Systematic errors in orthology inference and their effects on evolutionary analyses.

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Comparative genomics enables the identification of clade-specific genes, crucial for understanding evolutionary novelties and gene ages (phylostratigraphy).
• Accurate prediction of orthologs is fundamental for these evolutionary reconstructions and analyses.

Purpose of the Study:

• To investigate the impact of orthology prediction errors on phylogenetic analyses using simulated data.
• To assess whether simulated orthology prediction errors recapitulate patterns observed in empirical evolutionary studies.

Main Methods:

• Simulated gene sets with no gains or losses were generated to isolate the effects of orthology prediction errors.
• Phylogenetic trees were reconstructed, gene gains and losses were counted, and phylostratigraphy was performed using these simulated ortholog sets.

Main Results:

• Orthology prediction errors increase with higher rates of molecular evolution.
• Simulated data, containing only orthology prediction errors, closely mirrored findings from analyses of empirical data.
• Downstream analyses of gene evolution may be substantially influenced by these prediction errors.

Conclusions:

• Errors in orthology prediction are a significant factor that can mimic expected patterns of gene evolution.
• Researchers should be aware of and account for potential orthology prediction errors when interpreting phylogenetic and evolutionary studies.