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1,509 results for “Calibrations”
Fossilization processes have little impact on tip-calibrated divergence time analyses
<p>The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian Total-Evidence Dating methods which utilise fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non-random distribution of missing data. The impact of non-random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip-calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimise the impact of taphonomy on divergence time estimation.</p>
Data from: Proxies in practice: calibration and validation of multiple indices of animal abundance
The abundance of individuals in a population is a fundamental metric in basic and applied ecology, but sampling protocols yielding precise and unbiased estimates of abundance are often cost prohibitive. Proxies of abundance are therefore common, but require calibration and validation. There are many ways to calibrate a proxy, and it is not obvious which will perform best. We use data from eight populations of Chinook salmon (Oncorhynchus tshawytscha) on the Oregon coast where multiple proxies of abundance were obtained contemporaneously with independent mark-recapture estimates. We combined multiple proxy values associated with a single level of abundance into a univariate index and then calibrated that index to mark-recapture estimates using several different techniques. We tested our calibration methods using leave-one-out cross validation and simulation. Our cross-validation analysis did not definitively identify a single best calibration technique for all populations, but we could identify consistently inferior approaches. The simulations suggested that incorporating the known mark-recapture uncertainty into the calibration technique added bias and imprecision. Cross validation techniques should be used to test multiple methods of calibrating multiple proxies to an estimate of abundance. Critical uncertainties with the application of calibrated proxies still exist, and cost-benefit analysis should be performed to help identify optimal monitoring designs.
Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
Data from: Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees
Background: Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns ("broom" clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon – Australian grass trees (Xanthorrhoea) – whose substitution rate is slower than in its sister groups, as determined by relative rate tests. Results: In the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3-6 Ma versus 25-35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model. Conclusions: The choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.
Dynamic re-calibration of perceived size in fovea and periphery through predictable size changes
<p>Dataset relative to the following publication:</p> <p>Valsecchi, M. & Gegenfurtner, K.R (2016). Dynamic re-calibration of perceived size in fovea and periphery through predictable size changes. Current Biology, 26, 59-63.</p> <p>Each folder contains the data relative to one experiment and the script that was used to generate them. </p> <p>Each data folder contains a description of the data format which should be sufficient to replicate the analyses as performed in the paper. </p> <p>Additional info can be deducted fromt he experimental scripts.</p>
M Dwarf Flare Continuum Variations on One-Second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices
<p>These files contain the ULTRACAM light curves, the ULTRACAM flare color indices, the APO/DIS spectral data, and the NMSU 1-m U-band photometry from "M Dwarf Flare Continuum Variations on One-Second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices", Kowalski, A. F., Mathioudakis, M., Hawley, S. L., Wisniewski, J. P., Dhillon, V. S., Marsh, T. R., Hilton, E. J., & Brown, B. P., 2016, Astrophysical Journal in press. See the included ReadMe file for detailed information on the files.</p>
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 in The phylogenetIc posItIon and taxonomIc status of the RaInbow Tree Snake Gonyophis margaritatus (Peters, 1871) (Squamata: ColubrIdae)
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 (Drummond et al. 2012) with node support values representing posterior probability (left) and bootstrap support (right) from inferred Maximum Likelihood tree. Dashes for bootstrap values indicate low support or not supported by ML tree. Family Colubridae and subfamily Colubrinea are highlighted by red arrows. Taxa in genera Gonyosoma, Rhadinophis, Gonyophis, and Rhynchophis are highlighted in the red square on the tree.
FIGURES 3–4 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURES 3–4. Wing venation of (A) Pareronia Bingham, 1907 (Pieridae), and (B) Hasora Moore, 1881 (Hesperiidae). See text for explanation.
FIGURE 22 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 22. Fossils marked on phylogenetic tree of "redefined" butterflies (Heikkilä et al. 2011), with family trees according to Simonsen et al. (2011, Papilionidae), Warren et al. (2009, Hesperiidae), Wahlberg et al. (2014, Pieridae), Wahlberg et al. (2005, Lycaenidae), and Espeland et al. (2015, Riodinidae).
FIGURE 2 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 2. Apomorphies, their placement on a tree, and the assignment of calibration points. See text for explanation.
FIGURES 11–13 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURES 11–13. Ƒanessa pluto Heer, 1849. Figures copied from (1875), Plate II, figures 1, 17 and 7, respectively. (A), copied by Scudder from original description by Heer; (B) and (C), figures sent to Scudder by Mr. Brunner de Wattenwyl, made after the same object. Note differences in wing shape and other details. Figs 14–16. Thaites ruminiana Scudder, 1875. Figures copied from Scudder (1875), Plate III, figures 9, 1 and 3, respectively. (A), underside of fossil; (B), reconstruction of venation; (C), reconstruction of markings. In (A) two separate subcostal veins have been drawn in the forewing, an impossible configuration in Lepidoptera, and apparently a mistake, corrected in (B) and (C). Fig. 17. Cyllo sepulta Boisduval, 1841, wing venation after Scudder (1875). Fig. 18. Butterfly fossil recorded by Wangrin (1939), but shown to be a fraud by Ansorge (2015). Photo kindly provided by J. Ansorge, Horst, Germany (see text for explanation).
