Supplementary material and supplementary data files for: Handling logical character dependency in phylogenetic inference: Extensive performance testing of assumptions and solutions using simulated and empirical data

Tiago R. Simões, Oksana Vernygora, Bruno A. S. Medeiros & April M. Wright
Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological datasets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in datasets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become...
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