What can mitochondrial genomics do for bivalve phylogeny?

Molecular phylogenetics of Bivalvia mainly inferred from nuclear ribosomal and COI sequences, though yielding some valuable results, has not resolved important questions like, e.g., the relationships of the major taxa. Complete mitochondrial genome sequences are valuable sources for phylogenetic signal providing both nucleotide and genomic data, i.e. gene content and gene order. Contrasting vertebrates and arthropods, molluscan mitochondrial gene order varies considerably, especially within the Bivalvia. We present phylogenetic analyses of complete mitochondrial genomes of 18 bivalve and 16 other molluscan species. The gene order in Bivalvia is highly heterogeneous. Even closely related species show several rearrangements, and none except for Nucula, the single protobranch representative, resembles the putative plesiomorphic condition in molluscs. With the Nucula gene order differing by only two rearrangements from that of the polyplacophoran Katharina, the high rearrangement rates must have arisen within Bivalvia. Consequently, phylogenetic inference using gene order data with the present taxon sample and analysis methods yield unreliable results. Maximum likelihood and Bayesian inference of nucleotide and amino acid data yield robust Autobranchia, Pteriomorpha, and Heterodonta. Bivalve monophyly is not supported as Nucula clusters with Haliotis and Katharina at the base of the tree. This notable similarity of gene order and sequence trees suggests a rate correlation of nucleotide substitutions and gene rearrangements. Given these initial results, what can mitochondrial genomics do for bivalve phylogeny? The trees based on the combined sequences of the protein coding genes yield much better results than studies using COI alone and match those based on 18S rRNA and morphology data. Especially within the Heterodonta the resolution is likely to be superior to all other available data sets. Little hope remains, however, that gene order data will resolve the sistergroup of bivalves. Improving both the taxon sampling and analysis methods will show the taxonomic level - or time window - gene order data contain robust phylogenetic signal. With a growing number of complete genomes, in particular that of closely related species, additional genomic characters, such as gene duplication and loss, rearrangement hotspots, and occurrence of doubly uniparental inheritance, are likely to be assessed.