A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny

• Published in: Molecular phylogenetics and evolution Vol. 69; no. 2; pp. 352 - 364
• Main Authors: Bernt, Matthias, Bleidorn, Christoph, Braband, Anke, Dambach, Johannes, Donath, Alexander, Fritzsch, Guido, Golombek, Anja, Hadrys, Heike, Jühling, Frank, Meusemann, Karen, Middendorf, Martin, Misof, Bernhard, Perseke, Marleen, Podsiadlowski, Lars, von Reumont, Björn, Schierwater, Bernd, Schlegel, Martin, Schrödl, Michael, Simon, Sabrina, Stadler, Peter F., Stöger, Isabella, Struck, Torsten H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2013
• Subjects: Amino Acid Substitution; amino acids; Amino Acids - genetics; Animal phylogeny; Animals; Arthropoda; Bayes Theorem; Bilateria; data collection; expressed sequence tags; Gene Order; Gene Rearrangement; genes; genetics; Genome, Mitochondrial; Hexapoda; Likelihood Functions; Metazoa; Mitochondrial genomes; Models, Genetic; Mollusca; Nematoda; nucleotides; Nucleotides - genetics; Phylogeny; Platyhelminthes; Sequence Alignment; vertebrates; Animal phylogeny; Mitochondrial genomes
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2013.05.002

[Display omitted] •A huge amino acid alignment from mitochondrial genomes of Metazoa was considered.•Maximum likelihood and Bayesian analyses failed to give support for many high-ranking taxa.•Some reasons for misleading phylogenetic signals have been identified.•There is a correlation between gene order differences and branch lengths.•Amino acid substitution rates strongly differ between genes encoded on heavy and light strand. About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.