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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Gene trees and species trees: irreconcilable differences.

Krister M Swenson¹, Nadia El-Mabrouk

¹Département d'Informatique, DIRO, Université de Montréal, H3C 3J7 Canada. swensonk@iro.umontreal.ca

BMC Bioinformatics

|January 4, 2013

Summary

Gene tree reconciliation can lead to inaccurate duplication-loss histories, even with accurate gene trees. This study introduces a conservative method to improve evolutionary history inference, using the interleukin-1 gene family as a model.

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Area of Science:

Evolutionary biology
Bioinformatics
Genomics

Background:

Reconciliation is a classical method for inferring gene duplication and loss history.
This method relies on embedding gene trees into species trees, with incongruence indicating evolutionary events.
Accuracy is highly dependent on the quality of both species and gene trees.

Purpose of the Study:

To demonstrate that errors in gene tree reconstruction are not the sole cause of inaccurate duplication-loss histories.
To prove that even well-supported gene trees can lead to incorrect reconciliation under certain biological assumptions.
To provide theoretical foundations for a more conservative approach to inferring evolutionary histories.

Main Methods:

Proving that even accurate gene trees can lead to erroneous reconciliation under specific hypotheses.
Developing theoretical underpinnings for a conservative inference approach.
Applying the novel method to the mammalian interleukin-1 (IL) gene family.

Main Results:

Errors in gene tree reconstruction are not the only source of inaccurate duplication-loss history inference.
Even a well-supported gene tree can yield a reconciliation that does not reflect the true evolutionary history.
A conservative approach is proposed for inferring histories from gene trees.

Conclusions:

The study highlights limitations in classical gene tree reconciliation methods.
It emphasizes the need for conservative approaches to account for potential inaccuracies beyond gene tree errors.
The findings have implications for understanding gene family evolution, exemplified by the IL gene family.