Table 1.
Taxon sampling and availability.
Fig 1.
Mitochondrial maps of two muscoid flies.
Circular maps were drawn with GCView [53] with the unsequenced portion of each genome indicated. Gene arrangement is shown on the outermost circle with arrows indicating the orientation of gene transcription. tRNAs are are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). GC content was plotted (in black) using a sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted (positive skew in green, negative skew in purple) as the deviation from the average GC-skew of the entire sequence. The innermost cycle indicates size.
Table 2.
Mitochondrial nucleotide composition in six muscoid flies.
Fig 2.
Predicted secondary structure of the lrRNA gene in muscoid flies.
Gene sequence from Delia mt genome. Inferred Watson–Crick bonds are illustrated bylines, GU bonds by dots. Roman numerals denote the conserved domain structure. The darker circles indicate the conserved sites among all six muscoid species while the lighter circles indicate the unconserved sites.
Fig 3.
Predicted secondary structure of the srRNA gene in muscoid flies.
Gene sequence from Delia mt genome. Inferred Watson–Crick bonds are illustrated bylines, GU bonds by dots. Roman numerals denote the conserved domain structure. The darker circles indicate the conserved sites among all six muscoid species while the lighter circles indicate the unconserved sites.
Fig 4.
Phylogenetic tree based on mt genome data.
Cladogram of relationships resulting from Bayesian analyses with datasets PCG123 & PCG12RNA and ML analyses with datasets PCG12, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities≥ 0.90 or ML bootstrap≥ 70, white indicates posterior probabilities< 0.90 or ML bootstrap< 70, ‘ns’ = not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. The Bayesian tree of datasets PCG123 and PCG12RNA as well as ML tree of datasets PCG12 and PCG123. B. Part of the Bayesian tree of dataset PCG123RNA as well as ML tree of datasets PCG123RNA and PCG12RNA. C. Part of the Bayesian tree of dataset PCG12.
Fig 5.
Evolutionary timescale for Calyptratae inferred from a mitochondrial PCG123 dataset.
Numbers at nodes indicate mean estimated divergence times (in mya) and node bars indicate 95% credibility intervals. In the geological time scale: Pala indicates Palaeocene; Eoce indicates Eocene; Oligo indicate Oligocene; Mioc indicated Miocene.