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.

Rooting the tree of life: the phylogenetic jury is still out

“…Importantly, contrary to the naive, yet commonly held view that open problems eventually get solved through the accumulation of more sequence data, incongruencies still persist in the genomic era (e.g. for streptophytes [11 -16]) or Bilateria [17][18][19][20][21][22]). Indeed, while phylogenomics helps in decreasing stochastic error (due to small sample sizes), it actually makes systematic error more apparent.…”

Phylogenetic analysis of the complete mitogenome sequence of the raspberry weevil, Aegorhinus superciliosus (Coleoptera: Curculionidae), supports monophyly of the tribe Aterpini

“…Characteristics of this molecular resource such as the lack of introns, unambiguous orthology, lack of recombination, broadly uniform rate of molecular evolution and phylogenetic signal at diverse taxonomic ranks have led many to consider it a reliable tool for investigating molecular divergence and deep evolutionary relationships (Bernt et al, 2013;Botero-Castro et al, 2013;Gaitán-Espitia et al, 2013;Papadopoulou et al, 2010;Zhang and Hewitt, 1996). For weevils, phylogenetic analyses using mitogenomes have supported the monophyly of most of the families of curculionids (with the exception of Curculionidae) and indicated a convergent evolution of specialized wood-boring behavior in the subfamilies Scolytinae, Platypodinae, and Cossoninae (Gillett et al, 2014;Haran et al, 2013).…”

Syllidae mitochondrial gene order is unusually variable for Annelida

“…The analysis of the sequences and the order in which these genes are organized provide valuable information that has been widely used to resolve phylogenetic relationships of different taxa at different levels (Vallès and Boore 2006). The mt genomes have been shown to be quite suitable for younger divergences, though less informative for deep phylogenies (Bernt et al 2013a). …”