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677 results for “Inversion”
Data from: Reproductive isolation and local adaptation quantified for a chromosome inversion in a malaria mosquito
Chromosome inversions have long been thought to be involved in speciation and local adaptation. We have little quantitative information, however, about the effects that inversion polymorphisms have on reproductive isolation and viability. Here we provide the first estimates from any organism for the total amount of reproductive isolation associated with an inversion segregating in natural populations. We sampled chromosomes from 751 mosquitoes of the malaria vector Anopheles funestus along a 1421 km transect in Cameroon that traverses savannah, highland, and rainforest ecological zones. We then developed a series of population genetic models that account for selection, migration, and assortative mating, and fit the models to the data using likelihood. Results from the best-fit models suggest there is strong local adaptation, with relative viabilities of homozygotes ranging from 25% to 130% compared to heterozygotes. Viabilities vary qualitatively between regions: the inversion is underdominant in the savannah, while in the highlands it is overdominant. The inversion is also implicated in strong assortative mating. In the savannah, the two homozygote forms show 92% reproductive isolation, suggesting that this one inversion can generate most of the genetic barriers needed for speciation.
Data from: Vanishing chromosomal inversion clines in Drosophila subobscura from Chile: is behavioral thermoregulation to blame?
Chromosomal inversion clines paralleling the long-standing ones in native Palearctic populations of Drosophila subobscura evolved swiftly after this species invaded the Americas in the late 1970s and early 1980s. However, the new clines did not consistently continue to converge on the Old World baseline. Our recent survey of Chilean populations of D. subobscura shows that inversion clines have faded or even changed sign with latitude. Here, we investigate the hypothesis that this fading of inversion clines might be due to the Bogert effect, namely, that flies' thermoregulatory behavior has eventually compensated for environmental variation in temperature, thus buffering selection on thermal-related traits. We show that latitudinal divergence in thermal preference (Tp) has evolved in Chile for females, with higher-latitude flies having a lower mean Tp. Plastic responses in Tp also lessen latitudinal thermal variation because flies developed at colder temperatures prefer warmer microclimates. Our results are consistent with the idea that active behavioral thermoregulation might buffer environmental variation and reduce the potential effect of thermal selection on other traits as chromosomal arrangements.
Data from: Chromosomal inversions in the Atlantic cod genome: implications for management of Canada's Northern cod stock
Following stock collapse and over twenty years of moratoria, the state of Canada's Northern Atlantic cod (Gadus morhua) remains precarious. To test if recent stock growth was of endogenous or exogenous origin, we performed a whole genome scan (ddRAD) on 135 adults captured in 2015 at three offshore spawning locations spanning the range of the offshore stock along the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre Dame Channel and Bonavista Corridor), with an additional 105 adults from three more southern locations (St. Anns Bank, Browns Bank and Bay of Fundy). Population structure analysis using 5,077 single nucleotide polymorphisms (SNPs) detected a distinct genetic break off the coast of Nova Scotia near 45 °N. Gene flow between groups north and south of this divide appears to be limited despite the presence of several northern-type and admixed individuals present in the southern area. North of the genetic divide, allele frequencies of neutral loci were indicative of a panmictic population. Several outlier SNPs were found to be associated with ecologically relevant physical characteristics (visual pigments, fin development, response to hypoxia, and various metabolic processes), which may be indicative of different ecological niches.
Data from: How much can history constrain adaptive evolution? A real time evolutionary approach of inversion polymorphisms in Drosophila subobscura
Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes.
Data from: An inversion supergene in Drosophila underpins latitudinal clines in survival traits
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation, and survival upon cold shock). We generated homokaryon lines, either carrying the inverted or standard chromosomal arrangement, isolated from populations approximating the endpoints of the North American cline (Florida, Maine), and phenotyped the flies at two growth temperatures (18°C, 25°C). Across both temperatures, high-latitude flies from Maine lived longer and were more stress resistant than low-latitude flies from Florida, as previously observed. Interestingly, we find that this latitudinal pattern is partly explained by the clinal distribution of the In(3R)P polymorphism, which is at ~50% frequency in Florida but absent in Maine: inverted karyotypes tended to be shorter-lived and less stress resistant than uninverted karyotypes. We also detected an interaction between karyotype and temperature on survival traits. Since In(3R)P influences body size and multiple survival traits, it can be viewed as a 'supergene', a cluster of tightly linked loci affecting multiple complex phenotypes. We conjecture that the inversion cline is maintained by fitness trade-offs and balancing selection across geography; elucidating the mechanisms whereby this inversion affects alternative, locally adapted phenotypes across the cline is an important task for future work.
Data from: Molecular Inversion Probes for targeted resequencing in non-model organisms
Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.
