Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 69, Issue 2, Pages 352-364Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2013.05.002
Keywords
Mitochondrial genomes; Animal phylogeny
Funding
- German Science foundation (DFG) [SPP 1174: BL 787/2-1, 2, BA 1520/10-1, 2, SCHO 442/8-1, 2, PO 765/4-3, STA 850/3-2, STA 850/2, STR-683/5-2, 6-1, SCHL 229/14-1, HA 1947/5, SCHR 667/9-1, WA530/34, MI 649/7, Schi-227/20, Schi-227/26-1]
- DFG [RE-3454/1-1]
- German Academic Exchange Service (DAAD)
- French-German PROCOPE Program [DAAD D/0628236, EGIDE PHC 1477011]
- French-German University (DFH-UFA) [CT-08-10]
- German Academic Exchange Service [DAAD D/10/43622]
- College Doctoral Europeen (CDE), Universite de Strasbourg
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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. (C) 2013 Elsevier Inc. All rights reserved.
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