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Updated: Jul 30, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Multiple outgroups can cause random rooting in phylogenomics.

Rob DeSalle¹, Apurva Narechania², Michael Tessler³

¹Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.

Molecular Phylogenetics and Evolution

|May 12, 2023

Summary

This summary is machine-generated.

Selecting distant or multiple outgroups in phylogenetics can lead to random tree rooting. For accurate phylogenetic analysis, use a single, closely related outgroup instead of multiple distant ones.

Keywords:

Animals Outgroup choice Phylogenetic accuracy Phylogenetic analysis Phylogenomics Raw distance

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Last Updated: Jul 30, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

Phylogenetics and Phylogenomics
Computational Biology
Evolutionary Biology

Background:

Outgroup selection is a persistent challenge in phylogenetics, impacting tree topology.
This issue remains critical in the phylogenomic era with large datasets.

Purpose of the Study:

To investigate the influence of outgroup selection on phylogenetic tree topology.
Utilize large-scale animal phylogenomic datasets to assess this impact.

Main Methods:

Analysis of large phylogenomic animal datasets.
Examination of concatenated and coalescent-based phylogenetic methods.
Evaluation of different outgroup selection strategies.

Main Results:

Distant outgroups were found to cause random tree rooting.
The common practice of using multiple outgroups also frequently results in random rooting.
Both concatenated and coalescent-based methods are susceptible to this issue.

Conclusions:

The standard practice of using multiple outgroups should be discontinued.
A single, most closely related outgroup is recommended for robust phylogenetic inference.
Exceptions exist when multiple outgroups are similarly related to the ingroup.