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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.

Paschalia Kapli¹, Ioanna Kotari^1,2, Maximilian J Telford¹

¹Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK.

Systematic Biology

|June 27, 2023

Summary

DNA sequences may be as effective as protein sequences for inferring deep phylogenies. This finding challenges long-held beliefs and suggests DNA data analysis offers computational advantages for evolutionary studies.

Keywords:

Amino acid models codon models deep phylogeny nonhomogeneous processes nucleotide substitution phylogenetic information

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Evolutionary biology
Bioinformatics
Computational phylogenetics

Background:

Deep phylogenetic inference traditionally favors protein sequences over DNA due to perceived lower rates of homoplasy and saturation.
Concerns about compositional heterogeneity in DNA sequences have historically limited their use in deep phylogenetic analyses.

Purpose of the Study:

To challenge the prevailing notion that protein sequences are superior to DNA sequences for deep phylogenetic inference.
To evaluate the utility of both DNA and protein sequences for reconstructing deep phylogenies using various evolutionary models.

Main Methods:

A simulation study was conducted using codon evolution models under an idealized genetic code.
Protein-coding data were generated incorporating heterogeneous substitution processes across sites and lineages.
Analyses were performed using nucleotide, amino acid, and codon substitution models on both simulated and empirical metazoan data.

Main Results:

Analysis of DNA sequences using nucleotide substitution models recovered the correct phylogeny as effectively as protein sequence analysis using amino acid models.
Both simulated and empirical data analyses indicated that DNA sequences are comparable to protein sequences for deep phylogeny inference.
DNA data analysis under nucleotide models demonstrated significant computational advantages over protein data analysis.

Conclusions:

DNA sequences are as valuable as protein sequences for inferring deep phylogenies and should not be excluded from such analyses.
The perceived limitations of DNA sequences in phylogenetic inference may be misconceptions.
The computational efficiency of DNA data analysis facilitates the application of advanced models for phylogenetic reconstruction.