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29 results for “Bayesian tip dating”
Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process
<p>Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life.</p>
Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process
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Figure 21 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 21. Dorsoposterior and lateral views of mesosoma. A, Holophris huberi; B, Parnopes grandior; C, E, Allocoelia capensis (Smith) (NHMUK 010576396); D, Caenochrysis nigropolita (Bischoff); F, Allocoelia emarginata Edney (NHMUK 010576397). Scale bars: 0.2 mm (A); 0.5 mm (B, D); 1 mm (C, E, F). Images of A. capensis and A. emarginata available under Creative Commons License 4.0. Natural History Museum: data.nhm.ac.uk. Arrowheads indicate morphological conditions coded as character-states.
Figure 19 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 19. Dorsal view of mesosoma. The axillae are colour-marked. A, Parnopes grandior (Pallas), male; B, Exallopyga guatemalensis (Cameron), female; C, Allocoelia emarginata Edney, female (NHMUK 010576397); D, Caenochrysis crotonis (Ducke), female. Scale bars (A, B, D): 0.5 mm; (C): 1 mm. Image of A. emarginata available under Creative Commons License 4.0. Natural History Museum: data.nhm.ac.uk. Arrowheads indicate morphological conditions coded as character-states.
Figure 18 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 18. Comparative phylogenetic hypotheses on the evolutionary relationships among tribes of the Chrysidinae cuckoo wasps obtained from different sources. A, B, cladistic morphology-based hypotheses. C, D, molecularbased hypotheses. The uncertain position of Allocoeliini is represented as '?' (the placement of this taxon was not inferred by Niehuis & Wägele, 2004).
Figure 17 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 17. Scanning electron microscopy images of morphological structures of head. A, clypeus and mandibles of Adelphe brasiliensis, male; B, clypeus of Pleurochrysis postica (Brullé); C, clypeus and mandibles of Elampus gayi (Spinola), female; D, clypeus and mandibles of Holopyga wagnerella du Buysson, female; E–H, anterior surface of mandibles: E, Caenochrysis nigropolita (Bischoff), female; F, Hedychridium periotoi Lucena, female; G, Muesebeckidium paraensis (Ducke), female; H, H. wagnerella, female. I–K, C. nigropolita, female, frontal view of scapal basin with the facial fovea shown in amplified views. Arrowheads indicate morphological conditions coded as character-states.
Figure 14 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 14. Lateral view of female metasoma. A, Cleptidea sp.; B, Adelphe sp.; C, Exallopyga guatemalensis (Cameron); D, Spintharina vagans Radoszkowski; E, Exochrysis spinigera (Spinola); F, Neochrysis carina (Brullé); G, Ipsiura myops (du Buysson); H, Chrysis brasiliensis Brullé; I, Stilbum cyanurum (Förster). Scale bars (A, B): 1 mm; (C–I): 0.5 mm.
Figure 12 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 12. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Chrysidinae: Chrysidini partim. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'.
Figure 10 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 10. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Chrysidinae: Parnopini and Allocoeliini. Character state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the top, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among Chrysidini species (Clade 5) are shown in detail in Figures 11–12.
Figure 8 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 8. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Loboscediliinae and Amiseginae. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers.
Figure 7 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 7. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Cleptinae and extinct Chrysididae taxa. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among other subfamilies of Chrysididae (Clades 2 and 3) are shown detail in Figures 8–12.
Figure 6. Maximum credibility Bayesian tree obtained from a in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 6. Maximum credibility Bayesian tree obtained from a combined analysis of a partitioned dataset of 300 morphological characters employing a relaxed morphological clock model with tip-dating. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among Chrysididae (Clade 1) are shown in detail in Figures 7–12.
Figure 4 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 4. Chronogram for Chrysidinae, partim (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 chrysidine clade connects to the remaining tree of Chrysididae in Figure 3; phylogenetic relationships among the species of Chrysidini are shown in the Figure 5. 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.
Figure 5 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 5. Chronogram for Chrysidini (Chrysididae: Chrysidinae) derived from a combined Bayesian analysis of a partitioned dataset of 300 morphological characters employing a relaxed morphological clock model with tip-dating. The clade herein represented connects to the remaining tree of Chrysidinae in Figure 4. Branch lengths are drawn proportional to time from the present (timescale on the bottom), highest posterior density (HPD) 95% intervals for the ages of selected 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.
Figure 13 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 13. Maximum credibility Bayesian dated tree calculated for the Chrysididae and distribution of terminals in biogeographic divisions of the world. The charts on tips represent the true geographical range for the genus or lineage being considered. Widespread taxa are represented on tips by multicolour charts. The pruned tree was obtained from a maximum credibility Bayesian dated tree considering all compatible groups (contype = allcompat in MrBayes). Groups of species were combined into lineages representing monophyletic genera or other taxon combinations. Monophyletic groups are represented by their genus names only. Non-monophyletic taxa are represented multiple times. Biogeographic reconstruction of the history of Chrysididae was conducted using the DEC model as implemented in BioGeoBEARS. Pie charts at nodes show the relative probability of the possible states (areas or combinations of areas) indicated by asterisk those higher than 50%; combinations of areas are indicated by grey slices; black slices represent a fraction of the reconstructions with high ambiguity.
Figure 11 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 11. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Chrysidinae: Chrysidini partim. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among other Chrysidini species (Clades 6 and 7) are shown in detail in Figure 12.
Figure 2 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 2. Comparison between phylogenetic hypotheses for extant groups of Chrysididae and closely related taxa of Chrysidoidea: A, summary of morphology-based hypotheses (Kimsey & Bohart, 1991; Carpenter, 1999; Lucena & Melo, 2018; Melo & Lucena, 2020); B, summary of the DNA-based hypothesis by Pauli et al. (2019, 2021). The phylogenetic position of Loboscelidiinae (Chrysididae) is indicated with a question mark because it was not inferred by Pauli et al. (2019, 2021). Fossil taxa not included in the molecular analyses are represented by dashed lines.
Figure 1 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 1. Summary of the phylogenetic relationships and valid genera of Chrysididae based on Kimsey & Bohart (1991) with recent amendments. The placement of Kimseya and †Eochrysis are considered herein as uncertain within the Chrysidinae. The main groups being considered in the family are colour-coded. Fossil taxa are indicated by daggers.
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 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.
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