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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Rooting with Multiple Outgroups: Consensus Versus Parsimony.

Véronique Barriel^1,2, Pascal Tassy³

¹URA 9948 CNRS, Institut de Paléontologie Humaine, Muséum national d'Histoire naturelle, Paris, France.

Cladistics : the International Journal of the Willi Hennig Society

|December 14, 2021

Summary

Rooting phylogenetic trees with multiple outgroups can yield conflicting results, affecting basal branching patterns. Using a strict consensus of equally parsimonious trees offers a robust alternative to selecting a single prime outgroup.

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Area of Science:

Phylogenetics
Systematics
Evolutionary Biology

Background:

Phylogenetic trees are commonly rooted using outgroup(s) to infer evolutionary relationships and test ingroup monophyly.
Unconstrained simultaneous analysis with multiple outgroups is favored for its potential to rigorously test ingroup monophyly.

Discussion:

Contradictory outgroup data can lead to unstable basal node resolution in rooted trees.
The order of outgroups in the data matrix, specifically the prime outgroup, can arbitrarily influence tree topology, even with exhaustive searches.
Permuting prime outgroups can result in different, equally parsimonious rooted trees (cladograms).

Key Insights:

Selecting a single outgroup to root a tree introduces an assumption that may not reflect true evolutionary history.
The strict consensus of multiple equally parsimonious rooted trees provides a less assumption-laden alternative for tree rooting.
This consensus approach avoids the arbitrary choice of a prime outgroup but may result in a less resolved tree.

Outlook:

Future phylogenetic analyses should consider consensus methods to mitigate biases from outgroup selection.
Further research into robust methods for resolving basal relationships in the presence of conflicting outgroup data is warranted.
Developing standardized protocols for outgroup selection and tree rooting could enhance phylogenetic reproducibility.