DOI: 10.5061/dryad.2ss46
title: Data from: Phylogenies, the comparative method, and the conflation of tempo and mode

description: The comparison of mathematical models that represent alternative
 hypotheses about the tempo and mode of evolutionary change is a common
 approach for assessing the evolutionary processes underlying phenotypic
 diversification. However, because model parameters are estimated
 simultaneously, they are inextricably linked, such that changes in tempo,
 the pace of evolution, and mode, the manner in which evolution occurs, may
 be difficult to assess separately. This may potentially complicate
 biological interpretation, but the extent to which this occurs has not yet
 been determined. In this study, we examined 160 phylogeny × trait
 empirical data sets, and conducted extensive numerical phylogenetic
 simulations, to investigate the efficacy of phylogenetic comparative
 methods to distinguish between models that represent different
 evolutionary processes in a phylogenetic context. We observed that, in
 some circumstances, a high uncertainty exists when attempting to
 distinguish between alternative evolutionary scenarios underlying
 phenotypic variation. When examining data sets simulated under known
 conditions, we found that evolutionary inference is straightforward when
 phenotypic patterns are generated by simple evolutionary processes that
 are represented by modifying a single model parameter at a time. However,
 inferring the exact nature of the evolutionary process that has yielded
 phenotypic variation when facing complex, potentially more realistic,
 mechanisms is more problematic. A detailed investigation of the influence
 of different model parameters showed that changes in evolutionary rates,
 marked changes in phylogenetic means, or the existence of a strong
 selective pull on the data, are all readily recovered by phenotypic model
 comparison. However, under evolutionary processes with a milder
 restraining pull acting on trait values, alternative models representing
 very different evolutionary processes may exhibit similar goodness-of-fit
 to the data, potentially leading to the conflation of interpretations that
 emphasize tempo and mode during empirical evolutionary inference. This is
 a mathematical and conceptual property of the considered models that,
 while not prohibitive for studying phenotypic evolution, should be taken
 into account and addressed when appropriate.
description: Online Appendix
 1AICC
 SCORES OF MODELS FIT TO EMPIRICAL DATASETSAppendix
 1_mar2015.docxOnline Appendix
 2BM
 SIMULATIONS UNDER VARYING MODEL PARAMETERSAppendix
 2_mar2015.docxOnline Appendix
 3SIMULATION EXPERIMENT
 DEMONSTRATING THE EQUIVALENCE BETWEEN THE CENSORED APPROACH (O’MEARA ET
 AL. 2006) AND THE RATE METHOD USING A DESIGN MATRIX FOR GROUP MEANS
 (THOMAS ET AL. 2006, 2009)Appendix
 3_mar2015.docxOnline Appendix
 4SIMULATION EXPERIMENT TO
 INVESTIGATE WHETHER R-PACKAGES OUWIE AND MOTMOT PROVIDE COMPARABLE
 PARAMETER ESTIMATES AND LIKELIHOOD SCORESAppendix
 4_mar2015.docxOnline Appendix
 5VARIATION IN
 EVOLUTIONARY RATES ESTIMATED BY DIFFERENT MODELS FIT TO DATA SIMULATED
 WHILE VARYING RELATIVE OPTIMA AND RELATIVE RATES
 PARAMETERSAppendix
 5_mar2015.docxR-codeR-code used for all tree
 and phenotypic data simulations, and for fitting different models to the
 simulated data. Please see the ReadMe file for details.Rcode.zip