A Memetic Algorithm Based on an NSGA-II Scheme for Phylogenetic Tree Inference

Abstract

Phylogenetic inference allows building a hypothesis about the evolutionary relationships between a group of species, which is usually represented as a tree. The phylogenetic inference problem can be seen as an optimization problem, searching for the most qualified tree among all the possible topologies according to a selected criterion. These criteria can be based on different principles. Due to the combinatorial number of possible topologies, diverse heuristics and meta-heuristics have been proposed to find approximated solutions according to one criterion. However, these methods may result in several phylogeny trees which could be in conflict with one another. In order to deal with this problem, models based on multiobjective optimization with different configurations have been used. In this paper, we propose an ad-hoc multiobjective memetic algorithm (MO-MA) to infer phylogeny using two objectives: 1) maximum parsimony and 2) likelihood. Several population operators and local search strategies are proposed and evaluated in order to measure their contribution to the algorithm. Additionally, we perform a comparison among different configurations and tree rearrangement strategies. The results show that the proposed MO-MA is able to identify a Pareto set of solutions that include new trees which were nondominated by solutions from the current state of the art single-objective optimization tools. Furthermore, the MO-MA improves the results presented in the literature for multiobjective approaches in all of the studied data sets. These results make our proposal a good alternative for phylogenetic inference.