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289 results for “natural variation”
Data from: Using controlled subsurface releases to investigate the effect of leak variation on above-ground natural gas detection
<p class="MsoNormal"><span>Pipelines transport natural gas (NG) in all stages between production and the end user. The NG composition, pipeline depth, and pressure vary significantly between extraction and consumption. As methane (CH<sub>4</sub>), the primary component of NG is both explosive and a potent greenhouse gas, NG leaks from underground pipelines pose both a safety and environmental threat. Leaks are typically found when an observer detects a CH<sub>4</sub> enhancement as they pass through the downwind above-ground NG plume. The likelihood of detecting a plume depends, in part, on the size of the plume, which is contingent on both environmental conditions and intrinsic characteristics of the leak. To investigate the effects of leak characteristics, this study uses controlled NG release experiments to observe how the above-ground plume width changes with changes in the gas composition of the NG, leak rate, and depth of the subsurface emission. Results show that plume width generally decreases when heavier hydrocarbons are present, the leak rate is reduced, and as leak depth decreases from 0.9 to 0.6 m. The above surface CH<sub>4</sub> plume is undetectable when leaks are 1.8 m deep. As most survey methods typically prioritize leaks based on the leak size, this study shows that the effect of NG density on above-ground plume width is only 4%, equivalent to the effect of leak rate. This suggests that reported leaks in areas with heavier hydrocarbons could currently be missed or underestimated. Furthermore, this study shows that leaks from pipelines laid in covers meeting minimum depth requirements of 0.9 m could be easier to detect compared to those buried shallower. Overall, this study illustrates that leak survey protocols for flowlines and gathering lines should be different from distribution pipelines and tailored to the compositions of the transported NG to report emissions accurately.</span></p>
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
<p>Although studies of <em>Saccharomyces cerevisiae</em> have provided many insights into mutagenesis and DNA repair, most of this work has focused on a few laboratory strains. Much less is known about the phenotypic effects of natural variation within <em>S. cerevisiae</em>'s DNA repair pathways. Here, we use natural polymorphisms to detect historical mutation spectrum differences among several wild and domesticated <em>S. cerevisiae</em> strains. To determine whether these differences are likely caused by genetic mutation rate modifiers, we use a modified fluctuation assay with a <em>CAN1</em> reporter to measure de novo mutation rates and spectra in 16 of the analyzed strains. We measure a 10-fold range of mutation rates and identify two strains with distinctive mutation spectra. These strains, known as AEQ and AAR, come from the panel's 'Mosaic beer' clade and share an enrichment for C > A mutations that is also observed in rare variation segregating throughout the genomes of several Mosaic beer and Mixed origin strains. Both AEQ and AAR are haploid derivatives of the diploid natural isolate CBS 1782, whose rare polymorphisms are enriched for C > A as well, suggesting that the underlying mutator allele is likely active in nature. We use a plasmid complementation test to show that AAR and AEQ share a mutator allele in the DNA repair gene <em>OGG1</em>, which excises 8-oxoguanine lesions that can cause C > A mutations if left unrepaired.</p>
Extreme natural size variation in both sexes of a sexually cannibalistic mantidfly
