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17 results for “chronogram”
Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character's evolution: R scripts and simulated trees
<p>All R scripts used in this study, and the set of simulated phylogenetic trees used in the study.</p> <p>1. Modern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.<br><br>2. In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (1) the effect of alternate branch lengths on ASE error, and (2) whether phylogenetic signal statistics and/or model-fit statistic can be used to select the branch lengths most correlated with a binary character.<br><br>3. In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model-fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model-fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favorable for model optimization, and when shape differences between alternate phylogenies are greater.<br><br>4. Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model-fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model fit.</p>
Figure 5. BEAST chronogram from a data set corresponding with Table 1 in Verifying Australian Nilotanypus Kieffer (Chironomidae) In A Global Perspective: Molecular Phylogenetic And Temporal Analyses, New Species And Emended Generic Diagnoses
Figure 5. BEAST chronogram from a data set corresponding with Table 1. Values at nodes are time to most recent common ancestor (tmrca) with HPD (95% Highest Posterior Density) intervals in parentheses. The time scale is in millions of years before present.
Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character’s evolution: R scripts and simulated trees
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Intaglio. Rectangular intaglio in cornelian with bevelled sides; engraved with a chronogram (?).
<p>Intaglio. Rectangular intaglio in cornelian with bevelled sides; engraved with a chronogram (?). British Museum 1892,1103.144.</p>
ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data
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Figure 5. Chronogram for Brachycera. A in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 5. Chronogram for Brachycera. A chronogram is the Bayesian topology resulting from analysis of the AP12R dataset. Branches have been separated by different colours (same as Fig. 4). Species of Vermileonidae are marked with a red asterisk. The numbers close to the branching points are the mean age. The bar through each node shows the time interval that contains 95% of the probability for the node age.
Figure 6. Chronogram resulting from Bayesian analysis employing a in Phylogeny indicates polyphyly in Cnodocentron (Trichoptera: Xiphocentronidae): biogeography and revision of New World species (Caenocentron)
Figure 6. Chronogram resulting from Bayesian analysis employing a relaxed clock. Most likely ancestral distribution recovered in DEC analysis and estimated mean age are displayed at the nodes. Dispersal events are indicated as a black line below the distribution boxes, vicariant events are indicated in a green line, as recovered in the biogeographic analysis. Highest posterior density (HPD) 95% intervals for the ages of the nodes are indicated by light blue bars. Timescale and global surface temperature estimated from δ18O benthic (Zachos et al., 2001) are displayed on the bottom. Eocene and Miocene thermal optimum are highlighted in grey. Cnodocentron and Caenocentron species distributions are shown in the maps.
Fig. 3 Chronogram showing the relationships and divergence times for 80 bears, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker
Fig. 3 Chronogram showing the relationships and divergence times for 80 bears, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.
Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker
Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.
Figure 3. Maximum clade credibility chronogram inferred from a in Diversification of low dispersal crustaceans through mountain uplift: a case study of Gammarus (Amphipoda: Gammaridae) with descriptions of four novel species
Figure 3. Maximum clade credibility chronogram inferred from a relaxed clock model based on the cytochrome c oxidase subunit I data set. The type specimens for nominal species are underlined. Node bars represent 95% posterior credibility intervals for nodes of interest. 1, Gammarus incoercitus sp. nov.; 2, Gammarus benignus sp. nov.; 3, Gammarus shanxiensis; 4, Gammarus monticellus sp. nov.; 5, Gammarus pisinnus sp. nov.; 6, Gammarus clarus; 7, Gammarus nekkensis.
Figure 2. Simplified maximum clade credibility chronogram obtained from BEAST with 95 in Phylogenetic position of the endemic Mount Oku rat, Lamottemys okuensis (Rodentia: Muridae), based on molecular and morphological data
Figure 2. Simplified maximum clade credibility chronogram obtained from BEAST with 95% highest posterior density intervals.
Figure 3. Chronogram. The maximum clade credibility tree amongst 9000 in Vicariance and convergence in Magellanic and New Zealand long-looped brachiopod clades (Pan-Brachiopoda: Terebratelloidea)
Figure 3. Chronogram. The maximum clade credibility tree amongst 9000 trees from an uncorrelated lognormal relaxed clock analysis of the rDNA alignment. Nodes are labelled A–R and show mean node ages and 95% highest posterior density (HPD) ranges as wide black bars. See Table 1 for details of SDmean, 95% HPD confidence limits of mean ages, descriptions of nodes and of mean age agreement with external ages. Vertical lines labelled NZ (New Zealand), MAG (Magellanic), Laq (laqueoid) and Short (short-looped terebratulidine) mark the respective clades and the proximate and more distant outgroups. Evolutionary model for dating analysis: 18 taxa, 2833 sites, general time reversible with estimated frequency of invariant sites and gamma rate distribution (four rate categories) with empirical base frequencies; uncorrelated lognormal distribution. Priors: substitution rates, Jefferies; site model alpha and invariant, Normal, mean = 0.7, SD = 0.1, initial = 0.7; tree model root height, lognormal logx mean = 2.39, SD = 0.5; defined taxon sets, default tree prior. Markov chain Monte Carlo chain 107 cycles, sampled every 103. TreeAnnotator was used to identify the maximum clade credibility tree of 9000 trees after 1001 trees were discarded as burnin.
DNA matrix, phylogram and chronogram of Pepsini species
<p>This dataset submission consists of a DNA matrix and two tree files. The phylogeny file of UCE loci for 39 taxa was required to construct a Maximum Likelihood tree. The tree file was needed to examine the topology and the topology was used to examine the limits of two taxonomically challenging genera within the tribe Pepsini, <em>Cryptocheilus</em> and <em>Heterodontonyx</em>. The time-calibrated tree was built with MCMCTree program to estimate the divergence pattern and timing of the group. </p>
DNA matrix, phylogram and chronogram of Pepsini species
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Figure 3. Chronogram for Chrysididae derived from a in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 3. Chronogram for Chrysididae derived from a combined Bayesian analysis of a partitioned dataset of 300 morphological characters employing a relaxed morphological clock model with tip-dating. The maximum credibility tree was calculated considering only clades higher than 50% of Bayesian posterior probability resulting from the analysis of 173 species representing Chrysididae and outgroups. Branch lengths are drawn proportional to time from the present (timescale on the bottom), highest posterior density (HPD) 95% intervals for the ages of select nodes are indicated by horizontal blue bars, and node support values correspond to Bayesian posterior probabilities. Lowercase letters indicate clades of major interest (discussed in the text) with their respective estimated ages. Fossil taxa are indicated by daggers. Phylogenetic relationships among Chrysidinae species are shown in Figures 4 and 5.
Fig. 4 Phylogenetic chronogram, a in Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the Marsh Warbler Acrocephalus palustris (Aves: Acrocephalidae)
Fig. 4 Phylogenetic chronogram, a coalescent analysis implemented in BEAST with lognormal relaxed clock (uniform distribution and 0.01105– 0.02500 substitutions per million years) and population expansion model as priors. Thick horizontal bars represent the 95 % HDP of the age of major nodes and numbers indicate node posterior probability values
Figure 2. BEAST chronogram from a in Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring
Figure 2. BEAST chronogram from a data set of single representatives per species/clade that corresponds with Table 1. Lettered nodes are those for which time to most recent common ancestor (tmrca) was estimated and correspond with Table 1; black stars indicate nodes to which prior calibrations were applied. The time scale is in millions of years before present.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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
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