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Wiley InterScience | |||||||||
  Systematic EntomologyVolume 32 Issue 1, Pages 40 - 59 Published Online: 15 Sep 2006 Journal compilation © 2010 The Royal Entomological Society
Abstract | References | Full Text: HTML, PDF (Size: 606K) | Supporting Information | Related Articles | Citation Tracking  A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision *Many taxonomic groups recognized previously within Diptera are now known to be paraphyletic evolutionary grades. Throughout this paper, these terms have been retained to allow ready comparison with older literature and are designated by being placed in quotation marks. †Three additional dipteran mitochondrial genomes have become available recently on GenBank – Dermatobia hominis (Oestridae), Haematobia irritans (Muscidae) and Aedes albopictus (Culicidae) – but have not yet been published. We have not included these sequences so as not to pre-empt other workers. Further, as close relatives of each have already been published, their inclusion is not critical to this study. ‡A secondary structure model for the mt rRNA genes of Apis will be published shortly (Gillespie et al., 2006), and its application to other insect groups will no doubt greatly improve the alignments of insect mt rRNA genes for phylogenetic studies. Copyright 2006 The Authors Journal compilation ABSTRACTAbstract. Mitochondrial genomes provide a promising new tool for understanding deep-level insect phylogenetics, but have yet to be evaluated for their ability to resolve intraordinal relationships. We tested the utility of mitochondrial genome data for the resolution of relationships within Diptera, the insect order for which the most data are available. We sequenced an additional three genomes, from a syrphid, nemestrinid and tabanid, representing three additional dipteran clades, 'aschiza', non-heteroneuran muscomorpha and 'basal brachyceran', respectively. We assessed the influence of optimality criteria, gene inclusion/exclusion, data recoding and partitioning strategies on topology and nodal support within Diptera. Our consensus phylogeny of Diptera was largely consistent with previous phylogenetic hypotheses of the order, except that we did not recover a monophyletic Muscomorpha (Nesmestrinidae grouped with Tabanidae) or Acalyptratae (Drosophilidae grouped with Calliphoridae). The results were very robust to optimality criteria, as parsimony, likelihood and Bayesian approaches yielded very similar topologies, although nodal support varied. The addition of ribosomal and transfer RNA genes to the protein coding genes traditionally used in mitochondrial genome phylogenies improved the resolution and support, contrary to previous suggestions that these genes would evolve too quickly or prove too difficult to align to provide phylogenetic signal at deep nodes. Strategies to recode data, aimed at reducing homoplasy, resulted in a decrease in tree resolution and branch support. Bayesian analyses were highly sensitive to partitioning strategy: biologically realistic partitions into codon groups produced the best results. The implications of this study for dipteran systematics and the effective approaches to using mitochondrial genome data are discussed. Mitochondrial genomes resolve intraordinal relationships within Diptera accurately over very wide time ranges (1–200 million years ago) and genetic distances, suggesting that this may be an excellent data source for deep-level studies within other, less studied, insect orders. Accepted 1 March 2006 | 
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