DOI: 10.5061/dryad.1n14c
title: Data from: Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Paleogene boundary

description: NOTE: Please also see Slater (2014) published in Methods in Ecology and
 Evolution at http://dx.doi.org/10.1111/2041-210X.12201 1. Phylogenetic
 comparative methods provide a powerful way of addressing classic questions
 about tempo and mode of phenotypic evolution in the fossil record, such as
 whether mammals increased in body size diversity after the
 Cretaceous-Paleogene (K-Pg) extinction. 2. Most often, these kinds of
 questions are addressed in the context of variation in evolutionary rates.
 Shifts in the mode of phenotypic evolution provides an alternative and, in
 some cases, more realistic explanation for patterns of trait diversity in
 the fossil record but these kinds of processes are rarely tested for. 3.
 In this study, I use a time-calibrated phylogeny of living and fossil
 Mammaliaformes as a framework to test novel models of body size evolution
 derived from paleontological theory. Specifically, I ask whether the K-Pg
 extinction resulted in a change in rates of body size evolution or release
 from a constrained adaptive zone. 4. I found that a model comprising an
 Ornstein-Uhlenbeck process until the K-Pg event and a Brownian motion
 process from the Cenozoic onwards was the best supported model for these
 data. Surprisingly, results indicate a lower absolute rate of body size
 evolution during the Cenozoic than during the Mesozoic. This is explained
 by release from a stationary OU process that constrained realized
 disparity. Despite a lower absolute rate, body size disparity has in fact
 been increasing since the K-Pg event 5. The use of time-calibrated
 phylogenies of living and extinct taxa and realistic, process-based models
 provides unparalleled power in testing evolutionary hypotheses. However,
 researchers should take care to ensure that the models they use are
 appropriate to the question being tested, and that the parameters
 estimated are intepreted in the context of the best-fitting model.
description: mammal_nexusNexus file containing molecular and morphological data for living and fossil Mammaliaformes, plus outgroups. Also contains MrBayes block with constraints, node calibrations, and tip agesmammaliforme_combinded.nexMCCTMaximum clade credibility tree from simultaneous phylogenetic and dating analysis of living and fossil mammals. extant clade names reflect those in Meredith et al.mammaliaforme_combinded.trebody_massa csv file containing mean and standard errors for ln body mass in living and fossil mammals and mammaliaformesmammal_mass.csvfitContinuous_paleoModelsA corrected version of the functions used in Slater (2013) to fit mode shift models to phylogenetic data. This version uses direct conversion of the variance covariance matrix to fit OU models to non-ultrametric data.fitContinuous_paleo_CORRECTED.Rmammaliaformes treeThe pruned, renamed tree used in model fittingmammal.phyfit_mammal_modelsAn R script that allows the user to repeat model fitting analyses performed in the manuscript using the pruned and renamed mammal tree.mammal_mass_posteriormammaliaforme body mass data with row names corresponding to those in the posterior distribution of trees. Used when fitting models to posterior distribution.pfileparameter (.p) file from dating analysis of living and fossil mammals conducted in MrBayes. This file is required to rescale branch lengths in the posterior distribution of treestfileposterior distribution of time calibrated mammaliaforme trees from MrBayes analysisfit_models_posteriorR script to fit macroevolutionary models to trees from MrBayes Posterior distribution