Reconciling multiple genes trees via segmental duplications and losses

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macroevolutionary events, where segmental duplication events and losses are associated with cost δ and λ, respectively. We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 0 and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ/ λ and the number d of segmental duplications, of time complexity O(⌈δ/λ ⌉d · n δ/λ ). Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.