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29 results for “Bayesian tip dating”
Selecting and averaging relaxed clock models in Bayesian tip dating of Mesozoic birds
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Bayesian tip-dated phylogenetics in paleontology: topological effects and stratigraphic fit
<p>The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip dating are outliers when compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio and The Stratigraphic Completeness Index. This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favours tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favours trees with a higher Gap Excess Ratio compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two datasets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data.</p>
Data from: Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds
Recently, comprehensive morphological datasets including nearly all the well-recognized Mesozoic birds became available, making it feasible for statistically rigorous methods to unveil finer evolutionary patterns during early avian evolution. Here, we exploited the advantage of Bayesian tip dating under relaxed morphological clocks to estimate both the divergence times and evolutionary rates while accounting for their uncertainties. We further subdivided the characters into six body regions (i.e., skull, axial skeleton, pectoral girdle and sternum, forelimb, pelvic girdle, and hindlimb) to assess evolutionary rate heterogeneity both along the lineages and across partitions. We observed extremely high rates of morphological character changes during early avian evolution and the clock rates are quite heterogeneous among the six regions. The branch subtending Pygostylia shows extremely high rate in the axial skeleton, while the branches subtending Ornithothoraces and Enantiornithes show notably high rates in the pectoral girdle and sternum, and moderately high rates in the forelimb. The extensive modifications in these body regions largely correspond to refinement of the flight capability. This study reveals the power and flexibility of Bayesian tip dating implemented in MrBayes to investigate evolutionary dynamics in deep time.
Data from: Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds
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Bayesian tip-dated phylogenetics in paleontology: topological effects and stratigraphic fit
Open the record for dataset details and reuse information.
Figure 20 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 20. Scanning electron microscopy images of mesosoma habitus with amplified views of metapleuron/propodeum. Yellow arrows indicate propodeal spiracles, black arrows indicate the metapleural processes. A, C, Elampus gay (Spinola); B, D, Neochrysis inseriata (Mocsáry).
Figure 15 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 15. Fore- and hindwings. Rectangles indicate areas in higher magnification on right. A, Cleptidea xanthomelas (Mocsáry), female; B, Adelphe sp., male. Scale bars: 1 mm (forewing) and 0.5 mm (hindwing). Arrowheads indicate morphological conditions coded as character-states.
Figure 16 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 16. Frontal view of heads and amplified view of mandibles. A, D, Cladobethylus insularis Kimsey & Dewhurst, female; B, E, C. insularis, male; C, F, Duckeia cyanea Costa Lima, female; G, H, Adelphe brasiliensis Kimsey, male. Scale bars: (A, B, C, G): 0.5 mm; (D, E, F, H): 0.2 mm. Arrowheads indicate morphological conditions coded as character-states.
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.
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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
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.