DOI: 10.5061/dryad.3ffbg79qx
title: Data from: Phylogenetic paradigm shifts in early amniote evolution

description: The dichotomy within Amniota (mammals and reptiles) was recognized early
 in the history of phylogenetic systematics, and with it developed a
 canonical understanding of the evolutionary relationships of
 early-diverging clades. In recent years, the relationships of these clades
 have shifted dramatically among studies, which has profound effects on how
 researchers interpret evolutionary patterns in early amniotes. To gain a
 fuller understanding of the early evolution of amniotes, we compiled the
 largest amniote-wide phylogenetic dataset to date, including 590 fully
 illustrated characters and 150 taxa representing all the major clades of
 “pelycosaurian” stem mammals, pan-reptiles, and several outgroups. We
 analyzed this dataset under Bayesian and parsimony frameworks, which
 resulted in different topologies, particularly among stem mammals and
 near-crown and within-crown Reptilia. To explore the effect sampling has
 on tree topology, we conducted three series of exclusion experiments, each
 consisting of ten analyses, each with ten fewer taxa than the previous, as
 well as 26 exclusion analyses removing one clade or individual at a time.
 This experiment showed that taxon sampling has a major effect on early
 amniote tree topology, and many of the topologies recovered bear striking
 similarities to those reported in recent publications. Furthermore, we
 identify and discuss several unique effects that taxon exclusion may have
 on phylogenies. To address poorly resolved (i.e., polytomies) and unstable
 portions of amniote phylogeny, where branches frequently move or dismantle
 depending on sampling and choice of analytical technique, we encourage
 more detailed anatomical work on early amniotes, particularly stem
 mammals.
description: # Data from: Phylogenetic paradigm shifts in early amniote evolution
 [https://doi.org/10.5061/dryad.3ffbg79qx](https://doi.org/10.5061/dryad.3ffbg79qx) Three folders are included within this Supplement: (1) Full_Analysis.zip - This folder contains 6 subfolders. Each subfolder contains the results from a phylogenetic analysis using the full taxon-character matrix, including all Parsimony analyses (Equal Weights, K = 3, 6, 9, 12) and Bayesian analysis (Fossilized Birth Death). (2) Random_Revomval.zip - Three series (Series A, B, C) of random removal experiments were conducted in both Parsimony and Bayesian frameworks. Nine subfolders are found within this folder with the original mesquite files, parsimony results, and Bayesian results for this experiment. (3) Selective_Removal.zip - 26 selective removal experiments were conducted in both Parsimony and Bayesian frameworks. Two subfolders are found within this folder, one for all Parsimony results and one for all Bayesian results. The complete, unaltered matrix is labeled as "Full_Matrix.tnt". Word documents related to matrix construction (i.e., taxa included in the analysis, illustrated character matrix) and the experimental removals, clade definitions, and synapomorphies can be found in the Supplementary Material hosted on *Systematic Biology*'s website.