Data from: Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity

Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. Although methods for identifying evolutionary rate shifts in continuous characters have attracted recent attention (e.g. Eastman et al., 2011, Stack et al., 2011), such methods for discrete characters have only very recently been developed (Beaulieu et al., 2013, Beaulieu and O'Meara 2014) and have yet to be widely used. However, ancestral state reconstructions of discrete characters are being performed on increasingly large phylogenies, where it is likely that evolutionary rates will vary greatly between different clades (Beaulieu and O'Meara 2014). Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree, split BiSSE estimates separate rate parameters for pre-specified clades, and the hidden rates model partitions each character state into a number of rate categories. The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles. Additionally, simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades).Fig1 - Expanded pdf versionExpanded pdf version of Figure 1 (main text), with name and reproductive state for each terminal taxon.Fig1_Expanded.pdfFig2 - Expanded pdf versionExpanded pdf version of Figure 2 (main text), with name and reproductive state for each terminal taxon, and posterior probability of reconstructed state for each node.Fig2_Expanded.pdfFigures S1 to S6 and captionsFigures S1 to S6 and captions, in a single Word (docx) file.Figures_S1-S6.docxTables_S1-S8 and captionsTables S1 to S8 and captions, in a single Word (docx) file.Tables_S1-S8.docxFile S1 - BEAST executable file for Analysis 1BEAST file for Analysis 1 (focal analysis - see file S2). File is in xml format and runs on BEAST 1.8.x (not BEAST 2).S1_BEAST_executable.xmlFile S2 - BEAST Random Local Clock settingsBEAST Random Local Clock (RLC) settings for all analyses of the empirical data. Word (docx) format.S2_BEAST_RLCsettings.docxFile S3 - BEAST tree in Figtree formatBEAST consensus tree from Analysis 1 (focal analysis). This file can be opened in Figtree and will show estimated evolutionary rate (mean and 95% HPD), and posterior probability for reconstructed state, at each node.S3_BEAST_figtree.treeFile S4 - R Code for SimulationsR Code for simulations, in plain text file. See annotations for further description.S4_Simulations_RCode.rFile S5 - Results of simulationsFull results of the 4 simulation scenarios (5 replicates each), in a pdf file (~98 MB).S5_SimulationResults.pd