186 Works

Data from: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

Dataset marmoset Snowdrift

Alejandro Sanchez Amaro, Judith Burkart & Federico Rossano
Social primates constantly face situations in which their preferences collide and they need to engineer strategies to overcome conflicts of interest. Studies with chimpanzees have found that they use competitive strategies to overcome social dilemmas, maximizing their own benefits while minimizing the loss of rewards. However, little is known about how other primates that rely more on cooperation would overcome similar dilemmas. We therefore presented male-female pairs of common marmosets (cooperative breeders) with two experiments...

Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus

Felipe S. Barreto, Sean D. Schoville & Ronald S. Burton
Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are...

Data from: Seasonal changes in plankton food web structure and carbon dioxide flux from Southern California reservoirs

Emily M. Adamczyk & Jonathan B. Shurin
Reservoirs around the world contribute to cycling of carbon dioxide (CO2) with the atmosphere, but there is little information on how ecosystem processes determine the absorption or emission of CO2. Reservoirs are the most prevalent freshwater systems in the arid southwest of North America, yet it is unclear whether they sequester or release CO2 and therefore how water impoundment impacts global carbon cycling. We sampled three reservoirs in San Diego, California, weekly for one year....

Data from: Pollution-tolerant invertebrates enhance greenhouse gas flux in urban wetlands

Andrew S. Mehring, Perran L.M. Cook, Victor Evrard, Stanley B. Grant, Lisa A. Levin & Perran L. M. Cook
One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if their effects can be detected in highly variable conditions in a field setting. Here we use an extensive dataset on carbon dioxide...

Data from: Monarch butterfly population decline in North America: identifying the threatening processes

Wayne E. Thogmartin, Ruscena Wiederholt, Karen Oberhauser, Ryan G. Drum, Jay E. Diffendorfer, Sonia Altizer, Orley R. Taylor, John Pleasants, Darius Semmens, Brice Semmens, Richard Erickson, Kaitlin Libby & Laura Lopez-Hoffman
The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids)....

Data from: Ear mite removal in the Santa Catalina Island fox (Urocyon littoralis catalinae): controlling risk factors for cancer development

Megan E. Moriarty, T. Winston Vickers, Deana L. Clifford, David K. Garcelon, Patricia M. Gaffney, Kenneth W. Lee, Julie L. King, Calvin L. Duncan & Walter M. Boyce
Ear mites (Otodectes cynotis) and ear canal tumors are highly prevalent among federally endangered Island foxes (Urocyon littoralis catalinae) living on Santa Catalina Island off the coast of Southern California. Since studies began in the 1990s, nearly all foxes examined were found to be infected with ear mites, and ceruminous gland tumors (carcinomas and adenomas) were detected in approximately half of all foxes ≥ 4 years of age. We hypothesized that reduction of ear mite...

Data from: Lethal and sublethal synergistic effects of a new systemic pesticide, flupyradifurone (Sivanto®) on honey bees

Simone Tosi & James Nieh
The honey bee (Apis mellifera L.) is an important pollinator and a model for pesticide effects on insect pollinators. The effects of agricultural pesticides on honey bee health have therefore raised concern. Bees can be exposed to multiple pesticides that may interact synergistically, amplifying their side-effects. Attention has focused on neonicotinoid pesticides, but flupyradifurone (FPF) is a novel butenolide insecticide that is also systemic and a nicotinic acetylcholine receptor (nAChR) agonist. We therefore tested the...

Data from: Crossing the line: tunas actively exploit submesoscale fronts to enhance foraging success

Stephanie Snyder, Peter J. S. Franks, Lynne D. Talley, Yi Xu & Suzanne Kohin
Fronts – i.e., the boundaries between water masses – are ubiquitous in the world oceans and have been shown to significantly influence pelagic ecosystems with enhanced local productivity and increased abundances of forage fish and top predators. Here we use data from archival tags to document how four juvenile albacore tunas foraged at and exploited a thermal front. Of the 3,098 observed trips, the albacore mainly swam across the front between the warm side above...

