Collapsed Site Coalescent Facilitates Detection of Adaptive Divergences Between Segmental Duplicates

Collapsed Site Coalescent (CSC) enables ARG inference across segmental duplicates by collapsing paralogous sites into pseudo-sites, supporting detection of adaptive “IGC havens” when IGC and selection are strong.

• Why it matters: Segmental duplications are common and evolutionary important, but population genetic inference has been blocked by high identity and by interlocus gene conversion that breaks standard coalescent and ARG assumptions.
• What they did: The authors model each paralogous site pair as a collapsed pseudo-site with its own genealogy, then develop a haplotype-copying inference method to estimate IGC parameters from population samples.
• The result: In simulations, estimated IGC parameters closely track true IGC rates, and under strong IGC and selection the method detects IGC havens, enabling population-genetic study of gene duplicate evolution.