Comparative Mitogenomics of Flesh Flies: Implications for Phylogeny

Abstract

Flesh flies (Diptera: Sarcophagidae) represent a rapid radiation belonging to the Calyptratae. With more than 3000 known species, they are extraordinarily diverse in terms of their breeding habits and are therefore of particular importance in human and veterinary medicine, forensics, and ecology. To better comprehend the phylogenetic relationships and evolutionary characteristics of the Sarcophagidae, we sequenced the complete mitochondrial genomes of five species of flesh flies and performed mitogenomic comparisons amongst the three subfamilies. The mitochondrial genomes match the hypothetical condition of the insect ancestor in terms of gene content and gene arrangement. The evolutionary rates of the subfamilies of Sarcophagidae differ significantly, with Miltogramminae exhibiting a higher rate than the other two subfamilies. The monophyly of the Sarcophagidae and each subfamily is strongly supported by phylogenetic analysis, with the subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). This study suggests that phylogenetic analysis based on mitochondrial genomes may not be appropriate for rapidly evolving groups such as Miltogramminae and that the third-codon positions could play a considerable role in reconstructing the phylogeny of Sarcophagidae. The protein-coding genes ND2 and ND6 have the potential to be employed as DNA markers for species identification and delimitation in flesh flies.

Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications

“…The circular map of the P. casei mt genome is shown in Figure 1 a and is generally consistent with the mt genomes of eight other Diptera, such as P. megastigmata (15,410 bp) ( Figure 1 b), Bactrocera dorsalis (15,915 bp) ( Figure 1 c), Liriomyza bryoniae (16,183 bp) ( Figure 1 e), and Anopheles oryzalimnetes (15,422bp) ( Figure 1 f). The difference in mt genome length between these five species is mainly due to the differences in the size of the control region (from a minimum of 388bp to a maximum of 1354 bp), as previously observed between Diptera species [ 42 ]. In Diptera, the mt genomes of some species, such as Zeugodacus caudatus (15,311 bp) ( Figure 1 d), Homoneura interstincta (16,351 bp) ( Figure 1 g), and Tropidia scita (15,739 bp) ( Figure 1 f) are arranged differently than most species.…”

“…The RSCU of P. casei and P. megastigmata show a similar bias, with only minor differences in the use of a few codons, such as CGC, CUC, and ACG. As with other Diptera, the mt genome of Piophilidae is more biased toward the use of amino acids encoded by codons with A or T in the third position [ 42 ]. The amino acid use frequencies of PCGs in the mt genomes of P. casei and P. megastigmata were counted and showed that the number of 20 amino acids varied, but both had the highest frequency of leucine (Leu) usage, followed by isoleucine (Ile), serine (Ser), and glycine (Gly) ( Figure 4 c,g).…”

“…Judging by the evolutionary branch lengths, the P. megastigmata has longer branch lengths, reflecting its greater degree of genetic variation and a higher degree of evolution. The divergence between P. casei and P. megastigmata was inferred at 7.28 MYA (95% HPD: 3.64–18.20 MYA) around the late Cenozoic Tertiary during the Miocene [ 42 ]. These results may provide a valuable basis for the study of the evolution of the P. casei gene family, population transmission, and biodefense potential [ 57 , 58 , 59 ].…”