DOI: 10.5061/dryad.pt3qm
title: Data from: Taxonomy and phylogeny can yield comparable results in comparative palaeontological analyses

description: Many extinct taxa with extensive fossil records and mature taxonomic
 classifications have not yet been the subject of formal phylogenetic
 analysis. Here, we test whether the taxonomies available for such groups
 represent useful (i.e., non-misleading) substitutes for trees derived from
 matrix-based phylogenetic analyses. We collected data for 52 animal clades
 that included fossil representatives, and for which a recent cladogram and
 pre-cladistic taxonomy were available. We quantified the difference
 between the time-scaled phylogenies implied by taxonomies and cladograms
 using the matching cluster distance metric. We simulated phenotypic trait
 values and used them to estimate a series of commonly used,
 phylogenetically explicit measures (phylogenetic signal [Blomberg's
 K], phylogenetic generalized least squares [PGLS], mode of evolution
 [Brownian vs. Ornstein–Uhlenbeck], and phylogenetic clustering of
 extinction [Fritz and Purvis' D]) in order to determine the degree to
 which they co-varied on taxonomic and cladistic trees. With respect to
 topology taxonomies are good approximations of the underlying evolutionary
 relationships as recorded in inferred cladograms. Detection of
 phylogenetic clustering of extinction could not be properly assessed. For
 all other evolutionary analyses, results from taxonomy-based phylogenies
 (TBPs) co-varied with those from cladogram-based phylogenies (CBPs), but
 individual comparisons could be misleading. The relative length of
 terminal branches (influenced by stratigraphy and sampling rate) is a key
 control on the shared information between, and therefore the relative
 performance of, TBP and CBP. Collectively these results suggest that under
 particular circumstances and after careful consideration some taxonomies,
 or composite trees that incorporate taxonomic information, could be used
 in place of a formal analytical solution, but workers must be cautious.
 This opens certain parts of a previously inaccessible section of the
 fossil record to interrogation within an explicit comparative framework,
 which will help to test many classical macroevolutionary hypotheses
 formulated for groups that currently lack formal phylogenetic estimates.
description: DataAll cladograms,
 taxonomies and range data used in analyses.Online appendix
 1Sources and details of
 all data sets used in analysesOnline Appendix
 2Methods flow
 chartScriptScript of R code used to
 run all the analysesExampleTaxonomyAn example taxonomy in the correct format to be converted to a cladogram in R using the function provided in the file tax2tree.txttax2treeR script of function to convert a taxonomy in the format shown in the file ExampleTaxonomy.txt, to a cladogram in Newick formatOnline appendix 3Methods and results from analyses of phylogenetic clustering of extinctionAdditional FiguresAdditional figures as mentioned in manuscript. Includes p-values for phylogenetic signal analysis, results of extended range analyses and results of OU model analysis with alpha proportional to tree heightResults