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14 results for “fossilized birth-death process”
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 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.
Data from: Total-evidence dating under the fossilized birth-death process
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of datasets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants and bees). Previous total-evidence dating analyses of this dataset were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push towards more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
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: Total-evidence dating under the fossilized birth-death process
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Data from: A simulation-based evaluation of tip-dating under the fossilized birth-death process
Open the record for dataset details and reuse information.
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