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Related Experiment Video

Updated: Oct 24, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Accuracy in Near-Perfect Virus Phylogenies.

Joel O Wertheim¹, Mike Steel², Michael J Sanderson³

¹Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.

Systematic Biology

|August 16, 2021

Summary

Phylogenetic tree accuracy can be high even with short edges. In near-perfect conditions, the false positive rate for discovering clades is low, especially for viruses like SARS-CoV-2.

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Area of Science:

Phylogenetics
Computational Biology
Evolutionary Biology

Background:

Real-world phylogenetic trees often have short edges, leading to incomplete resolution and reduced accuracy.
Theoretical models suggest that accurately reconstructing trees requires a number of sites inversely proportional to the square of the shortest edge length.

Purpose of the Study:

To redefine and assess "accuracy" in phylogenetic inference when short edges are present.
To analyze the false positive rate of clade discovery in "near-perfect" phylogenetic parameter spaces.
To compare bootstrap support measures with actual false positive rates.

Main Methods:

Analytical derivation for maximum parsimony.
Theoretical analysis and simulations for maximum likelihood.
Comparison of bootstrap resampling support with false positive rates.

Main Results:

Accuracy can remain high even with short edges if defined by false split discovery rate.
In near-perfect parameter spaces, the expected false positive rate is low (less than ξ/3), often below 5%.
Bootstrap support measures tend to underestimate clade reliability compared to actual false positive rates in near-perfect trees.

Conclusions:

The "near-perfect" model accurately reflects empirical data from human virus outbreaks (e.g., Ebolavirus, Zika virus, SARS-CoV-2).
Phylogenetic inference can be reliable in scenarios with low substitution rates relative to high transmission/sampling rates.
This work provides a more nuanced understanding of phylogenetic accuracy and support measures.