Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes

Abstract

The evolutionary history of living species is usually inferred through the phylogenetic analysis of molecular and morphological information using various mathematical models. New challenges in phylogenetic analysis are centered mostly on the search for accurate and efficient methods to handle the huge amounts of sequence data generated from newer genome sequencing. The next major challenge is the determination of relationships between the evolution of structural elements and their functional implementation, which is largely ignored in previous analyses. Here, we described the discovery of structural elements in metazoan mitochondrial genomes, termed key K-strings, that can serve as a basis for phylogenetic tree construction. 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 our 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 novelty and potential importance of key K-strings lead us to believe that they are essential evolutionary elements. As such, they may play important roles in the process of species evolution and their physical existence. Further studies could lead to discoveries regarding the relationship between evolution and processes of speciation.

Figure 1. Critical points of the L-curve.

The critical point represents a 90% reduction in the maximum variation value, and points above the critical point correspond to key K-strings. The curves were generated based on randomly selected datasets with different numbers of species, (20, 40, 80, 100, or 200). Points with serial numbers greater than 35,000 do not appear under zoom.

Figure 2. Phylogenetic trees constructed from our key K-strings and complete K-strings using the CVTree method.

Both trees contain 87 species that were randomly selected from each phylum (Table S2). (a) The phylogenetic trees constructed from our 23,223 key K-strings; (b) The phylogenetic trees constructed from the complete set of 20⁵ K-strings using the CVTree method. Bootstrap support values above 40% from 100 replicates were show in the figure.

Figure 3. Single amino acid compositions of the key K-strings in each phylum.

The compositional patterns of 8 groups of phylum-specific key K-strings are illustrated using different colors.

Figure 4. The composition patterns of phylum-specific key K-strings in different groups.

The 8 phyla are arranged according to the traditional view of phylogeny: Porifera, Coelenterata, Platyhelminthes, Nematoda, Annelida, Crustacea, Echinodermata and Vertebrata. Single amino acids, dimers and triplets containing the amino acids A, P or T displayed one distribution pattern, whereas those containing C exhibited a different distribution pattern.

Figure 5. Distribution of conserved regions and regions in which key K-strings accumulated for complete protein sequences.

Thirteen protein sequences are aligned in order and linked head-to-tail for the 10 chosen vertebrates. The curve models the distribution of sequence conservativity, and gray regions represent regions in which key K-strings accumulate.