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A Practical Guide to Phylogenetics for Nonexperts

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DO PHYLOGENETIC METHODS PRODUCE TREES WITH BIASED SHAPES?

John P Huelsenbeck¹, Mark Kirkpatrick¹

¹Department of Zoology, University of Texas, Austin, Texas, 78712.

Evolution; International Journal of Organic Evolution

|June 1, 2017

Summary

This summary is machine-generated.

Phylogenetic methods often overestimate tree asymmetry. This study reveals bias in common methods, especially with high evolutionary rates, and proposes a corrected tree shape test.

Keywords:

Cladogenesis UPGMA extinction maximum likelihood neighbor joining parsimony phylogenetic tree speciation tree balance tree shape tree symmetry

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Area of Science:

Phylogenetics and Evolutionary Biology
Computational Biology

Background:

Phylogenetic methods are crucial for reconstructing evolutionary history.
Estimating tree shape provides insights into speciation and extinction dynamics.
The random branching model serves as a null hypothesis for tree shape analysis.

Purpose of the Study:

To assess the bias in commonly used phylogenetic methods regarding tree shape estimation.
To compare the performance of five distinct phylogenetic methods under simulated conditions.
To identify the factors influencing bias in tree shape estimates.

Main Methods:

Computer simulations were employed to evaluate phylogenetic methods.
Five methods were tested: maximum parsimony, neighbor joining, UPGMA (with and without an outgroup), and maximum likelihood.
Tree shape was analyzed in relation to the random branching model.

Main Results:

All tested phylogenetic methods exhibited a bias towards estimating more asymmetrical trees than the true evolutionary history.
This bias was particularly pronounced when high rates of evolution were simulated.
The study identified a systematic overestimation of asymmetry across methods.

Conclusions:

Common phylogenetic methods can introduce bias in tree shape estimation, particularly under rapid evolution.
A simple explanation for this bias was elucidated.
A modified tree shape test was proposed to correct for the identified bias.