DOI: 10.5061/dryad.cj2fg
title: Data from: Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity

description: 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).
description: 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.pdf