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Updated: Jun 12, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Homoplasy and clade support.

Matthew C Brandley¹, Dan L Warren, Adam D Leaché

¹Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720-3160, USA.

Systematic Biology

|June 8, 2010

Summary

Homoplasy, or shared traits not from common ancestry, can skew phylogenetic tree inference. Bayesian methods, unlike bootstrap analyses, minimize this clade size bias, especially in deep phylogenetic studies.

Area of Science:

Phylogenetics
Evolutionary Biology
Bioinformatics

Background:

Distinguishing phylogenetic signal from homoplasy is crucial for accurate evolutionary tree inference.
Homoplasy can negatively impact common clade support measures like bootstrap proportions and Bayesian posterior probabilities.

Purpose of the Study:

To investigate how homoplasy affects clade support measures in phylogenetic analyses.
To determine if clade size influences the accuracy of support values.
To compare the performance of different phylogenetic methods in the presence of homoplasy.

Main Methods:

Data simulation and analysis of 38 empirical phylogenetic datasets.
Evaluation of clade support measures including bootstrap proportions and Bayesian posterior probabilities.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Development and application of the clade disparity index (CDI) to quantify clade size effects.

Main Results:

High homoplasy affects all clade support measures, with smaller bipartitions receiving disproportionately higher support.
This effect is linked to random tree inclusion in resampling and the proportion of small bipartitions.
Bayesian Markov chain Monte Carlo (MCMC) methods effectively overcome the clade size effect, even with minimal phylogenetic signal.
The clade disparity index (CDI) indicates Bayesian MCMC analyses are less affected by homoplasy than parsimony or likelihood bootstrap analyses.

Conclusions:

Bayesian MCMC methods provide more reliable clade support estimates, uncorrelated with clade size, compared to bootstrap methods.
The clade disparity index (CDI) is a useful tool for assessing the impact of homoplasy and clade size on phylogenetic inference.
These findings are particularly relevant for deep phylogenetic studies, such as reconstructing the tree of life, where homoplasy is prevalent.