Data from: Audience affects decision-making in a marmoset communication network

Camille R. Toarmino, Lauren Wong & Cory T. Miller
An audience can have a profound effect on the dynamics of communicative interactions. As a result, non-human primates often adjust their social decision-making strategies depending on the audience composition at a given time. Here we sought to test how the unique vocal behaviour of multiple audience members affected decisions to communicate. To address this issue, we developed a novel experimental paradigm in which common marmosets directly interacted with multiple ‘virtual monkeys’ (VMs), each of whom...

Data from: Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change

Elizabeth Sibert, Richard Norris, Jose M. Cuevas, Lana G. Graves & Jose Cuevas
While the history of taxonomic diversification in open ocean lineages of ray-finned fish and elasmobranchs is increasingly known, the evolution of their roles within the open ocean ecosystem remains poorly understood. To assess the relative importance of these groups through time, we measured the accumulation rate of microfossil fish teeth and elasmobranch dermal denticles (ichthyoliths) in deep-sea sediment cores from the North and South Pacific gyres over the past 85 million years (Myr). We find...

Data from: Effects of sea ice cover on satellite-detected primary production in the Arctic Ocean

Mati Kahru, Zhongping Lee, Brian Greg Mitchell & Cynthia D. Nevison
The influence of decreasing Arctic sea ice on net primary production (NPP) in the Arctic Ocean has been considered in multiple publications but is not well constrained owing to the potentially large errors in satellite algorithms. In particular, the Arctic Ocean is rich in coloured dissolved organic matter (CDOM) that interferes in the detection of chlorophyll a concentration of the standard algorithm, which is the primary input to NPP models. We used the quasi-analytic algorithm...

Data from: Integrating abundance and diet data to improve inferences of food web dynamics

Jake M. Ferguson, , Brianna H. Witteveen, John B. Hopkins & Briana H. Witteveen
1. Both population abundances and chemical tracers are useful tools for studying consumer-resource interactions. Food web models parameterized with abundances are often used to understand how interactions structure communities and to inform management decisions of complex ecological systems. Unfortunately, collecting abundance data to parameterize these models is often expensive and time-consuming. Another approach is to use chemical tracers to estimate the proportional diets of consumers by relating the tracers in their tissues to those found...

Data from: Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous–Palaeogene mass extinction

Elizabeth Sibert, Matthew Friedman, Pincelli Hull, Gene Hunt, Richard Norris & Matt Friedman
Molecular phylogenies suggest some major radiations of open-ocean fish clades occurred roughly coincident with the K/Pg boundary, however the timing and nature of this diversification is poorly constrained. Here we investigate evolutionary patterns in ray-finned fishes across the Cretaceous-Palaeogene (K/Pg) Mass Extinction 66 million years ago (Ma), using microfossils (isolated teeth) preserved in a South Pacific sediment core spanning 72-43 Ma. Our record does not show significant turnover of fish tooth morphotypes at the K/Pg...

Data from: Extinction risk in extant marine species integrating paleontological and biodistributional data

Katie S. Collins, Stewart M. Edie, Gene Hunt, Kaustuv Roy & David Jablonski
Extinction risk assessments of marine invertebrate species remain scarce, which hinders effective management of marine biodiversity in the face of anthropogenic impacts. In order to close this information gap, we developed a metric of relative extinction risk that combines paleontological data, in the form of extinction rates calculated from the fossil record, with two known correlates of risk in the modern day: geographic range size and realized thermal niche. We test the performance of this...

Data from: Human-like Cmah inactivation in mice increases running endurance and decreases muscle fatigability: implications for human evolution

Jonathan Okerblom, William Fletes, Hemal H. Patel, Simon Schenk, Ajit Varki & Ellen C. Breen
Compared to other primates, humans are exceptional long-distance runners, a feature that emerged in genus Homo ~2 million years ago (mya) and is classically attributed to anatomical and physiological adaptations such as an enlarged gluteus maximus and improved heat dissipation. However, no underlying genetic changes have currently been defined. Two-three mya, an exon deletion in the CMP-Neu5Ac Hydroxylase (CMAH) gene also became fixed in our ancestral lineage. Cmah loss in mice exacerbates disease severity in...

