Structural Elements in Metazoan Mitochondrial Genomes Play Important Roles in Reconstructing the Metazoan Phylogenetic Tree and Determining the Evolutionary Trajectory of Species

The evolutionary history of living species can be inferred via the phylogenetic analysis of molecular and morphological information using various mathematical models. Recent years, the CVTree method has been successfully implemented for plant phylogenetic analysis based on whole chloroplast proteomes and for prokaryote phylogenetic analysis based on whole prokaryote proteomes. CVTree infers phylogenetic relationships among organisms based on the oligopeptide contents (namely K-strings) of protein sequences or from the oligonucleotide contents of DNA sequences. As dimension reduction improves prediction performance, the use of key K-strings could lead to the construction of more rational phylogenetic trees.

Therefore, researchers performed dimensional reduction on a collection of high-dimensional data (taking K=5, yielding 20⁵ protein strings) and obtained a cluster of key K-strings from a dataset of the whole mt genome sequences of all metazoans available. Using these key K-strings, researchers reconstructed the metazoan phylogenetic tree, which they then compared with the tree constructed using the CVTree method and with trees constructed using many other methods. Researchers also implemented further structural analyses of these K-strings to determine the distribution pattern of amino acid compositions. Researchers then analyzed the genetic characters of conservativity, hydrophobicity, and the special motif structure of these key K-strings. Finally, researchers attempted to deduce the potential biological implication of these key K-strings.

According to the results, although comprising only a small fraction (0.73%) of all K-strings, these key K-strings are pivotal to the tree construction because they allow for a significant reduction in the computational time required to construct phylogenetic trees, and more importantly, they make significant improvement to the results of phylogenetic inference. The trees constructed from the key K-strings were consistent overall to the current view of metazoan phylogeny and exhibited a more rational topology than the trees constructed by using other conventional methods. Surprisingly, the key K-strings tended to accumulate in the conserved regions of the original sequences, which were most likely due to strong selection pressure.

Furthermore, the special structural features of the key K-strings should have some potential applications in the study of the structures and functions relationship of proteins and in the determination of evolutionary trajectory of species. The key K-strings may play important roles in the process of species evolution and their physical existence. The study was published in PLOS ONE on 20 January 2014.