Suitability of path distances for horizontal gene transfer within PLR

Investigate whether species-tree path distances are appropriate for comparing nodes undergoing horizontal gene transfer in reconciled gene trees within the PLR framework, and ascertain necessary adaptations if path distances are inadequate.

Background

PLR incorporates a path-distance component on the species tree and an event-labeling component for duplications and speciations. In settings with horizontal gene transfer (HGT), reconciliation models use different time-consistency notions and include transfer events, raising concerns about whether species-tree path distances appropriately quantify discrepancies for transferred genes.

Determining the suitability of path distances for HGT comparisons—and, if needed, proposing modifications—would broaden PLR’s applicability to reconciliation models that include transfer events.