An experimentally determined evolutionary model dramatically improves phylogenetic fit.


Abstract

All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.

Submission Details

ID: zAqktrSK

Submitter: Shu-Ching Ou

Submission Date: March 1, 2019, 5:26 p.m.

Version: 1

Publication Details
Bloom JD,Mol Biol Evol (2014) An experimentally determined evolutionary model dramatically improves phylogenetic fit. PMID:24859245
Additional Information

Number of data points 9464
Proteins Nucleoprotein
Unique complexes 9463
Assays/Quantities/Protocols Experimental Assay: Preference
Libraries Variants for Nucleoprotein
Sequence Assay Result Units