title: The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes.
abstract: Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene.
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Shuangmei
authors.initials: S
authors.lastname: Ding
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Xuankun
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China; Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Wang
authors.affiliation: Earth, Environmental and Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia.
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Cameron
authors.affiliation: Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.
authors.forename: Meng
authors.initials: M
authors.lastname: Mao
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Yuyu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Yuqiang
authors.initials: Y
authors.lastname: Xi
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Ding
authors.initials: D
authors.lastname: Yang
mesh_terms: D000818:Animals; D004175:Diptera / Q000235:genetics*; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry
chemical_list: D012313:RNA