A Probabilistic Algorithm for Gene–Species Reconciliation with Segmental Duplications

Reconciliations are a mathematical tool to compare the phylogenetic trees of genes to the species that contain them, accounting for events such as gene duplication and loss. Traditional reconciliation methods have predominantly relied on parsimony to infer gene-only evolutionary events and usually make the hypothesis that genes evolve independently. Recently, more advanced models have been developed that account for complex gene interactions stemming from phenomena such as segmental duplications, where multiple genes undergo simultaneous duplication. In this article, we study the NP-hard problem of reconciling gene trees to a species tree with segmental duplications, without the aid of synteny information. We address this problem by proposing a novel probabilistic approach, imposing a Boltzmann distribution over the space of reconciliations. This allows for a Gibbs sampling-like Markov chain Monte Carlo algorithm that uses simulated annealing to effectively find or approximate the most parsimonious reconciliation, as demonstrated through rigorous simulations and re-analysis of empirical datasets. Our findings present a promising new framework for addressing NP-hard reconciliation challenges in phylogenetics, enhancing our understanding of gene evolution and its relationship with species evolution.