Distinguishing punctuated and continuous-time models of character evolution for discrete characters and its implications for macroevolutionary theory

The recent proliferation of quantitative models for assessing anatomical character evolution all assume that character change happens continuously through time. However, the punctuated equilibrium model posits that character change should be coincide with cladogenetic events, and thus should be tied to origination rates. Rates of cladogenesis are important to quantitative phylogenetics, but typically only for establishing prior probabilities in the tree model component of phylogenetic analyses. Here, we modify existing character-likelihood models to use the local cladogenesis rates from Bayesian analyses to generate amounts of character change over time dependent on origination rates, as expected under the punctuated equilibrium model. In the case of strophomenoid brachiopods from the Ordovician, Bayesian analyses strongly favor punctuated models over continuous-time models, with elevated rates of cladogenesis early in the clade’s history inducing frequencies of change despite constant ..., Simply use these scripts as you would any RevBayes script. Do note that the primary code calls upon several external scripts and datasets, which are segregated into particular folders. The code assumes that these folders are in the \"main\" directory that RevBayes is using at that time. , # Data from: Distinguishing punctuated and continuous-time models of character evolution for discrete characters and its implications for macroevolutionary theory

Dataset DOI: [10.5061/dryad.dfn2z35f3](10.5061/dryad.dfn2z35f3)

## Description of the data and file structure

RevBayes code plus example data sets for conducting Bayesian phylogenetic analyses with either punctuated (= pulsed, speciational, etc.) or continuous (gradual, Darwinian, phyletic, etc.) character change.

### Files and folders

The zip file (`forPub_Final_2.zip`) contains two folders.

#### RevBayes

The RevBayes folder contains the code relevant to the analyses of the paper. Note that the scripts and datasets are partitioned into folders. The main script calls upon scripts and datasets within these folders; if the directory is set to the RevBayes folder when running RevBayes and this folder structure is maintained, then it should not be necessary to alter the directory commands pointing to the relevant files and ..., ,