Infer Species Phylogenies Using Self-Organizing Maps

Abstract

With rapid advances in genomics, phylogenetics has turned to phylogenomics due to the availability of large amounts of sequence and genome data. However, incongruence between species trees and gene trees remains a challenge in molecular phylogenetics for its biological and algorithmic complexities. A state-of-the-art gene concatenation approach was proposed to resolve this problem by inferring the species phylogeny using a random combination of widely distributed orthologous genes screened from genomes. However, such an approach may not be a robust solution to this problem because it ignores the fact that some genes are more informative than others in species inference. This paper presents a self-organizing map (SOM) based phylogeny inference method to overcome its weakness. The author’s proposed algorithm not only demonstrates its superiority to the original gene concatenation method by using same datasets, but also shows its advantages in generalization. This paper illustrates that data missing may not play a negative role in phylogeny inferring. This study presents a method to cluster multispecies genes, estimate multispecies gene entropy and visualize the species patterns through the self-organizing map mining.