Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Mitochondria, originating from endosymbiosis, have undergone significant gene loss.
• Numerous hypotheses exist for mitochondrial genome evolution, but lack data-driven validation.
• A consensus on selective pressures shaping mitochondrial DNA (mtDNA) is absent.

Purpose of the Study:

• To infer the ordering of evolutionary events in mitochondrial gene loss.
• To identify the selective pressures driving mtDNA gene retention and loss.
• To develop a data-driven method for analyzing evolutionary trajectories.

Main Methods:

• Developed HyperTraPS, a methodology combining stochastic modeling and Bayesian inference.
• Analyzed 2015 complete mitochondrial genomes to infer evolutionary trajectories.
• Investigated selective pressures including GC content and protein hydrophobicity.

Main Results:

• Identified preferential retention of electron transport chain core proteins in mitochondrial genomes across eukaryotes.
• Found that high GC content and high protein hydrophobicity are key factors in mtDNA gene retention.
• Demonstrated that a model incorporating these pressures predicts artificial gene transfer success.

Conclusions:

• The study provides a general method for inferring the order of evolutionary events.
• Distinct features shaping present-day mitochondrial genomes have been identified.
• Selective pressures like GC content and hydrophobicity are crucial for understanding mtDNA evolution.