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Updated: Jan 22, 2026

A Practical Guide to Phylogenetics for Nonexperts
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Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest

Benedict King1

  • 1Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The Netherlands.

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Summary

A new method identifies characters driving conflicting phylogenetic trees from morphological data. For early fish, Bayesian analysis favors a specific group, driven by just two traits, ignoring others.

Keywords:
Bayesianbiasosteichthyansparsimonyphylogenetics

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Area of Science:

  • Phylogenetics
  • Evolutionary Biology
  • Paleontology

Background:

  • Reconstructing the tree of life from morphological data involves debate over optimal methods.
  • Identifying characters responsible for topological differences between phylogenetic trees is crucial but often overlooked.
  • Existing methods for character support analysis are limited, particularly within model-based frameworks.

Purpose of the Study:

  • Introduce a procedure to find characters supporting conflicting tree topologies in a model-based framework.
  • Apply this procedure to resolve phylogenetic discrepancies in early osteichthyans ('psarolepids').
  • Investigate the influence of character completeness on phylogenetic inference in Bayesian analyses.

Main Methods:

  • Developed a novel procedure for character support analysis within a model-based phylogenetic framework.
  • Applied the procedure to morphological data of 'psarolepid' osteichthyans.
  • Compared phylogenetic results from parsimony and Bayesian analyses.

Main Results:

  • The 'psarolepid' group is weakly supported as stem osteichthyans under parsimony but strongly as sarcopterygians in Bayesian analysis.
  • The Bayesian result is driven by two characters related to the intracranial joint.
  • Characters like the absence of tooth enamel have minimal impact in the Bayesian framework due to sampling completeness bias.

Conclusions:

  • The introduced procedure effectively identifies characters driving conflicting phylogenetic hypotheses.
  • Bayesian analysis of morphological data can exhibit bias towards characters with complete sampling.
  • Critical appraisal of character support is essential for robust phylogenetic analyses, especially with morphological datasets.