The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes.

Shuangmei Ding,Ding Yang,Stephen L Cameron,Ning Wang,Meng Mao,Xuankun Li,Yuyu Wang,Yuqiang Xi

doi:10.1371/journal.pone.0134170

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.

Highlights

Muscoidea, with approximately 7000 described species, is nearly 5% of the known specieslevel diversity of the Diptera, the true flies [1], and includes the following four families: PLOS ONE | DOI:10.1371/journal.pone.0134170 July 30, 2015The Phylogeny of Muscoidea Based on Mt Genomes
The Euryomma sp. specimen used for DNA extraction was collected by Jinying Yang and Lei Zhang from Gaoshang, Jining, Shandong, China (N35°0500.94@ E116°19034.92@) in May 2013, the Delia platura specimen was collected by Yuqiang Xi from Huangniupu, Fengxian, Shaanxi, China (N34°11047.11@ E106°49034.12@) in August 2013. They were initially preserved in 95% ethanol in the field, and transferred to -20°C for the long-term storage upon the arrival at the China Agricultural University (CAU)
Total DNA was purified from muscle tissues of the thorax using TIANamp Genomic DNA Kit (TIANGEN)

Summary

Introduction

With approximately 7000 described species, is nearly 5% of the known specieslevel diversity of the Diptera, the true flies [1], and includes the following four families: PLOS ONE | DOI:10.1371/journal.pone.0134170 July 30, 2015The Phylogeny of Muscoidea Based on Mt Genomes. Based on four mitochondrial and four nuclear genes from 127 exemplar species of Muscoidea, Kutty et al (2008) found that Muscoidea was paraphyletic, with the clade (Anthomyiidae + Scathophagidae) sister to a monophyletic Oestroidea.

Results

Conclusion