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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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New Phylogenetic Markov Models for Inapplicable Morphological Characters.

Sergei Tarasov¹

¹Finnish Museum of Natural History, Pohjoinen Rautatiekatu 13, FI-00014 Helsinki, Finland.

Systematic Biology

|February 14, 2023

Summary

This study introduces novel Markov models for phylogenetic inference, specifically designed for complex morphological characters with anatomical dependencies. These models enhance evolutionary analyses by accurately representing character evolution under hierarchical constraints.

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Area of Science:

Evolutionary Biology
Computational Biology
Phylogenetics

Background:

Phylogenetic inference often struggles with morphological characters exhibiting complex dependencies.
Existing models may not adequately capture anatomical constraints where character evolution is state-dependent.

Purpose of the Study:

To propose novel Markov models for phylogenetic inference that explicitly handle anatomically dependent morphological characters.
To provide tools and recommendations for implementing these models in Bayesian phylogenetic analyses.

Main Methods:

Development of two new types of Markov models tailored for character hierarchies.
Implementation of functions for custom character hierarchy construction within the R package rphenoscate.
Assessment of model performance through theoretical analysis and simulations.

Main Results:

The proposed Markov models effectively represent anatomically dependent characters.
The R package rphenoscate facilitates the creation of custom character hierarchies.
Simulations demonstrate the utility and performance of the new models in phylogenetic inference.

Conclusions:

The new Markov models offer a significant advancement for phylogenetic inference with complex morphological data.
Practical guidance is provided for applying these models using RevBayes for Bayesian phylogenetic analyses.
These models improve the accuracy of evolutionary reconstructions when dealing with inapplicable or state-dependent characters.