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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Hypothetical Ancestors and Rooting in Cladistic Analysis.

Harold N Bryant¹

¹Provincial Museum of Alberta, 12845-102 Avenue, Edmonton, Alberta, T5N 0M6, Canada.

Cladistics : the International Journal of the Willi Hennig Society

|December 16, 2021

Summary

Hypothetical ancestors can root cladistic trees, but combining outgroup comparison with ontogenetic or paleontological methods is invalid. Synthesizing these methods requires taxonomic congruence for accurate phylogenetic analysis.

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Area of Science:

Systematic Biology
Phylogenetics
Evolutionary Biology

Background:

Hypothetical ancestors are commonly used to root phylogenetic trees in cladistic analyses.
These ancestors can summarize character-state data from outgroup taxa.
Alternative methods for rooting include ontogenetic and paleontological approaches to polarizing character transformations.

Purpose of the Study:

To evaluate the validity of using a single hypothetical ancestor that combines different methods of rooting cladograms.
To clarify the distinct applicability of outgroup comparison versus ontogenetic/paleontological methods for rooting.
To propose a valid method for synthesizing information from multiple rooting strategies.

Main Methods:

Analysis of character-state transformations in cladistic analyses.
Comparison of rooting inferences from outgroup comparison, ontogenetic, and paleontological methods.
Application of the Lundberg method for rooting with hypothetical ancestors derived from ontogenetic/paleontological data.

Main Results:

Combining outgroup comparison with ontogenetic or paleontological methods in a single hypothetical ancestor for rooting is invalid.
Inferences from outgroup comparison apply to the outgroup node, while ontogenetic/paleontological methods apply to the ingroup node.
The Lundberg method provides a valid approach for rooting using hypothetical ancestors inferred from ontogenetic and paleontological data.

Conclusions:

A single hypothetical ancestor cannot validly combine rooting inferences from outgroup comparison with ontogenetic or paleontological methods.
Direct combination of these rooting strategies is not possible due to differing application points (outgroup vs. ingroup nodes).
Synthesizing information from all three rooting methods into a single phylogenetic tree necessitates the use of taxonomic congruence.