Study of mitogenomes provides implications for the phylogenetics and evolution of the infraorder Muscomorpha in Diptera

The Muscomorpha is one of the most species-rich brachyceran groups in Diptera, with many species serving as important disease vectors; however, its high-level phylogenetic relationships have long been controversial and unsolved. This study comparatively analyzed the characteristics of mitogenomes of 131 species that represent 18 superfamilies in Muscomorpha, in which mitogenomes of 16 species have been newly sequenced and annotated, demonstrating that their gene composition, order, AT bias, length variation, and codon usage are consistent with documented dipteran mitogenomes. The phylogenetic topologies demonstrated that the robustness of Muscomorpha and major clades within Muscomorpha are monophyletic: Cyclorrhapha, Schizophora, and Calyptratae. A clade of Empidoidea were recovered as the sister-group to Cyclorrhapha. Within Cyclorrhapha, Platypezoidea and Syrphoidea were sequentially placed as basal groups of the Cyclorrhapha. The remaining cyclorrhaph superfamilies gathered as two ma..., Our phylogenetic analysis included published sequences from 131 muscomorpha, representing 53 families from 18 superfamilies. Multiple sequence alignment precedes matrix generation, we employed the codon-aware program MACSE v2.06 for 13 PCGs and MAFFT version 7.0 with the G-INS-i strategy for 2 rRNAs, thereafter, the 13 PCGs were subjected to trimming using Gblocks under the invertebrate mitochondrial genetic code, while the two rRNA sequences underwent trimming using trimAl v1.2rev57, subsequently, all individual alignments were concatenated into a supermatrix using the Phylosuite\_v1.2.3 platform with default settings. We constructed 4 datasets for phylogenetic analyses: (1) PCGsrRNA, the combination of 13 protein-coding genes plus two rRNA genes, resulting in a total sequence length of 12,641 nucleotides; (2) PCGs12rRNA, to mitigate substitution saturation, the third codon positions of 13 PCGs were excluded; (3) PCGs, all codon positions; and (4) AA, amino acids translated by PCGs. Be..., , # Study of mitogenomes provides implications for the phylogenetics and evolution of the infraorder Muscomorpha in Diptera

[https://doi.org/10.5061/dryad.wwpzgmsvm](https://doi.org/10.5061/dryad.wwpzgmsvm)

## Description of the data and file structure

**FILE LIST**

**File S1.txt** BioGeoBEARS (output generated by BioGeoBEARS, which was used to perform biogeographical analysis on phylogenetic trees) result file of Name

**Fig.s1.tiff** Predicted secondary structures of 22 tRNAs in the mitogenomes of *Loxoneura* sp.. The tRNAs are labelled with their corresponding amino acids.

**Fig.s2.tiff** Predicted secondary structures of 22 tRNAs in the mitogenomes of *Systropus daiyunshanus*. The 22 tRNAs are labelled with their corresponding amino acids.

**Fig.s3.pdf** Phylogenetic relationships of 131 species inferred from PCGsRNA dataset. Numbers beside the nodes are the ultrafast bootstrap value (BS) / the approximate likelihood ratio test support (SH-aLRT) for partitioned maximum likelihoo...