Developing and Applying RNA Empirical Models With Secondary Structure Insights for Orthoptera Phylogenetics

Area of Science:

• Evolutionary biology
• Bioinformatics
• Molecular biology

Background:

• RNA secondary structures have distinct evolutionary patterns in ring and stem regions.
• RNA evolutionary models incorporating secondary structure are scarce but crucial for accurate phylogenetics.
• Conserved secondary structures in mitochondrial RNAs of Orthoptera show significant coevolution and selection signals.

Purpose of the Study:

• To develop novel RNA evolutionary models that incorporate secondary structure information.
• To assess the performance of these models in phylogenetic analyses of Orthoptera mitochondrial RNAs.
• To improve the reliability of phylogenetic trees constructed from RNA sequences.

Main Methods:

• Reconstruction of conserved secondary structures for 22 mitochondrial tRNAs and two rRNAs in Orthoptera.
• Development of three RNA substitution models: mtRNA16 (16-state, pairing-specific), mtRNA7 (7-state), and mtRNA6 (6-state) using maximum likelihood estimation.
• Phylogenetic analyses comparing trees generated by new models against a universal model.

Main Results:

• The 16-state model (mtRNA16) showed the best fit to the Orthoptera dataset.
• Phylogenetic trees generated using the new models, especially mtRNA16, significantly outperformed those from a universal model.
• Stronger coevolution and selection signals were detected in paired RNA regions.

Conclusions:

• Incorporating RNA secondary structure into evolutionary models enhances phylogenetic accuracy.
• The developed 16-state model provides precise phylogenetic relationships for Orthoptera.
• These findings highlight the potential of structure-aware models for broader RNA-based phylogenetic studies.