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A covarion model for phylogenetic estimation using discrete morphological datasets.

Basanta Khakurel^1,2, Sebastian Höhna^1,2

¹Department of Earth and Environmental Sciences, Paleontology, and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.

Systematic Biology

|February 23, 2026

Summary

This summary is machine-generated.

The new covariomorph model accounts for varying evolutionary rates across lineages and characters in morphology. This approach improves phylogenetic inference accuracy by capturing complex rate shifts, unlike traditional models.

Keywords:

Bayesian phylogenetics RevBayes covariomorph covarion morphology

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Area of Science:

Evolutionary Biology
Phylogenetics
Computational Biology

Background:

Morphological character evolution rates are heterogeneous across phylogenies and vary among characters.
Traditional phylogenetic models often assume time-homogeneous Markov processes, failing to capture lineage-specific rate variation.
Existing models with among-character rate variation do not address lineage-specific dynamics for individual characters.

Purpose of the Study:

To extend the covarion model for molecular data to morphological character evolution, termed the covariomorph model.
To implement and apply the covariomorph model in RevBayes to diverse morphological datasets.
To investigate the impact of lineage- and character-specific rate shifts on phylogenetic inference.

Main Methods:

Developed the covariomorph model, utilizing multiple rate categories from a discretized probability distribution to scale rate matrices.
Allowed characters to evolve within and switch between rate categories during the evolutionary process.
Validated the model through simulations and applied it to 164 empirical morphological datasets.

Main Results:

The covariomorph model was successfully implemented and verified via simulations.
Approximately half of the empirical datasets showed rate heterogeneity patterns consistent with covarion-like dynamics.
Analysis of focal datasets revealed that the covariomorph model significantly impacts tree topology and branch lengths compared to traditional models.

Conclusions:

The covariomorph model offers a more nuanced approach to incorporating rate variation across lineages and characters in morphological phylogenetics.
Accounting for lineage- and character-specific rate shifts enhances the accuracy of phylogenetic inference.
The model's sensitivity to branch lengths highlights its importance for divergence time estimation and evolutionary rate calculations.