Supplementary materials from: Phylogeny of Athyridida (Brachiopoda): A comparison of methods of inference

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).
, , # 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 eac...,