DOI: 10.5061/dryad.5st8m
title: Data from: Comparing evolutionary rates between trees, clades, & traits

description: 1. The tempo of evolutionary change through time is among the most heavily
 studied dimensions of macroevolution using phylogenies. 2. Here, we
 present a simple, likelihood-based method for comparing the rate of
 phenotypic evolution for continuous characters between trees. Our method
 is derived from a previous approach published by Brian O’Meara and
 colleagues in 2006. 3. We examine the statistical performance of the
 method and find that it suffers from the typical downward bias expected
 for maximum likelihood estimates of the variance, but only for very small
 trees. We find that evolutionary rates are estimated with minimal bias for
 trees of even relatively modest size. 4. We also find that type I error
 rates based on a likelihood-ratio test are minimally elevated above the
 nominal level, even for small phylogenies. The type I error rate can be
 reduced to a level at or below its nominal value by substituting a
 test-statistic distribution obtained via simulation under the null
 hypothesis of no difference in evolutionary rate among trees. 5. We
 discuss the consequences of failing to account for uncertainty in the
 estimation of species means or in the phylogeny, and describe strategies
 for taking this uncertainty into consideration during estimation. We also
 identify how our approach is related to previous methods for comparing the
 rate of evolution among different clades of a single tree or between
 different phenotypic traits. Finally, we describe how the method can be
 applied to different evolutionary models and to discrete characters –
 options that are already implemented in software. 6. Evolutionary
 biologists continue to be intrigued by changes in the tempo of phenotypic
 evolution across the tree of life. The method described herein should be
 useful for contexts in which changes in the evolutionary rate or process
 between two or more clades of distant or unknown relationship are of
 interest.
description: R markdown for
 reproducible workflowR markdown file
 containing the fully reproducible workflow of the
 study.Revell-etal-2018.MEE.RmdBuilt reproducible workflowBuilt reproducible workflow containing all analyses of the study including (low quality versions of) all figures & tables.Revell-etal-2018.MEE.htmlPhenotypic dataPhenotypic data file used for empirical example of study. Data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers AØ (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660piguanids.csvPhylogeny of lizard tribe LiolaeminiFile containing phylogeny of lizard tribe Liolaemini. Phylogeny data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers AØ (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660pliolaeminipl.phyPhylogeny of lizard subfamily PhrynosomatinaeFile containing phylogeny of lizard subfamily Phrynosomatinae. Phylogeny data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers AØ (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660pphrynosomatpl.phy