title: A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.
abstract: 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.
authors.affiliation: Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany. Electronic address: bernt@informatik.uni-leipzig.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bernt
authors.forename: Christoph
authors.initials: C
authors.lastname: Bleidorn
authors.forename: Anke
authors.initials: A
authors.lastname: Braband
authors.forename: Johannes
authors.initials: J
authors.lastname: Dambach
authors.forename: Alexander
authors.initials: A
authors.lastname: Donath
authors.forename: Guido
authors.initials: G
authors.lastname: Fritzsch
authors.forename: Anja
authors.initials: A
authors.lastname: Golombek
authors.forename: Heike
authors.initials: H
authors.lastname: Hadrys
authors.forename: Frank
authors.initials: F
authors.lastname: Jühling
authors.forename: Karen
authors.initials: K
authors.lastname: Meusemann
authors.forename: Martin
authors.initials: M
authors.lastname: Middendorf
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
authors.forename: Marleen
authors.initials: M
authors.lastname: Perseke
authors.forename: Lars
authors.initials: L
authors.lastname: Podsiadlowski
authors.forename: Björn
authors.initials: B
authors.lastname: von Reumont
authors.forename: Bernd
authors.initials: B
authors.lastname: Schierwater
authors.forename: Martin
authors.initials: M
authors.lastname: Schlegel
authors.forename: Michael
authors.initials: M
authors.lastname: Schrödl
authors.forename: Sabrina
authors.initials: S
authors.lastname: Simon
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Isabella
authors.initials: I
authors.lastname: Stöger
authors.forename: Torsten H
authors.initials: TH
authors.lastname: Struck
mesh_terms: D019943:Amino Acid Substitution; D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001499:Bayes Theorem; D023061:Gene Order; D015321:Gene Rearrangement; D054629:Genome, Mitochondrial; D016013:Likelihood Functions; D008957:Models, Genetic; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D000596:Amino Acids; D009711:Nucleotides
keywords: Animal phylogeny; Mitochondrial genomes