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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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How many characters are needed to reconstruct a phylogeny?

Alessio Capobianco^1,2

¹GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich 80333, Germany.

Biology Letters

|October 14, 2025

Summary

Accurate Bayesian phylogenetics requires 100-500 discrete characters for reliable tree topology estimation, especially with morphological data. Multistate and labile characters improve accuracy for larger datasets.

Keywords:

Bayesian phylogenetics Mkv RevBayes character matrix dataset size molecular characters morphological characters simulation systematics

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Published on: July 11, 2025

Area of Science:

Evolutionary biology
Computational phylogenetics
Systematics

Background:

Bayesian phylogenetics is increasingly used for macroevolutionary studies.
Morphological datasets are typically smaller than molecular datasets, raising questions about their sufficiency for phylogenetic inference.
The number of discrete characters needed for accurate phylogenetic tree estimation in a Bayesian framework remains unclear.

Purpose of the Study:

To investigate the impact of the number of discrete characters on the accuracy and precision of Bayesian phylogenetic tree topology estimation.
To explore this relationship under varying conditions, including the number of taxa, tree length, and character states.

Main Methods:

A simulation study was conducted using the software RevBayes.
The study manipulated the number of sampled discrete characters, number of taxa, average number of state changes per character (tree length), and number of states per character.
Phylogenetic accuracy and precision were assessed based on these parameters.

Main Results:

Between 100 and 500 variable discrete characters are generally needed for sufficient accuracy and precision with up to 20 taxa.
Multistate characters yielded slightly more accurate estimates than binary characters.
More labile characters (more state changes) improved accuracy for trees with over 50 taxa.

Conclusions:

A minimum of 100-500 discrete characters is recommended for robust Bayesian phylogenetic analyses, particularly with morphological data.
The type of character (multistate vs. binary, labile vs. conservative) influences phylogenetic accuracy.
There is an ongoing need to characterize and digitize morphological diversity for phylogenetic research.