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A Practical Guide to Phylogenetics for Nonexperts

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Should Networks Supplant Tree Building?

Rob DeSalle¹, Margaret Riley²

¹Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.

|August 7, 2020

Summary

This summary is machine-generated.

Rumors of the bacterial tree of life's demise are exaggerated. Network methods may not fully replace traditional tree-building for analyzing bacterial and archaeal evolutionary relationships.

Keywords:

bacterial phylogeny horizontal gene transfer networks

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Area of Science:

Evolutionary Biology
Phylogenetics
Genomic Analysis

Background:

Recent proposals advocate for network methods over traditional tree-building in genealogical analysis.
These proposals cite non-bifurcating evolutionary processes in bacteria and archaea and the perceived circularity of tree-building algorithms.
The validity of these arguments challenges the foundational methods of phylogenetic analysis.

Purpose of the Study:

To critically evaluate the arguments suggesting the obsolescence of tree-building in phylogenetic analysis.
To reassess the suitability of network methods versus tree-building for representing bacterial and archaeal evolutionary history.
To address the claim that tree-building is inherently circular and unscientific.

Main Methods:

Review and critical analysis of existing literature on phylogenetic methods.
Examination of the assumptions and limitations of both tree-building and network approaches.
Evaluation of evolutionary processes in bacterial and archaeal lineages in the context of different analytical frameworks.

Main Results:

The arguments for supplanting tree-building with network methods are not fully substantiated.
Bacterial and archaeal evolutionary processes, while complex, do not entirely preclude the utility of tree-like representations.
The perceived circularity of tree-building is a mischaracterization of the scientific process.

Conclusions:

The bacterial tree of life remains a relevant and valuable concept.
Tree-building methods, despite limitations, continue to be essential tools in phylogenetic analysis.
Claims regarding the end of tree-building in phylogenetics are premature and overstated.