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Total-Evidence Dating Under The Fossilized Birth–Death Process, Chi Zhang, Tanja Stadler, Serena Klopfstein, Tracy A. Heath, Fredrik Ronquist

Tracy Heath

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 …

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Boosting The Performance Of Bayesian Divergence Time Estimation With The Phylogenetic Likelihood Library, Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis

Tracy Heath

We present a substantially improved and parallelized version of DPPDiv, a software tool for estimating species divergence times and lineage-specific substitution rates on a fixed tree topology. The improvement is achieved by integrating the DPPDiv code with the Phylogenetic Likelihood Library (PLL), a fast, optimized, and parallelized collection of functions for conducting likelihood computations on phylogenetic trees. We show that, integrating the PLL into a likelihoodbased application is straight-forward since it took the first author (DD) a programming effort of only one month, without having prior knowledge of DPPDiv, nor the PLL. We achieve sequential speedups that range between a …

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Phylotastic! Making Tree-Of-Life Knowledge Accessible, Reusable And Convenient, Arlin Stoltzfus, Hilmar Lapp, Helena Deus, Brian Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O. Webb, Luke J. Harmon, Megan Pirrung, Brian O'Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenburg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane Mctavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan

Tracy Heath

Background

Scientists rarely reuse expert knowledge of phylogeny, in spite of years ofeffort to assemble a great “Tree of Life” (ToL). A notableexception involves the use of Phylomatic, which provides tools togenerate custom phylogenies from a large, pre-computed, expert phylogeny ofplant taxa. This suggests great potential for a more generalized systemthat, starting with a query consisting of a list of any known species, wouldrectify non-standard names, identify expert phylogenies containing theimplicated taxa, prune away unneeded parts, and supply branch lengths andannotations, resulting in a custom phylogeny suited to the user’sneeds. Such a system could become a sustainable community resource ifimplemented …

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Full-Text Articles in Life Sciences

Total-Evidence Dating Under The Fossilized Birth–Death Process, Chi Zhang, Tanja Stadler, Serena Klopfstein, Tracy A. Heath, Fredrik Ronquist

Tracy Heath

Boosting The Performance Of Bayesian Divergence Time Estimation With The Phylogenetic Likelihood Library, Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis

Tracy Heath

Tracy Heath