A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast

Area of Science:

• Evolutionary biology
• Genomics
• Population genetics

Background:

• Interlocus gene conversion (IGC) is a mechanism that homogenizes repetitive DNA sequences.
• The evolutionary significance of IGC in repeat-rich genomes remains largely uncharacterized.
• Novel statistical methodologies are required to accurately assess the impact of IGC.

Purpose of the Study:

• To develop and apply a composite likelihood strategy for integrating IGC into existing probabilistic models of sequence evolution.
• To quantify the proportion of nucleotide substitutions attributable to IGC versus point mutations in yeast ribosomal protein-coding genes.
• To validate the robustness of the proposed IGC detection method against potential model misspecification artifacts.

Main Methods:

• Development of a composite likelihood framework to model sequence evolution incorporating IGC.
• Estimation of IGC contribution to nucleotide substitutions across 14 yeast ribosomal protein gene families.
• Application of a model misspecification artifact assessment procedure.
• Simulation studies to evaluate the performance of the IGC statistical approach.

Main Results:

• Estimated IGC contribution to nucleotide substitutions ranged from 20% to 38% in the studied yeast gene families.
• Artifact assessment procedures confirmed the validity of the IGC estimates.
• Simulations demonstrated the utility and reliability of the developed IGC detection method.

Conclusions:

• IGC is a substantial evolutionary force in yeast ribosomal protein gene families, contributing significantly to sequence homogenization.
• The proposed statistical framework provides a robust tool for investigating IGC's role in multigene family evolution.
• IGC should be considered in evolutionary studies of multigene families, challenging conventional approaches.