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1,509 results for “Calibrations”
Pseudo-observational datasets for testing projection calibration methods (EUCP WP2)
<p>Pseudo-observational datasets, produced by standardising and anonymising output from climate model data from the CMIP6 archive. </p> <p>Each folder "PSEUDOobs_*.tar.gz" contains the data required for the different EUCP Work Package 2 methods to calibrate projections (see, e.g., initial comparison of methods presented in Brunner et al., Journal of Climate, 2020, <em>in revision</em>).</p> <p>All data is in netcdf format.</p> <p> </p> <p><em>References:</em></p> <p>Brunner, L., et al., "Comparing methods to constrain future European climate projections using a consistent framework", Journal of Climate, <em>in revision.</em></p>
Hydraulic hysteresis of unsaturated pyroclastic soils: experimental investigation and model calibration
<p>In many geotechnical applications, especially in the study of weather-induced landslides, a reliable soil hydraulic characterization under unsaturated conditions is required. Currently, the experimental techniques neglecting hydraulic hysteresis represent the greatest limitation to landslide forecasting. Here, experimental data from a new procedure to obtain an unsaturated soil hydraulic characterization are reported. These allows us to evaluate the soil hydraulic properties not only along the main drying path but also along wetting/drying cycles. Pyroclastic soil samples collected at a test site located at Mount Faito in the Campania region (southern Italy) were tested. The experimental investigation consisted of a forced evaporation test followed by a number of wetting-drying cycles. </p>
Calibration of a Parameterization for Near-Inertial Waves
<p>We use these data to calibrate a parameterization for near-inertial waves.</p>
Pressure Correction in the Calibration of Heat Dissipation Sensors
<p>Heat dissipation sensors (HDSs) infer soil matric potential based on the measured rate of temperature rise from a heat source. The process for calibrating these sensors may use a pressure plate apparatus (PPA) to remove water to a certain calibration point that is controlled by pressure. Conventionally, the pressure within the PPA is released before the temperature change calibration points are measured (D<i>T</i><sub>0</sub>). This conventional HDS calibration approach can take several weeks. We propose that the equilibrated temperature change at pressure (D<i>T</i><sub>p</sub>) can be corrected empirically to the value at zero pressure. Based on measurements of 14 HDSs between 0.02 and 0.1 MPa, D<i>T</i><sub>p</sub> was on average 6.2% larger than D<i>T</i><sub>0</sub>. After pressure correction, using an empirical equation, the difference between the corrected D<i>T</i><sub>p</sub> and D<i>T</i><sub>0</sub> was only 0.28%. These results demonstrate that this empirical approach provides sufficient accuracy to achieve HDS calibration without performing a PPA pressure release.</p>
Multicamera calibration for multiobject tracker for mice
<p>Noninvasive tracking of all individuals in unmarked mouse group using multicamera fusion and deep learning</p>
Data from: Image Calibration and Analysis Toolbox – a free software suite for measuring reflectance, colour, and pattern objectively and to animal vision
1. Quantitative measurements of colour, pattern, and morphology are vital to a growing range of disciplines. Digital cameras are readily available and already widely used for making these measurements, having numerous advantages over other techniques, such as spectrometry. However, off-the-shelf consumer cameras are designed to produce images for human viewing, meaning that their uncalibrated photographs cannot be used for making reliable, quantitative measurements. Many studies still fail to appreciate this, and of those scientists who are aware of such issues, many are hindered by a lack usable tools for making objective measurements from photographs. 2. We have developed an image processing toolbox that generates images that are linear with respect to radiance from the RAW files of numerous camera brands, and can combine image channels from multispectral cameras, including additional ultraviolet photographs. Images are then normalised using one or more grey standards to control for lighting conditions. This enables objective measures of reflectance and colour using a wide range of consumer cameras. Furthermore, if the camera's spectral sensitivities are known, the software can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox also provides image analysis tools that can extract luminance (lightness), colour, and pattern information. Furthermore, all processing is performed on 32-bit floating point images rather than commonly used 8-bit images. This increases precision and reduces the likelihood of data loss through rounding error or saturation of pixels, while also facilitating the measurement of objects with shiny or fluorescent properties. 3. All cameras tested using this software were found to demonstrate a linear response within each image and across a range of exposure times. Cone-catch mapping functions were highly robust, converting images to several animal visual systems and yielding data that agreed closely with spectrometer-based estimates. 4. Our imaging toolbox is freely available as an addition to the open source ImageJ software. We believe that it will considerably enhance the appropriate use of digital cameras across multiple areas of biology, in particular researchers aiming to quantify animal and plant visual signals.
Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.
