Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic "cal3" time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.suppFigure_09-17-13120 supplemental figures, with the analysis, simulation scenario and data sources labeled. See the ReadMe for more detail.rdata_workspaces_12-29-13A zip file containing 15 .Rdata saved workspaces, each containing the analytical results from a respective simulation scenario, as indicated in the file names. Can be used with the figure-making scripts to remake the majority of the analytical figures in the main paper and all of the figures shown in the supplement.methodTest_analysisThe main simulation "workhorse" script, for the computer language R. Called and run with the runMethodTest R script to perform the different simulation scenarios and saves the analytical results as a workspace to an .rdata file.runMethodTest_03-05-13A script for the R programming language, which runs analyses in the 15 simulation scenarios described in the main paper, via calls to the methodTest script.making_mainfigures_12-06-13R script which, if given the 15 workspaces contained in the zip file included in this archive, will generate figures 2-9 in the main paper. (Unfortunately, the final-final figures I submitted had to be converted to a different file format and resized in GIMP, so they may not be 100% identical).make_supp_files_09-15-13R script which, if given the 15 workspace files contained in the zip file included in this archive, will generate the 120 supplemental figures for this paper, and save them as a single PDF file, which should be identical to the PDF file containing the supplemental figures already included here on Dryad.ZLB_tests_01-23-13An R script for running and recreating the figures related to zero-length branch simulations described in the Discussion section of the main paper, and was used to create Figure 10. If the attached 'ZLB' workspace file is used, it should be able to recreate Figure 10 exactly.ZLB_test_01-23-13The saved R workspace (as an .Rdata file) from the zero length branch simulations described in the Discussion of the paper, and produced using the ZLB_test R script. Can be used with the same script to recreate Figure 10 from the main paper