<p><span>In sexually cannibalistic animals, the relative sizes of potential mates often predict the outcome of aggressive encounters. Mantidflies are spider egg predators as larvae and generalist predators as adults. Unlike most cannibalistic species, individual mantidflies can be substantially larger than other individuals, regardless of sex. Using preserved collections of <em>Dicromantispa sayi</em>, we focused on three body size metrics that we found to be positively correlated and accurately measured across researchers. We found extreme size variation in both sexes: the largest 10% of females were 1.72x larger than the smallest 10%, and the largest 10% of males were 1.65x larger than the smallest 10%. On average, females were 7.94% larger than males. In exploring possible causes of this variation, we uncovered differences among populations. To explore the effect of spider egg sac size on adult mantidfly size, we reared mantidfly larvae on egg sacs from two jumping spider species with small or large egg sacs. Mantidfly larvae reared on small egg sacs were smaller than those reared on large egg sacs. This study provides the groundwork to design ecologically relevant experiments exploring the causes and consequences of extreme size variation in an understudied system with intriguing natural history. </span></p>
Data from: Soil variation among natural habitats alters glucosinolate content in a wild perennial mustard
<p>The archive Wagner_Mitchell-Olds_Zenodo_SoilPlast.zip contains a README file describing the contents.</p> <p>These data are described in the Journal of Experimental Botany: <a href="https://doi.org/10.1093/jxb/erac520">https://doi.org/10.1093/jxb/erac520</a></p> <p>Funding: National Science Foundation, IOS-<span>2016351</span></p>
Ecology and evolution of competitive trait variation in natural phytoplankton communities under selection
<p>Competition for limiting resources is a major force structuring ecological communities. Species minimum resource requirements (<em>R*</em>s) can predict competitive outcomes and evolve under selection in simple communities under controlled conditions. However, whether <em>R*</em>s predict competitive outcomes or demonstrate adaptive evolution in naturally complex communities is unknown. We subjected natural phytoplankton communities to three types of resource limitation (nitrogen, phosphorus, light) in outdoor mesocosms over ten weeks. We examined the community composition weekly and isolated 21 phytoplankton strains from seven species to quantify responses to selection of R* for these resources. We investigated evolutionary change in R*s in the dominant species, <em>Desmodesmus armatus</em>. <em>R*</em>s were good predictors of species changes in relative abundance, though this was largely driven by the success of <em>D. armatus </em>across several treatments. This species also demonstrated evolutionary change in <em>R*</em>s under resource limitation, supporting the potential for adaptive trait change to modify competitive outcomes in natural communities.</p>
A high-resolution speleothem record of Marine Isotope Stage 11 as a natural analog to Holocene Asian summer monsoon variations
<p>A full-spectrum characterization of past interglacial climate is a necessary prerequisite for the detection and attribution of climate changes during the current interglacial. Here we present a speleothem record of Asian summer monsoon (ASM) during Marine Isotope Stage (MIS) 11 interglacial (MIS 11c), from Yongxing cave, China. The record’s unprecedented chronologic constraints and decadal-scale temporal resolution allow a precise and direct comparison of ASM between the MIS 11c and the Holocene. Our data suggest that orbital–centennial patterns of ASM were remarkably similar during both interglacial, including their pacing and structure. Notably, a multi-millennial stronger monsoon late in MIS 11c, the ‘Late-MIS 11c shift’, is similar to the Late Holocene strengthening of the ASM, the ‘2-kyr shift’. Thus the multi-centennial ASM weakening at the end of the ‘Late-MIS 11c shift’ could imply that the current century-long ASM waning trend may persist into the future, if only natural forcings are considered.</p>
Natural temperature variation at the origin site can determine coral resistance to thermal stress
<p>This repository contains data files and scripts used in the research paper titled <em>"Natural temperature variation at the origin site can determine coral resistance to thermal stress."</em> The provided materials support the analysis and results presented in the study.</p>
Genome-wide association analysis identifies naturally segregating genetic variation associated with the rapid evolution of diapause in Aedes albopictus, an invasive vector mosquito.
