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Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene

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Summary

We developed PoMoBalance, a new model to detect balancing selection, a key evolutionary process maintaining genetic diversity. This tool analyzes genomic data to reveal selection pressures over long evolutionary timescales.

Keywords:
Bayesian inference with MCMCGC-biased gene conversionbalancing selectionpolymorphism-aware phylogenetic modelssite frequency spectrumspecies trees

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Area of Science:

  • Evolutionary Biology
  • Population Genetics
  • Phylogenetics

Background:

  • Balancing selection is vital for maintaining genetic variation but notoriously difficult to detect.
  • Existing models often struggle to resolve balancing selection on timescales relevant to species divergence.

Purpose of the Study:

  • To introduce PoMoBalance, a novel model extending the Polymorphism-aware phylogenetic Models (PoMos) framework.
  • To disentangle complex evolutionary forces, including balancing selection, mutation, drift, and GC-biased gene conversion.
  • To quantify balancing selection pressures over ultra-long evolutionary timescales using multi-individual genomic data.

Main Methods:

  • Developed the PoMoBalance model, incorporating ancestral polymorphisms and frequency-dependent selection parameters.
  • Implemented PoMoBalance within the RevBayes Bayesian software for phylogenetic inference and selection quantification.
  • Validated the model using simulated data (SLiM, custom Moran model) and analyzed real Drosophila population genomic data.

Main Results:

  • PoMoBalance successfully quantifies balancing selection and other evolutionary pressures.
  • The model accounts for ancestral polymorphisms, crucial for accurate inference of selection.
  • Analysis of Drosophila erecta revealed frequency-dependent balancing selection in regions associated with sex-limited color dimorphism.

Conclusions:

  • PoMoBalance provides a powerful new tool for studying balancing selection over long evolutionary periods.
  • The model's ability to infer frequency-dependent selection offers deeper insights into evolutionary dynamics.
  • Findings highlight the role of balancing selection in shaping genetic diversity, exemplified by Drosophila dimorphism.