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).