DOI: 10.5061/dryad.wwpzgmsvm
title: Data from: Study of mitogenomes provides implications for the phylogenetics and evolution of the infraorder Muscomorpha in Diptera

description: 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
 main clades. Ephydroidea were, in most cases, placed as the sister-group
 to Calyptratae. Within Calyptratae, Hippoboscoidea were sister to an
 assemblage of lineages composed of a Oestroid grade and Muscoidea. The
 Muscomorpha was proposed to originate in the early Jurassic, and the main
 clade diversified near the Cretaceous–Paleogeneextinction event, estimated
 using the MCMCtree and six fossil calibration points. The ancestral area
 of origin and geographic range of Muscomor- pha was deduced to be the
 Palaearctic region with 56.9% probability using the RASP software based on
 a dated tree.
description: 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. Before phylogenetic analyses, the substitution
 saturation of each codon position of the 13 mitochondrial PCGs was
 assessed using the index (Iss) with DAMBE v.6. the completeness of
 multiple sequence alignments was quantified by AliStat, and the
 heterogeneity of sequence was visualized using AliGROOVE v.1.08. To
 determine the optimal partitioning schemes and corresponding nucleotide
 substitution models for each dataset, we employed ModelFinder to select
 the best-fit substitution model for each partition in maximum likelihood
 (ML) analysis. To avoid the influence of heterotachous evolutionary
 sequences on phylogenetic inference, we used the single topology (GHOST)
 model in IQ-TREE, the Bayesian information criterion (BIC) and the
 'greedy' algorithm were used, with branch lengths estimated as
 'unlinked', to search for the best-fit scheme in the partition
 model. To mitigate the effects of long-branch attraction (LBA) artefacts,
 the posterior mean site frequency (PMSF) model was manipulated in IQ-TREE
 too. In the concatenated analyses, support values were assessed using the
 ultrafast bootstrap (UFBoot), the approximate likelihood ratio test
 (SH-aLRT), and a Bayes test.
description: # 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 likelihood analysis. **Fig.s4.pdf** Phylogenetic relationships of 131 species inferred from PCGsRNA dataset. Numbers beside the nodes are the ultrafast bootstrap value (BS)/a bayes test support (PP) for GTR+FO*H4 maximum likelihood analysis. **Fig.s5.pdf** Phylogenetic relationships of 131 species inferred from PCGs dataset. Numbers beside the nodes are the ultrafast bootstrap value (BS)/the approximate likelihood ratio test support (SH-aLRT) for partitioned maximum likelihood analysis. **Fig.s6.pdf** Phylogenetic relationships of 131 species inferred from PCGs dataset. Numbers beside the nodes are the ultrafast bootstrap value (BS)/a bayes test support (PP) for GTR+FO*H4 maximum likelihood analysis. **Fig.s7.pdf** Phylogenetic relationships of 131 species inferred from PCGs12RNA dataset. Numbers beside the nodes are the ultrafast bootstrap value (BS)/the approximate likelihood ratio test support (SH aLRT) for partitioned maximum likelihood analysis. **Table S1.doc** Collect information on 16 newly sequenced species in Muscomorpha.  **Table S2.xlsx** A total of 131 species of mitogenomes were selected for comparative and phylogenetic analyses in the infraorder Muscomorpha, with 16 species in 11 families being newly sequenced in this study.  **Table S3.xlsx** Calibration point, fossil information, calibrating scheme and references used in the analyses for estimating divergence dates.  **Table S4.xlsx** The distribution information for ancestral state estimation in the present study. A (Afrotropical region), B (Palaearctic region), C (Oriental region), D (Australasian), E (Nearctic region) and F (Neotropical region) respectively.  **Table S5.xlsx** The results of model test for inferring biogeographic history.  **Table S6.xlsx** The long branch scores of the phylogenetic tree are based on the PCGsRNA dataset.  **Table S7.xlsx** Summary of support values that support specific taxonomic groups in 6 phylogenetic analyses. **matirx.zip** all matrix used in this paper (this folder consists of 4 NEX files namely PCGsRNA, AA, PCGs, and PCGs12RNA) **Abbreviations** Mitogenome: mitochondrial genome; PCGs: protein-coding genes; rRNAs: ribosomal RNA genes; tRNAs: transfer RNA genes; CR: control region; PCGsRNA: dataset of 13 protein-coding genes plus two rRNA genes; PCGs12RNA: dataset of 13 protein-coding genes removing 3rd coding site then plus two rRNA genes; AA: amino acid translated by 13 protein-coding genes; ML: maximum likelihood; BP: bootstrap value; SH: aLRT SH-like supports value; K-Pg: the Cretaceous–Paleogene; HPD: highest posterior density.