Journal ArticleDOI
A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision
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TLDR
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.Abstract:
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.read more
Citations
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Journal ArticleDOI
Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny
TL;DR: Insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes, and greater integration of nuclear and mt genomic studies is necessary to further the understanding of insect genomic evolution.
Journal ArticleDOI
The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths.
TL;DR: Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, n ad4 and nad5.
Journal ArticleDOI
The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae)
TL;DR: The mitochondrial genome of O. lunifer is the first representative of superfamily Noctuoidea that account for about 40% of all described Lepidoptera and shares many features with other known lepidopteran genomes, differs however for its low A+T content and marked C-skew.
Journal ArticleDOI
A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles
TL;DR: Six new complete mitochondrial genome descriptions are presented, including a representative of each suborder, and the evolution of mtgenomes from a comparative framework using all available coleopteran mt Genomes is analyzed.
Journal ArticleDOI
How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research
TL;DR: The aims of this review are to describe in detail the various sequencing methods used on insect mt genomes, and to improve the re-annotation of previously sequenced mt genomes used in systematic or comparative research.
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