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A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

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Total evidence, average consensus and matrix representation with parsimony: what a difference distances make.

Claudine Levasseur¹, François-Joseph Lapointe

¹Département de sciences biologiques, Université de Montréal, QC, Canada.

Evolutionary Bioinformatics Online

|May 21, 2009

Summary

Matrix Representation with Parsimony (MRP) is less accurate than average consensus trees in supertree reconstruction. Both total evidence and average consensus methods outperform MRP, with accuracy influenced by data characteristics.

Keywords:

Average consensus character congruence matrix representation with parsimony simulation study taxonomic congruence total evidence

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Area of Science:

Phylogenetics
Computational Biology
Systematics

Background:

Matrix Representation with Parsimony (MRP) is a popular method for combining phylogenetic trees.
Its classification as a consensus or total evidence method remains debated.
Previous studies yielded conflicting results regarding its relationship to consensus and total evidence approaches.

Purpose of the Study:

To investigate the hypothesis that MRP is equally related to total evidence and consensus methods.
To evaluate the accuracy of MRP in comparison to total evidence and consensus methods using simulations.

Main Methods:

A simulation study was conducted to compare the accuracy of different tree-building methods.
Methods compared included total evidence, average consensus (with branch lengths), and Matrix Representation with Parsimony (MRP).
The impact of factors like taxon number, data partitions, and data heterogeneity on accuracy was assessed.

Main Results:

Total evidence trees were not significantly more accurate than average consensus trees that account for branch lengths.
Both total evidence and average consensus methods performed better than MRP trees in a consensus setting.
The accuracy of all methods was similarly affected by the number of taxa, partitions, and data heterogeneity.

Conclusions:

MRP does not perform as well as average consensus methods in the consensus setting.
Average consensus methods, particularly those accounting for branch lengths, offer a viable alternative to total evidence approaches.
The choice of method can be influenced by the characteristics of the phylogenetic data.