Evolutionary histories of complex genomic loci underlying gene-level variation

Establish evolutionary histories for complex genomic loci that exhibit gene-level structural variation, in order to define biologically grounded target graphs for pangene-like representations.

Background

A biologically ‘correct’ pangene graph would ideally reflect the true evolutionary history of loci. However, complex processes such as convergent/divergent evolution, non-homologous recombination, and non-allelic gene conversion make such histories difficult to reconstruct.

The authors note that, beyond a few well-studied cases, these evolutionary histories remain unknown, limiting our ability to adjudicate among alternative graph representations or annotations.