Integrating Secondary Structure Information Enhances Phylogenetic Signal in Mitochondrial Protein Coding Genes

Abstract

Secondary structures have long been held to carry significant phylogenetic information, but the difficulty in collating primary sequence and structural information has frequently hindered its full application in phylogenetic studies. Here, we focus on the implementation of secondary structure information (inner, outer and transmembrane regions) to improve partitioning in datasets of mitochondrial Protein-Coding Genes for phylogenetic analysis. A new pipeline called TRAMPO was developed to partition alignment sites accordingly. The inclusion of this structural information in phylogenetic analyses was shown to produce an improvement in the phylogenetic signal of mitochondrial protein coding genes. We speculate that the observed, distinctive, compositional bias towards thymines in second codon sites of transmembrane regions, as well as selection, may be among the possible driving forces. This effect is especially relevant in lineages older than 50 Ma, where the signal of second codon positions becomes more relevant as first and third codon sites begin experiencing saturation.