Exact reconciliation of undated trees

TL;DR

This paper introduces an ILP-based method for exactly computing the most parsimonious, time-consistent reconciliation of gene and species trees without dating information, demonstrating improved efficiency over brute force methods.

Contribution

It presents a novel ILP formulation for the NP-hard problem of reconciliation without dating data, enabling exact solutions for small trees and advancing the field.

Findings

ILP approach is significantly faster than brute force search.

The method provides exact, parsimonious reconciliations without species dating.

Software ILPEACE is freely available for use.

Abstract

Reconciliation methods aim at recovering macro evolutionary events and at localizing them in the species history, by observing discrepancies between gene family trees and species trees. In this article we introduce an Integer Linear Programming (ILP) approach for the NP-hard problem of computing a most parsimonious time-consistent reconciliation of a gene tree with a species tree when dating information on speciations is not available. The ILP formulation, which builds upon the DTL model, returns a most parsimonious reconciliation ranging over all possible datings of the nodes of the species tree. By studying its performance on plausible simulated data we conclude that the ILP approach is significantly faster than a brute force search through the space of all possible species tree datings. Although the ILP formulation is currently limited to small trees, we believe that it is an important proof-of-concept which opens the door to the possibility of developing an exact, parsimony based approach to dating species trees. The software (ILPEACE) is freely available for download.