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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Predicting evolution from the shape of genealogical trees.

Richard A Neher¹, Colin A Russell², Boris I Shraiman³

¹Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany.

|November 12, 2014

Summary

Predicting the evolutionary future of asexual populations is possible by analyzing genome sequences. Genealogical tree branching patterns reveal relative fitness, enabling the prediction of successful strains, as demonstrated with influenza A/H3N2 virus evolution.

Keywords:

adaptive evolution evolutionary biology genomics population genetics vaccine strain selection viruses

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Area of Science:

Evolutionary biology
Genomics
Epidemiology

Background:

Predicting the evolutionary trajectory of asexual populations, such as viruses, is crucial for public health and biological research.
Understanding the factors driving successful strain emergence requires robust analytical methods.

Purpose of the Study:

To develop and validate a method for predicting the evolutionary future of asexual populations using genomic data.
To assess the predictability of successful strains based on genealogical tree branching patterns.

Main Methods:

Reconstruction of genealogical trees from asexual population genome sequences.
Analysis of branching patterns to infer relative sequence fitness.
Application of the method to historical seasonal influenza A/H3N2 virus data.

Main Results:

Genealogical tree branching patterns contain information about relative fitness.
The method successfully predicted the progenitor lineage of the upcoming influenza season in 30% of cases.
Informative predictions were made in 16 out of 19 influenza seasons analyzed.

Conclusions:

The evolutionary future of asexual populations can be predicted from genome sequences.
The findings imply persistent fitness variation among circulating influenza A/H3N2 viruses.
This approach offers a tool for predicting successful strains in asexual populations under selection.