Data from: A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles
True crocodiles (Crocodylus) are the most broadly distributed, ecologically diverse, and species-rich crocodylian genus, comprising about half of extant crocodylian diversity and exhibiting a circumtropical distribution. Crocodylus traditionally has been viewed as an ancient group of morphologically conserved species that originated in Africa prior to continental breakup. In this study, these long-held notions about the temporal and geographic origin of Crocodylus are tested using DNA sequence data of 10 loci from 76 individuals representing all 23 crocodylian species. I infer a time-calibrated species tree of all Crocodylia and estimate the spatial pattern of diversification within Crocodylus. For the first time, a fully resolved phylogenetic estimate of all Crocodylia is well-supported. The results overturn traditional views of the evolution of Crocodylus by demonstrating that the true crocodiles are not "living-fossils" that originated in Africa. Rather, Crocodylus originated from an ancestor in the tropics of the Late Miocene Indo-Pacific, and rapidly radiated and dispersed around the globe during a period marked by mass extinctions of fellow crocodylians. The findings also reveal more diversity within the genus than is recognized by current taxonomy.
Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa
1.) Applying phylogeny-based analyses of trait evolution and diversification in the fossil record generally involves transforming an unscaled cladogram into a phylogeny scaled to geologic time. Current methods produce single time-scaled phylogenies with artificial zero-length branches and no indication of the uncertainty in the temporal relationships. 2.) Here I present a stochastic algorithm for time-scaling phylogenies of fossil taxa by randomly sampling node ages from a constrained distribution, with the ultimate goal of producing large samples of time-scaled phylogenies for a given dataset as the basis for phylogeny-based analyses. I describe how this stochastic approach can be extended to consider potential ancestral relationships and resolve polytomies. 3) The stochastic selection of node ages in this algorithm is weighted by the probability density of the total inferable unobserved evolutionary history at single divergence events in a tree, a distribution dependent on rates of branching, extinction and sampling in the fossil record. 4) The combined time-scaling method must be calibrated with explicit estimates of three rates: branching, extinction and sampling, and thus is named the cal3 time-scaling method, included in the R library paleotree. I test the time-scaling capabilities of the cal3 and older time-scaling methods in simulations. cal3 produces samples of time-scaled trees that better bracket the uncertainty in the true node ages than existing time-scaling methods. This is true even in simulations under a 'terminal-taxon' model of differentiation that violates many of the assumptions of the cal3 method. 5) The cal3 method provides a new approach for time-scaling paleontological cladograms, calibrated to estimated sampling and diversification rates, allowing for better estimates of uncertainty in the phylogenetic time-scaling. The cal3 method is robust to relaxation of at least some model assumptions. Additional work is needed to analyze the impact of time-scaling approaches on macroevolutionary analyses and to integrate time-scaling with phylogenetic inference.
Data from: Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies
Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analysing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.
Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using 'early but risky' fossil constraints in addition to 'safe but late' constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown-group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical re-assessment of their phylogenetic position.
Data from: Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification
Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.
Data from: Not going with the flow: a comprehensive time-calibrated phylogeny of dragonflies (Anisoptera: Odonata: Insecta) provides evidence for the role of lentic habitats on diversification
Ecological diversification of aquatic insects has long been suspected to have been driven by differences in freshwater habitats, which can be classified into flowing (lotic) waters and standing (lentic) waters. The contrasting characteristics of lotic and lentic freshwater systems imply different ecological constraints on their inhabitants. The ephemeral and discontinuous character of most lentic water bodies may encourage dispersal by lentic species in turn reducing geographical isolation among populations. Hence, speciation probability would be lower in lentic species. Here, we assess the impact of habitat use on diversification patterns in dragonflies (Anisoptera: Odonata). Based on the eight nuclear and mitochondrial genes, we inferred species diversification with a model-based evolutionary framework, to account for rate variation through time and among lineages and to estimate the impact of larval habitat on the potentially nonrandom diversification among anisopteran groups. Ancestral state reconstruction revealed lotic fresh water systems as their original primary habitat, while lentic waters have been colonized independently in Aeshnidae, Corduliidae and Libellulidae. Furthermore, our results indicate a positive correlation of speciation and lentic habitat colonization by dragonflies: speciation rates increased in lentic Aeshnidae and Libellulidae, whereas they remain mostly uniform among lotic groups. This contradicts the hypothesis of inherently lower speciation in lentic groups and suggests species with larger ranges are more likely to diversify, perhaps due to higher probability of larger areas being dissected by geographical barriers. Furthermore, larger range sizes may comprise more habitat types, which could also promote speciation by providing additional niches, allowing the coexistence of emerging species.
GB GMOS gri-band coadded and fully calibrated FITS images
<p>These are the Gemini/GMOS-N and GMOS-S coadded FITS images, taken in gri filters, of the 17 Green bean galaxies published in Schirmer+ 2016.</p>
FIGURES 19–21 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURES 19–21. Three phylogenetic trees for Nymphalidae: Satyrinae. See text for explanation.
Calibration Data for Kinematic Stellar Age Models
<p>https://github.com/ssagear/KinematicAgePredictor</p>
bipl5: An R Package for Reactive Calibrated Axes PCA Biplots
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Methane sensor calibration dataset
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Calibration Data for "Sycamore" instrument in Lee Lab, Cambridge; Prime95B sCMOS cameras, Gain 3
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OpenNeuro
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