in Drosophila

Subhash Rajpurohit, Robert Hanus, Vladimir Vrkoslav, Emily L. Behrman, Alan O. Bergland, Dmitri Petrov, Josef Cvacka & Paul S. Schmidt
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore,...

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