FIGURE 23 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 23. Distribution of land, epicontinental seas (flooded continental areas) and oceans during the middle Paleocene (Thanetian Stage) at 60 Mya. From Smith, A.G., Smith, D.G. & Funnell, B.M. (1994); with permission of Cambridge University Press and University of East Anglia.
FIGURE 1 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 1. Localities of fossil butterflies plotted ion a modern map. See Table 1 for further, complementary information.
FIGURE 5 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 5. Ƒanessa amerindica Miller & Brown, 1989, holotype, collections of Invertebrate Paleontology, University of Florida. Photo by Roger Portell. Fig. 6. Pseudoneorina coulleti Nel & Descimon, 1984. France, Dép. Alpes-de-Haute- Provence, Dauphin, specimen in coll. M. Henrotay; photo by courtesy of M. Henrotay. Fig. 7. Archaeolycorea ferreirai Martins-Neto, 1989. Fig. 4A of original description. Fig. 8. Oligodonta florissantensis Brown, 1976, holotype, collections of Invertebrate Paleontology, University of Florida. Photo by courtesy of Akito Kawahara. Fig. 9. Neorinella garciae Martins- Neto, Kucera-Santos, de Moraes Vieira & de Campos Fragoso, 1993. Fig. 3A of original description. Fig. 10. Protocoeliades kristenseni de Jong, 2016, holotype, Zoologisk Museum, Copenhagen, Denmark. Photo by Department of Paleobiology, National Museum of Natural History, Washington DC, USA.
Calibration Bias Evaluation and Correction of S-Band Ground-Based Radar Reflectivity Using Ku-Band Space-Borne Radar Observations Along the East Coast of India
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Calibration and Measurements during a field campaign in Rende_Data from SirGalahad, Tekran SPeciation Unit, UT-3000 analyzers
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Supplementary material for the Hinode EIS calibration paper
<p>The files are associated with the paper describing the in-flight radiometric calibration of the<br>Hinode EIS instrument, see doi: 10.48550/arXiv.2308.06609<br> See the README file.</p> <p>The IDL save files contain a structure RETURN_STR with the results of the<br>fits of the single spectra, merged.</p> <p>The main array is return_str.total_counts which contains the<br>total counts in the lines for all the dates, in units of DN/s/1arc sec</p> <p>The array return_str.list_lambda has the expected wavelengths of the lines.</p> <p>The arrays in data_active_sfit_2023.save<br>return_str.eis_sw_ar_spectra and return_str.eis_lw_ar_spectra<br>contain the active region averaged spectra. </p> <p>The routine used to process Hinode EIS full spectral raster atlases<br>is process_atlas.pro</p> <p>The routine interpol_eis_ea.pro is to be used together with<br>the save file fit_eis_ea_2023-05-04_smooth.sav to obtain the<br>time and wavelength-dependent effective area.</p>
Data from: A Deep Learning Approach for Fast Muscle Water T2 Mapping with Subject Specific Fat T2 Calibration from Multi-Spin-Echo Acquisitions
<p>This repository contains the imaging data (in NIfTI) and analysis code to reproduce the work presented in <em>"A Deep Learning Approach for Fast Muscle Water T2 Mapping with Subject Specific Fat T2 Calibration from Multi-Spin-Echo Acquisitions"</em> by <strong>Marco Barbieri, Melissa T. Hooijmans, Kevin Moulin, Tyler E. Cork, Daniel B. Ennis, Garry E. Gold, Feliks Kogan and Valentina Mazzoli.</strong></p> <p>Citation: "Barbieri, M., Hooijmans, M.T., Moulin, K. <em>et al.</em> A deep learning approach for fast muscle water T2 mapping with subject specific fat T2 calibration from multi-spin-echo acquisitions. <em>Sci Rep</em> 14, 8253 (2024). https://doi.org/10.1038/s41598-024-58812-2"</p> <p>The source code for setting up the Deep Learning application can be found in the GitHub repository https://github.com/barma7/Deep_Learning_for_Muscle_T2_mapping.git</p>
Calibration data for Climate Change Tower temperature sensors - may 2017
<p>Calibration data for the temperature sensors hosted at Climate Change Tower in Ny-Ålesund, Svalbard, during May 2017. Each namefile contains the temperature point (e.g. m25 is -25 °C, while p5 is +5 °C) and the sensor type ("ref" for reference, "DUT" for Device under test).</p> <p>Reference files contain data for the 2 reference sensors employed, while DUT files contain data for the 4 CCT sensors.</p>
Figure 1. Calibrated phylogeny for the main avian taxa. Tree topology was obtained from O in Multivariate analysis of neognath skeletal measurements: implications for body mass estimation in Mesozoic birds
Figure 1. Calibrated phylogeny for the main avian taxa. Tree topology was obtained from O'Connor, Chiappe & Bell (2011) and divergence times are based on a 'literal' interpretation of the fossil record from Brockelhurst et al. (2012). Taxa abbreviations: Nth, Neornithes; Orph, Ornithuromorpha; Orn, Ornithothoraces; Orth, Ornithurae; Pyg, Pygostylia.
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