Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Recent advances in molecular phylogenetics are continuously changing our perception of decapod phylogeny. Although the two suborders Dendrobranchiata and Pleocyemata within the Decapoda are widely accepted, this taxonomic view is now challenged when using mitochondrial protein-coding genes to investigate the decapod phylogeny, especially for the basal pleocyematan groups. Here, we enhanced taxonomic coverage by sequencing the genomes of two basal decapod taxa Alpheus distinguendus and Panulirus ornatus, representing two infraorders, Caridea and Achelata, respectively. Based on these two and other available mitochondrial genomes, we evaluated the usefulness of protein-coding genes in resolving deep phylogenetic relationships of the Decapoda using maximum likelihood and Bayesian analyses. The mt genomic results revealed a novel gene order because of the reverse transposition of trnE (transfer, trn for Glutamate) and a pseudogene-like trnS (AGN) [trn for Serine (S-1, AGN)] in the mitochondrial genome of A. distinguendus, and a duplicate of 89 bp sequences in the putative noncoding region of P. ornatus. Our phylogenetic inferences suggest monophyly of the Decapoda and its two suborders, and that several lineages within the Reptantia are consistently recovered with high nodal supports. Our findings suggest that the best mitochondrial genome phylogeny can be found on the premise that systematic errors should be minimized as much as possible. (C) 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162, 471-481. doi: 10.1111/j.1096-3642.2010.00686.x