DOI: 10.5061/dryad.ksn02v7gf
title: Data from: Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data

description: Understanding the evolution and phylogenetic distribution of morphologic
 traits is fundamental to macroevolutionary research. Despite decades of
 major advances and key insights from molecular systematics, organismal
 anatomical features remain a key source of biological data for both
 inferring phylogenies and investigating patterns of trait evolution among
 fossil and extant species. In palaeobiology, morphologic characters are
 typically the only source of information available for reconstructing
 evolutionary trees. Systematists working with fossil data must make
 decisions regarding how morphological characters are modeled, whether they
 are coded as continuous or categorical, and how to address biological
 sources of rate variation. To determine the impact of how different models
 of morphological evolution influence phylogenetic inferences and
 downstream comparative analyses of fossil data, we competed a series of
 increasingly complex model configurations of character evolution to a
 dataset of Cambrian-Ordovician trilobites containing both discrete
 morphological characters and continuous traits. Competed models vary in
 complexity, ranging from simple constant rate scenarios with only discrete
 categorical traits, to complex evolutionary models including both discrete
 and quantitative traits across multiple ecological partitions while
 accounting for multiple sources of rate variation. We compared topological
 distributions across competed models by visualizing their distances in
 multidimensional treespace. Results indicate support for rate-variable
 models and partitioning characters. However, inclusion of continuous
 traits dramatically alters macroevolutionary inferences. Character model
 complexity also has a major impact on which regions of treespace are
 explored, suggesting a critical need to carefully model morphologic
 evolution even when systematists are only interested in patterns of
 phylogenetic relationships alone.
description: # Data from: Assessing the impact of character evolution models on
 phylogenetic and macroevolutionary inferences from fossil data Dataset
 DOI: [10.5061/dryad.ksn02v7gf](10.5061/dryad.ksn02v7gf) ## Description of
 the data and file structure Data comprise nexus files for morphologic
 character data from Monti and Confalonieri (2019) partitioned by character
 state and into ecologic vs. non-ecologic traits. Results of phylogenetic
 analyses are saved as .trees and .tre files, including the posterior
 sample and maximum clade credibility trees. R scripts are included to
 generate treespaces from the results. References: Monti, D.S. and
 Confalonieri, V.A., 2019. First cladistic analysis of the trilobite family
 Olenidae from the Furongian and Ordovician. *Lethaia*, *52*(3),
 pp.304-322. ## Code/software Data files can be viewed in a standard text
 editor. A custom R script includes functions for generating tree space
 visualizations. Any pdf viewer can be used to open
 *Wright_and_Hopkins__Supplementary_Information.pdf*. **R** is required to
 run the *Treespace.R* file that reproduces the treespace results, which
 requires *Functions.R* and all files ending with *.trees* to be in the
 same working directory. The files with the suffix *.trees* are named by
 the model configurations described in the main text. **RevBayes** is
 required to run files ending in *.Rev*, and require the character data
 files be included in the same working directory. Discrete character data
 are files ending in *.nex* and are named by the number of character states
 and an indicator for whether or not they were coded as ecologically
 significant traits. The continuous character data file
 is *olenid_cont.nex.* The file *OlenidaeScript.Rev* runs the phylogenetic
 analyses.