Reconciling multiple genes trees via segmental duplications and losses

Riccardo Dondi,Celine Scornavacca,Manuel Lafond

doi:10.1186/s13015-019-0139-6

Riccardo Dondi, Celine Scornavacca + Show 1 more

Open Access

https://doi.org/10.1186/s13015-019-0139-6

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Abstract

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 macro-evolutionary events, where segmental duplication events and losses are associated with cost delta and lambda , respectively. We show that the problem is polynomial-time solvable when delta le lambda (via LCA-mapping), while if delta > lambda the problem is NP-hard, even when lambda = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are delta /lambda and the number d of segmental duplications, of time complexity Oleft(lceil frac{delta }{lambda } rceil ^{d} cdot n cdot frac{delta }{lambda }right). 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 raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.

Highlights

It is nowadays well established that the evolution of a gene family can differ from that of the species containing these genes
We show that if δ ≤, an optimal reconciliation can be obtained by reconciling each gene tree separately under the usual LCA-mapping, even in the context of segmental duplications
We have presented an approach for the reconciliation of a set of gene trees and a species tree, based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost δ and, respectively

Summary

Introduction

It is nowadays well established that the evolution of a gene family can differ from that of the species containing these genes. This can be due to quite a number of different reasons, including gene duplication, gene loss, horizontal gene transfer or incomplete lineage sorting, to only name a few [22] While this discongruity between the gene phylogenies (the gene trees) and the species phylogeny (the species tree) complicates the process of reconstructing the latter from the former , every cloud has a silver lining: “plunging” gene trees into the species tree and analyzing the differences between these topologies, one can infer the macro-evolutionary events that shaped gene evolution. A more pertinent approach would be to reconcile the set of gene trees at once and consider segmental macro-evolutionary events, i.e. events that concern a chromosome segment instead of a single gene

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