Find research datasets worth reusing

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.

publicMar 2020View details →

dryad32/100

A Multi-Type Birth-Death model for Bayesian inference of lineage-specific birth and death rates

Open the record for dataset details and reuse information.

opencc-zeroDec 2014View details →

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.

opencc-zeroDec 2018View details →

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.

opencc-zeroJun 2019View details →

Data from: Exploring the power of Bayesian birth-death skyline models to detect mass extinction events from phylogenies with only extant taxa

Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth-death models has made it possible to detect their signature based on extant-taxa phylogenies. Most birth-death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree ("single pulse" approach), in contrast to the paleontological record, where MEEs have a time-duration. Here, we explore the power of a Bayesian Birth-Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a "time-slice" approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on phylogenies size and MEE intensity. Comparisons of BDSKY with the single-pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates.

publicOct 2015View details →

Data from: Total-evidence dating under the fossilized birth-death process

Open the record for dataset details and reuse information.

publicNov 2015View details →

Data from: No substitute for real data: a cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses

Open the record for dataset details and reuse information.

publicMay 2019View details →

Data from: A simulation-based evaluation of tip-dating under the fossilized birth-death process

Open the record for dataset details and reuse information.