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54 results for “tip dating”
Figure 22 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 22. Scanning electron microscopy images of ventral and dorsal views of metasomas, and posterior view of mesosomas. Metasomal carina is colour-indicated. A, Holopyga luzulina Dahlbom, female, ventral view of metasoma, higher magnification of the anterior area of metasoma is shown in C. B, Exochrysis leucostigma (Mocsáry), male, ventral view of metasoma, higher magnification of the anterior area of metasoma is shown in D. Dorsal views of T1: E, Exallopyga guatemalensis (Cameron), female; F, Neochrysis inseriata (Mocsáry), female. Posterior view of mesosomas: G, Holopyga wagnerella du Buysson, female; H, Caenochrysis paranaca (Linsenmaier), female. Arrowheads indicate morphological conditions coded as character-states.
Figure 7 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 7. Fossil diversity (species) of Evanioidea and Ichneumonoidea during the mid-Mesozoic and Cenozoic (data from
Figure 6 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 6. Keratodellitha kirin. Holotype IGR.BU-021 (female). A, head in left profile view. B, head in full-face view. C, wings. D, line drawing of wing venation with nomenclature. Scale bars: 0.5 mm.
Figure 4. Keratodellitha anubis. Holotype NIGP174739 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 4. Keratodellitha anubis. Holotype NIGP174739 (male). A, wing. B, line drawing of wing venation with nomenclature. Scale bars: 0.5 mm.
Figure 5 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 5. Keratodellitha kirin. Holotype IGR.BU-021 (female). A, habitus in left lateral view. B, habitus in right lateral view. Scale bars: 1 mm.
Figure 2. Keratodellitha basilisci. Holotype NIGP174738 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 2. Keratodellitha basilisci. Holotype NIGP174738 (female). A, head in full-face view. B, head in right profile view. C, head in dorsal view. D, wings. E, line drawing of wing venation with nomenclature. Scale bars: 0.5 mm.
Figure 3. Keratodellitha anubis. Holotype NIGP174739 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 3. Keratodellitha anubis. Holotype NIGP174739 (male). A, habitus in right lateral view. B, head in right lateral view. C, head in frontal view. Scale bars: 0.5 mm.
F i g u r e 1. K e r a t o d e l l i t h a b a s i l i s c i. H o l o t y p e NIGP174738 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
F i g u r e 1. K e r a t o d e l l i t h a b a s i l i s c i. H o l o t y p e NIGP174738 (female). A, habitus in right lateral view. B, habitus in left lateral view. Scale bars: 0.5 mm.
Figure 8 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process
Figure 8. Bayesian time-calibrated tree of Evanioidea. This tree was recovered from a Mkv+G, fossilized birth–death (FBD) model, with uniform distribution and samplestrat = fossiltip, combining extant and extinct species. Bars at each node represent the 95% highest posterior density in dating estimates. Dotted squares represent crown lineages. Abbreviations: L, Lower; Mid, Middle; Oligo, Oligocene; Paleo, Palaeocene; PP, Pliocene + Pleistocene.
Figure 12. Tip-dated Bayesian phylogenetic analyses. A, unconstrained phylogeny using hypothesis 1 in A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and 'archaic' South American ungulates
Figure 12. Tip-dated Bayesian phylogenetic analyses. A, unconstrained phylogeny using hypothesis 1 (H1) matrix. B, tip-dated topology constrained Bayesian phylogeny using hypothesis 1 (H1) matrix and constraining the node for the common ancestor of SANUs between the K/Pg boundary and the oldest age for the kollpaniines of Tiumpampa (66–65.075 Mya). The topological constraint in (B) was based on the topology of the undated Bayesian tree for H1. The trees in (A) and (B) represent a 50% majority rule in which tree support is indicated using Bayesian posterior probabilities in the nodes, and the node bars represent the 95% highest posterior density (HPD) for the estimated node ages. In (B), node support is only indicated for the node that was unconstrained (the undated tree presented a polytomy for that node). Litopterna is indicated with a star, but other nodes or tips of relevance are indicated in circles of different colours: blue, orders; black, families.
European origins of Squamata supported by biogeographic analysis of fossil-tip-dated phylogenies using paleocontinental plate-tectonic models
<p>Attached are the full results for the biogeographic analyses, with all tips labeled with taxon names. In addiiton, we have included the code utilized for all three trees used.</p>
Selecting and averaging relaxed clock models in Bayesian tip dating of Mesozoic birds
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Data from: New crinoids from the Baltic region (Estonia): fossil tip-dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)
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Data from: Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
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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: Multiple morphological clocks and total-evidence tip-dating in mammals
Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or 'pacemaker'. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.
Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
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: A simulation-based evaluation of tip-dating under the fossilized birth-death process
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa, but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.
Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a dataset. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical dataset and supply practical guidance for results interpretation.
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