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A Practical Guide to Phylogenetics for Nonexperts

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Using Genotype Abundance to Improve Phylogenetic Inference.

William S DeWitt^1,2, Luka Mesin³, Gabriel D Victora³

¹Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA.

Molecular Biology and Evolution

|February 24, 2018

Summary

Phylogenetic inference is improved by incorporating genotype abundance data. This method uses a stochastic process model and is validated in simulations and lineage tracing studies.

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Area of Science:

Evolutionary biology
Genetics
Computational biology

Background:

Modern biological techniques allow for dense genetic sampling, often resulting in multiple observations of the same genotype.
Incorporating genotype abundance data into phylogenetic inference is crucial for accurately reconstructing evolutionary histories.

Purpose of the Study:

To develop and validate a novel method for phylogenetic inference that integrates genotype abundance information.
To improve the accuracy of evolutionary tree estimation by leveraging multi-sample genotype data.

Main Methods:

Synthesized a stochastic process model with standard sequence-based phylogenetic optimality.
Incorporated genotype abundance data into the phylogenetic tree estimation process.
Validated the method using extensive simulations and a single-cell lineage tracing study.

Main Results:

Tree estimation accuracy was substantially improved by incorporating genotype abundance information.
The method demonstrated effectiveness in reconstructing evolutionary histories from dense genetic samples.
Successful application in a real-world biological system (B cell receptor affinity maturation).

Conclusions:

Integrating genotype abundance into phylogenetic inference significantly enhances tree estimation.
The developed stochastic process model offers a powerful tool for evolutionary studies with dense genetic data.
This approach has broad applicability in understanding evolutionary dynamics across various biological systems.