Testing for positive selection in multi-copy gene families using a reconciliation approach

Abstract

Multi-copy gene families evolve through dynamic processes of duplication, loss, and sequence divergence, often exhibiting complex paralogy and orthology relationships that complicate the detection of adaptive evolution. Traditional dN/dS-based positive selection analyses are typically limited to single-copy genes, overlooking most of the adaptive signal in multi-copy families. We present a novel pipeline that integrates existing tools to map branch-specific positive selection events from gene trees onto species phylogenies. Our approach incorporates a normalization procedure that corrects for biases caused by variable branch lengths, reducing false enrichment signals on longer branches. Applied to the odorant receptor repertoires of ants, the framework successfully identified branches of the species tree enriched for positive selection, revealing clade-specific adaptive patterns obscured by conventional methods. This reconciliation-based strategy enables detection of adaptive hotspots in complex gene families, providing a versatile tool for linking molecular evolution to species-level diversification.