Dataset for AMT paper "Ammonia emissions from a grazed field estimated by miniDOAS measurements and inverse dispersion modelling"
<p>Single excel file containing 30 minute averaged measurements and model outputs. Includes miniDOAS concentration measurements, sonic anemometer (Gill WindMaster) wind & turbulence, environmental measurements (relative humidity, rainfall, temperature, net radiation flux), deposition velocity resistance components (measured Ra and Rb and modelled Rc), and bLS-R model outputs (dispersion coefficients, also known as C/E ratios). These data provide the model inputs required to run the bLS-R dispersion model, (alternatively the WindTrax dispersion model can be used). The emissions from the field during both measuring periods can be determined from the measured horizontal concentration gradient and the simulated dispersion coefficients (Emissions = (Cdownwind-Cupwind)/Dispersion coefficient).</p>
An efficient 3D inversion scheme for continental scale Magnetotelluric data
<p>These zipped file contain 3D magnetotelluric dataset (synthetic and SAMTEX field data) and corresponding inverted model obtained using AP3DMT(RB) code<br>(Radiation Boundary version of the AP3DMT code) for the publications “3D inversion scheme for high-resolution analysis of continental scale Magnetotelluric<br>data”. </p>
Data for the paper "Assimilation of noble gas tracer concentrations with data space inversion in alluvial river-aquifer systems"
<p>This is the modelling data required to obtain results discussed in "Assimilation of noble gas tracer concentrations with data space inversion in alluvial river-aquifer systems".</p> <p> </p>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWLNETS (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Class-Inverse Relations-OWLNETS</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWL (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Class-Inverse Relations-OWL</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
[data]Pollution source detection with low-cost low-accuracy sensors through coupling forward data assimilation and inverse optimization
<p>The data used in the case study(Cases-S1,S2,S3)in manuscript "Pollution source detection with low-cost low-accuracy sensors through coupling forward data assimilation and inverse optimization"</p>
Inverse priority effects: A role for historical contingency during species losses
<p>Communities worldwide are losing multiple species at an unprecedented rate, but how communities reassemble after these losses is often an open question. It is well established that the order and timing of species arrival during community assembly shapes forthcoming community composition and function. Yet, whether the order and timing of species losses can lead to divergent community trajectories remains largely unexplored. Here, we propose a novel framework that sets testable hypotheses on the effects of the order of species losses inverse priority effects and suggests its integration into the study of community assembly. We propose that the order of species losses within a community can generate alternative reassembly trajectories, and suggest mechanisms that may underlie these inverse priority effects. To formalize these concepts quantitatively, we used a three-species Lotka-Volterra competition model, enabling to investigate conditions in which the order of species losses can lead to divergent reassembly trajectories. The inverse priority effects framework proposed here promotes the systematic study of the dynamics of species losses from ecological communities, ultimately aimed to better understand community reassembly and guide management decisions in light of rapid global change.</p>
Dataset for Estimating soil hydraulic properties from oven-dry to full saturation using inverse modeling and shortwave infrared imaging
<p>In this repository, we provide all the datasets that are needed to reproduce the analysis conducted in the paper entitled "Estimating soil hydraulic properties from oven-dry to full saturation using inverse modeling and shortwave infrared imaging."</p> <p><br> codes: This folder contains Python codes to run the forward and inverse modeling. Install the following packages.<br> notebook, fenics, numpy, pandas, matplotlib, scipy, numdifftools, and lmfit for inverse modeling (needs to be run on Linux).<br> data: This directory contains data used in the inverse modeling.<br> gif: This directory contains GIF movies of the upward infiltration experiments.</p> <p>readme.xlsx: This file explains which data are used for each figure in the paper.</p>
Quantifying Human Contributions to Near-Surface Temperature Inversions: Insights from COVID-19 Natural Experiments
<p>These are the processed data and code used to generate our analysis in the article: </p> <ul> <li>Zhang, Z., Wang, J., & Ge, Y. (2024). Quantifying Human Contributions to Near-Surface Temperature Inversions: Insights From COVID-19 Natural Experiments. Geophysical Research Letters, 51(6), e2023GL107964. https://doi.org/10.1029/2023GL107964</li> </ul> <p>If you have any question about our data or code used in the analysis, please contact us at zhangzy.20b@igsnrr.ac.cn</p>
Supporting data for "A method for non-linear inversion of the stellar structure applied to gravity-mode pulsators"
<p>These are the inlist and run_star_extras required to reproduce the stellar and asteroseismic models presented in 'A method for non-linear inversion of the stellar structure applied to gravity-mode pulsators', run with MESA r22.05.1.</p>
Data for Kinetic isotope effects during reduction of Fe(III) to Fe(II): Large normal and inverse isotope effects for abiotic reduction and smaller fractionations by phytoplankton in culture
<p>Supplemental data for the manuscript "Kinetic isotope effects during reduction of Fe(III) to Fe(II): Large normal and inverse isotope effects for abiotic reduction and smaller fractionations by phytoplankton in culture."</p>
UoE CO2 1x1 inversion dataset 2001-2022
Open the record for dataset details and reuse information.
CSEM data and inversion result
<p>The files contain information about the CSEM data and inversion results presented in the GJI paper.</p>
Responses, datasets used from the Geomagnetic Network of China, and the 3D inversion result of Geomagnetic depth sounding
Open the record for dataset details and reuse information.
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Allen Brain Atlas
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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.