Data from: The impact of pathological high-frequency oscillations on hippocampal network activity in rats with chronic epilepsy

Laura A. Ewell, Kyle B. Fischer, Christian Leibold, Stefan Leutgeb & Jill K. Leutgeb
In epilepsy, brain networks generate pathological high-frequency oscillations (pHFOs) during interictal periods. To understand how pHFOs differ from normal oscillations in overlapping frequency bands and potentially perturb hippocampal processing, we performed high-density single unit and local field potential recordings from hippocampi of behaving rats with and without chronic epilepsy. In epileptic animals, we observed two types of co-occurring fast oscillations, which by comparison to control animals we could classify as ‘ripple-like’ or ‘pHFO’. We compared...

Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae

Sean W. Graham, Joshua R. Kohn, Brian R. Morton, James E. Eckenwalder & Spencer C.H. Barrett
A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction-site survey) were used to reconstruct the phylogenetic history of the Pickerelweed family Pontederiaceae. The chloroplast data are converging to a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from the three chloroplast data sets were identical or extremely similar in shape to each other, mostly robustly supported and there was no evidence...

Data from: Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean Patagonia

Juan A. Ugalde, Maria J. Gallardo, Camila Belmar, Práxedes Muñoz, Nathaly Ruiz-Tagle, Sandra Ferrada-Fuentes, Carola Espinoza, Eric E. Allen & Victor A. Gallardo
The current study describes the taxonomic and functional composition of metagenomic sequences obtained from a filamentous microbial mat isolated from the Comau fjord, located in the northernmost part of the Chilean Patagonia. The taxonomic composition of the microbial community showed a high proportion of members of the Gammaproteobacteria, including a high number of sequences that were recruited to the genomes of Moritella marina MP-1 and Colwellia psycherythraea 34H, suggesting the presence of populations related to...

Data from: Parallel proteomic and phosphoproteomic analyses of successive stages of maize leaf development

Michelle R. Facette, Zhouxin Shen, Fjola R. Bjornsdotter, Steven P. Briggs & Laurie G. Smith
We carried out large-scale, quantitative analyses of the maize (Zea mays) leaf proteome and phosphoproteome at four developmental stages. Exploiting the developmental gradient of maize leaves, we analyzed protein and phosphoprotein abundance as maize leaves transition from proliferative cell division to differentiation to cell expansion, and compared these developing zones to one another and the mature leaf blade. Comparison of the proteomes and phosphoproteomes suggests a key role for post-translational regulation in developmental transitions. Analysis...

Data from: Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis

Lani U. Gleason & Ronald S. Burton
The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we...

Dataset for: Cascading effects of freshwater salinization on plankton communities in the Sierra Nevada

Emma Moffett, Henry Baker, Christine Bonadonna, Jonathan Shurin & Celia Symons
Runoff containing road salt (sodium chloride, NaCl) causes the salinization of inland freshwaters, with potentially severe impacts on aquatic species. We performed a mesocosm experiment to test the effects of salinization on plankton community structure in an oligotrophic mountain lake with a limited history of elevated salt concentrations. We exposed plankton communities to a gradient of 30 salt concentrations ranging from 1-2900 Cl– mg L-1 for six weeks. Adding salt increased zooplankton biomass at concentrations...

Data from: Training data from SPCAM for machine learning in moist physics

Guang Zhang, Yilun Han, Xiaomeng Huang & Yong Wang
Current moist physics parameterization schemes in general circulation models (GCMs) are the main source of biases in simulated precipitation and atmospheric circulation. Recent advances in machine learning make it possible to explore data-driven approaches to developing parameterization for moist physics processes such as convection and clouds. This study aims to develop a new moist physics parameterization scheme based on deep learning. We use a residual convolutional neural network (ResNet) for this purpose. It is trained...

Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence

Jessica A. Goodheart, Geetanjali Minsky, Mira N. Brynjegard-Bialik, Michael S. Drummond, J. David Munoz, Timothy R. Fallon, Darrin T. Schultz, Jing-Ke Weng, Elizabeth Torres & Todd H. Oakley
Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination...

Questioning to Resolve Transduction Problems

Eric Meinhardt, Anna Mai, Eric Bakovic & Adam McCollum

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