Phylogenetic paradigm shifts in early amniote evolution

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 co..., , , # 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...,