<p>The raw data for genotype calls, the output files from the genotype calls, the code to replicate the analysis, and the output of the analysis.</p>
Origin of the natural variation in the storage of dietary carotenoids in freshwater amphipod crustaceans
<p>Carotenoids are diverse lipophilic natural pigments which are stored in variable amounts by animals. Given the multiple biological functions of carotenoids, such variation may have strong implications in evolutionary biology. Crustaceans such as <i>Gammarus </i>amphipods store large amounts of these pigments and inter-population variation occurs. While differences in parasite selective pressure have been proposed to explain this variation, the contribution of other factors such as genetic differences in the gammarid ability to assimilate and/or store pigments, and the environmental availability of carotenoids cannot be dismissed. This study investigates the relative contributions of the gammarid genotype and of the environmental availability of carotenoids in the natural variability in carotenoid storage. It further explores the link of this natural variability in carotenoid storage with major crustacean immune parameters. We addressed these aspects using the cryptic diversity in the amphipod crustacean <i>Gammarus fossarum</i> and a diet supplementation protocol in the laboratory. Our results suggest that natural variation in <i>G. fossarum</i> storage of dietary carotenoids results from both the availability of the pigments in the environment and the genetically-based ability of the gammarids to assimilate and/or store them, which is associated to levels of stimulation of cellular immune defences. While our results may support the hypothesis that carotenoids storage in this crustacean may evolve in response to parasitic pressure, a better understanding of the specific roles of this large pigment storage in the crustacean physiology is needed.</p>
Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
<p>While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of <i>Drosophila pseudoobscura</i> from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a Q<sub>ST</sub>-F<sub>ST</sub> analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400kb scale, recombination rate appears to vary largely genome wide, rather than in specific intervals and (3) interpopulation differences in recombination rate may be the result of local adaptation.</p>
Integrated Study on the natural variation in Arabidopsis thaliana responses to alkaline salinity
<p>Supplementary Datasets of the doctoral thesis entitled "Integrated Study on the natural variation in <em>Arabidopsis thaliana</em> responses to alkaline salinity", comprising genomic and transcriptomic data from growth, nutritional and gene enrichment analyses of natural populations of A. thaliana in response to neutral and alkaline salinity treatments.</p>
Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature
<p class="MsoNormal">Pathogen life history theory assumes a positive relationship between pathogen load in host tissues and pathogen transmission. Empirical evidence for this relationship is surprisingly rare due to the difficulty of measuring transmission for many pathogens. The comparative method, where a common host is experimentally infected with a set of pathogen strains, is a powerful approach for investigating the relationships between pathogen load and transmission. The validity of such experimental estimates of strain-specific transmission is greatly enhanced if they can predict the pathogen population strain structure in nature.</p> <p class="MsoNormal"><em>Borrelia burgdorferi</em> is a multi-strain, tick-borne spirochete that causes Lyme disease in North America. This study used 11 field-collected strains of <em>B. burgdorferi</em>, a rodent host (<em>Mus musculus, </em>C3H/HeJ) and its tick vector (<em>Ixodes scapularis</em>) to determine the relationship between pathogen load in host tissues and lifetime host-to-tick transmission (HTT). Mice were experimentally infected via tick bite with 1 of 11 strains. Lifetime HTT was measured by infesting mice with <em>I. scapularis </em>larval ticks on 3 separate occasions. The prevalence and abundance of the strains in the mouse tissues and the ticks were determined by qPCR. We used published databases to obtain estimates of the frequencies of these strains in wild <em>I. scapularis</em> populations.</p> <p>Spirochete loads in ticks and lifetime HTT varied significantly among the 11 strains of <em>B. burgdorferi</em>. Strains with higher spirochete loads in the host tissues were more likely to infect feeding larvae, which molted into nymphs with a higher probability of <em>B. burgdorferi</em> infection (<em>i.e.</em>, higher HTT). Our laboratory-based estimates of lifetime HTT were predictive of the frequencies of these strains in wild <em>I. scapularis</em> populations. For <em>B. burgdorferi</em>, the strains that establish high abundance in host tissues and that have high lifetime transmission are the strains that are most common in nature.</p>
Using ecological context to interpret spatiotemporal variation in natural selection
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Data from: Pathogen susceptibility and fitness costs explain variation in immune priming across natural populations of flour beetles
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Data from: Personality variation in a marine snail and heterogeneous selection in natural populations
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Data from: Genetic independence of naturally correlated variation in resistance to endemic and novel pathogens
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Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature
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Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
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Data from: Precipitation drives global variation in natural selection
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Data from: Testing the optimal defense hypothesis in nature: variation for glucosinolate profiles within plants
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.