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

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Simultaneous Bayesian inference of phylogeny and molecular coevolution.

Xavier Meyer^1,2,3, Linda Dib³, Daniele Silvestro^4,3,5,6

¹Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; xav.meyer@gmail.com.

Proceedings of the National Academy of Sciences of the United States of America

|February 28, 2019

Summary

This study introduces a new Bayesian method to analyze molecular coevolution and phylogenetic history simultaneously. Accounting for dependent site evolution significantly improves the accuracy of phylogenetic tree inference.

Keywords:

Bayesian inference molecular coevolution phylogeny tree of life

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Area of Science:

Evolutionary Biology
Bioinformatics
Molecular Evolution

Background:

Molecular coevolution patterns reveal constraints in organic molecules.
Analyzing coevolution and phylogenetic history separately, due to computational convenience, reduces accuracy.
Disregarding dependent site evolution negatively impacts phylogenetic tree inference.

Purpose of the Study:

To develop a Bayesian method and software for simultaneous inference of molecular coevolution and phylogenetic relationships.
To distinguish between independent and pairwise dependent evolutionary processes at different sites.
To assess the impact of accounting for dependent site evolution on phylogenetic accuracy.

Main Methods:

A novel Bayesian approach was developed to infer evolutionary processes and phylogenetic relationships concurrently.
The method was validated using synthetic datasets and applied to the 16S rRNA molecule.
Phylogenetic tree accuracy was assessed using synthetic data, 16S rRNA, and eukaryotic protein-coding gene alignments.

Main Results:

The method successfully infers the number and type of evolutionary processes (independent or dependent) at different sites.
Predictions of coevolution for 16S rRNA were validated against its known molecular structure.
Accounting for dependent site evolution significantly improved phylogenetic tree estimates compared to methods assuming independence.

Conclusions:

Simultaneous analysis of molecular coevolution and phylogenetic history is crucial for accurate evolutionary inference.
The developed Bayesian method provides a more accurate approach to phylogenetic tree reconstruction.
Ignoring dependent site evolution leads to inaccuracies in understanding both evolutionary processes and phylogenetic relationships.