DOI: 10.5061/dryad.6m905qgcp
title: Supplementary materials from: Phylogeny of Athyridida (Brachiopoda): A comparison of methods of inference

description: Using Athyridida (Upper Ordovician-Lower Jurassic) as a case study, we
 utilize parsimony, Bayesian Mk, asymmetrical rates, and fossilized
 birth-death process models, with and without character partitions, to
 compare results from different methods of inference, to test previous
 phylogenetic hypotheses, and examine morphological character evolution in
 this long-lived group of extinct brachiopods. Because different
 phylogenetic methods utilize different models of evolution involving
 different sets of assumptions, they can result in different patterns of
 relationships, making it necessary to test multiple methods and then
 evaluate thoughtfully the various results obtained. We have chosen to
 illustrate and discuss the MCC consensus trees obtained, but include MAP
 consensus trees for comparison in the Supplemental Materials (SM1-9) as
 they can differ, sometimes significantly, in topology from the MCC trees
 (e.g., compare SM5 and SM8).
description: # Supplementary materials from: Phylogeny of Athyridida (Brachiopoda): A
 comparison of methods of inference Dataset DOI:
 [10.5061/dryad.6m905qgcp](10.5061/dryad.6m905qgcp) ## Description of the
 data and file structure **TIFF images of phylogenetic trees** ### Files
 and variables #### Files: * Carlsonetal_SupplementalMaterial1.tiff *
 Carlsonetal_SupplementalMaterial2.tiff *
 Carlsonetal_SupplementalMaterial3.tiff *
 Carlsonetal_SupplementalMaterial4.tiff *
 Carlsonetal_SupplementalMaterial5.tiff *
 Carlsonetal_SupplementalMaterial6.tiff *
 Carlsonetal_SupplementalMaterial7.tiff *
 Carlsonetal_SupplementalMaterial8.tiff *
 Carlsonetal_SupplementalMaterial9(1).tiff *
 Carlsonetal_SupplementalMaterial9(2).txt **Description:**  **Supplemental
 Material** **1.** Matrix 1, parsimony results. Fifty percent majority rule
 consensus tree of 630 equally most parsimonious (EWP) cladograms saved
 (out of 9300+ generated), characters equally weighted and unordered.
 Support values listed at each node; unlabeled nodes have 100% (1.0)
 support. **Supplemental Material** **2.** Matrix 1, Bayesian Mk analysis
 maximum *a posteriori* (MAP) consensus tree, which is the most likely tree
 given the priors and the likelihood of the data. Support values are listed
 at each node. **Supplemental Material** **3.** Matrix 2, parsimony
 results. Fifty percent majority rule consensus tree of 600 equally most
 parsimonious cladograms, characters equally weighted and unordered.
 Support values listed at each node; unlabeled nodes have 100% (1.0)
 support. **Supplemental Material** **4.** Matrix 2, Bayesian Mk analysis,
 MAP consensus tree, which is the most likely tree given the priors and the
 likelihood of the data. Support values are listed at each node.
 **Supplemental Material** **5.** Matrix 2, Mk partitioned MAP. Support
 values are listed at each node. **Supplemental Material** **6.** Matrix 2,
 Mk asymmetrical rates unpartitioned MAP.  Support values are listed at
 each node. **Supplemental Material** **7.** Matrix 2, FBD unpartitioned
 MAP. Support values are listed at each node. **Supplemental Material**
 **8.** Matrix 2, FBD partitioned MAP. Support values are listed at each
 node. **Supplemental Material** **9.** **(1)** Matrix 2, FBD results,
 unpartitioned MCC tree. Nodes numbered to correspond with **(2)** partial
 apomorphy list.