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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Retrieving a mitogenomic mammal tree using composite taxa.

Véronique Campbell¹, François-Joseph Lapointe

¹Département de Sciences biologiques, Université de Montréal, Montréal, Québec, Canada. veronique.campbell@umontreal.ca

Molecular Phylogenetics and Evolution

|December 8, 2010

Summary

The composite taxon approach effectively handles missing data in phylogenomic supermatrices. This method, creating composite sequences, shows comparable accuracy to traditional missing data methods while reducing computational time.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Published on: August 16, 2017

Area of Science:

Phylogenomics
Bioinformatics
Computational Biology

Background:

Supermatrices in phylogenomics often contain substantial missing data, complicating phylogenetic analyses.
The composite taxon approach, creating combined sequences from multiple species, is an emerging strategy to mitigate missing data.
The accuracy and utility of the composite taxon approach compared to traditional methods for handling missing data remain under-investigated.

Purpose of the Study:

To evaluate the accuracy of the composite taxon approach in phylogenomic analyses.
To compare the performance of composite taxon matrices with matrices containing coded missing data.
To assess the impact of missing data levels on phylogenetic congruence for both approaches.

Main Methods:

Applied the composite taxon approach to complete mitochondrial sequence matrices from 102 mammal species.
Constructed composite taxa by combining sequences to maximize gene representation.
Analyzed phylogenetic congruence of both composite and missing data matrices against model trees derived from complete data.

Main Results:

Composite taxon matrices and matrices with coded missing data exhibited similar congruence to model trees on average.
Phylogenetic congruence decreased for both approaches as the amount of missing data increased.
The composite taxon approach demonstrated comparable performance to traditional missing data handling.

Conclusions:

The composite taxon approach is a viable strategy for phylogenomic studies with significant missing data.
This method offers a practical solution that performs well and reduces computational demands.
Further consideration of the composite taxon approach is recommended in phylogenomic research.