CAM: an alignment-free method to recover phylogenies using codon aversion motifs.

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Traditional phylogenomic methods are time-consuming and rely on orthologous gene annotations.
• Alignment-free approaches use sequence composition (e.g., oligomer frequencies) for phylogenetic analysis.
• Codon aversion, the set of unused codons within genes, presents a novel character for phylogenetics.

Purpose of the Study:

• To introduce and evaluate CAM, an alignment-free phylogenomic approach based on codon aversion motifs.
• To assess the speed and accuracy of CAM compared to existing phylogenetic methods.
• To establish codon aversion as a phylogenetically conserved character.

Main Methods:

• Developed CAM, an alignment-free method comparing codon aversion motifs across genes within species.
• Calculated pairwise species distances based on shared and unique codon aversion motifs.
• Applied neighbor-joining algorithm to reconstruct phylogenies using calculated distances.
• Analyzed codon aversion across 229,742,339 genes from 23,428 species.

Main Results:

• CAM successfully recovered phylogenies comparable to established methods like maximum likelihood.
• The method demonstrated high accuracy, aligning well with reference phylogenies (Open Tree of Life, NCBI Taxonomy).
• CAM significantly outperforms maximum likelihood in speed while maintaining competitive accuracy with other alignment-free methods.

Conclusions:

• Codon aversion is a phylogenetically conserved character suitable for phylogenomic studies.
• CAM provides a rapid and accurate alignment-free framework for phylogenetic reconstruction.
• The CAM software is publicly available for further research.