DOI: 10.5061/dryad.292dd
title: Data from: Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites

description: Reconstructing the tree of life involves more than identifying
 relationships among lineages; it also entails accurately estimating when
 lineages diverged. Paleontologists typically scale cladograms to time a
 posteriori by direct reference to first appearances of taxa in the
 stratigraphic record. Some approaches use probabilistic models of
 branching, extinction, and sampling processes to date samples of trees,
 such as the recently developed cal3 method, which stochastically draws
 divergence dates given a set of rates for those processes. However, these
 models require estimates of the rates of those processes, which may be
 hard to obtain, particularly for sampling. Here, we contrast the use of
 cal3 and other a posteriori time-scaling approaches by examining a
 previous study that documented a decelerating rate of morphological
 evolution in pterocephaliid trilobites. Although aspects of the data set
 make estimation of branching, extinction, and sampling rates difficult, we
 use a multifaceted approach to calculate and evaluate the rate estimates
 needed for applying cal3. In agreement with previous simulation studies,
 we find that the choice of phylogenetic dating method impacts downstream
 macroevolutionary conclusions. We also find contradictory evolutionary
 inferences between analyses on ancestor–descendant contrasts (based on
 ancestor trait reconstruction methods) and maximum-likelihood parameter
 estimates. Ancestral taxon inference in cal3 corroborates previously
 hypothesized ancestor–descendant sequences, but cal3 suggests greater
 support for budding cladogenesis than anagenesis. This case study
 demonstrates the potential and wide applicability of the cal3 method and
 the benefits afforded by choosing cal3 over simpler a posteriori
 time-scaling approaches.
description: READMEREADME file describes
 the file type and contents of all files in this data
 repository.PteroGW-prunedThe pruned most-parsimonious tree of the pterocephaliid trilobites from Hopkins (2011) is provided as a NEXUS filePCscores-pterocephaliidThe principal component scores from a PCA of the geometric morphometric landmark data for those pterocephaliid taxa is provided as a tab-delimitted .txt tableFAD-LAD-rescaled-pterotab-delimited tables of first and last appearance dates across 100 CONOP solutions for just the pterocephaliidsFAD-LAD-rescaled-alltab-delimited tables of first and last appearance dates across 100 CONOP solutions for all taxaptero-minsamplingminimum number of horizons each taxon was found at for just pterocephaliids (tab-delimited)all-minsamplingminimum number of horizons each taxon was found at for just pterocephaliids (tab-delimited)trilobite_cal3_03-25-16Rmarkdown script used for all analyses in this studytrilobite_cal3_03-25-16.pdfPDF created by knitting the Rmarkdown script used for all analyses in this studytrilobite_workspace_03-25-2016R Workspace file created by running the Rmarkdown script used for all analyses in this studyfigures_08-12-16R script for recreating all figures in the manuscript from the saved workspace file.