Well-supported phylogenies using largest subsets of core-genes by discrete particle swarm optimization

TL;DR

This paper introduces a discrete particle swarm optimization method to identify the largest subset of core chloroplastic genes, enabling the construction of well-supported plant phylogenies from increasing genomic data.

Contribution

It presents a novel discrete and distributed PSO approach to efficiently select the largest gene subset for phylogenetic analysis, addressing computational challenges.

Findings

Successfully applied to Rosales core genes

Achieved well-supported phylogenetic trees

Demonstrated effectiveness of DPSO in gene subset selection

Abstract

The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a discrete and distributed Particle Swarm Optimization (DPSO) is proposed. It is finally applied to the core genes of Rosales order.