Gene tree species tree reconciliation with gene conversion

TL;DR

This paper introduces a new mathematical framework and randomized algorithm for gene tree/species tree reconciliation that includes gene conversion, a frequent biological event, improving the accuracy of evolutionary history modeling.

Contribution

It presents the first method to incorporate gene conversion into reconciliation, with a polynomial-time randomized algorithm for optimal solutions.

Findings

Algorithm efficiently finds reconciliations with gene conversion.

Reconciliation space extends traditional models to include gene conversion.

Method demonstrates biological relevance by modeling gene conversion events.

Abstract

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene tree nodes and species tree nodes or branches. Gene conversion is a very frequent biological event, which results in the replacement of a gene by a copy of another from the same species and in the same gene tree. Including this event in reconciliations has never been attempted because this changes as well the solutions as the methods to construct reconciliations. Standard algorithms based on dynamic programming become ineffective. We propose here a novel mathematical framework including gene conversion as an evolutionary event in gene tree/species tree reconciliation. We describe a randomized algorithm giving in polynomial running time a reconciliation minimizing the number of duplications, losses and conversions. We show that the space of reconciliations includes an analog of the Last Common Ancestor reconciliation, but is not limited to it. Our algorithm outputs any optimal reconciliation with non null probability. We argue that this study opens a wide research avenue on including gene conversion in reconciliation, which can be important for biology.