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.

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

“…Since it was specially analyzed by Ding et al [33], two more muscoidean families are included here (Anthomyiidae and Fanniidae), relationships within the Calyptratae will not be discussed in this paper. Although contrary to some previous mt genome trees of the Diptera [7], the monophyly of the included “orthorrhaphan” taxa (Nemestrinidae and Tabanidae) was not supported by most of our analyses (except the BI-P123 (dataset P123 with Bayesian analysis), ML-P123and ML-P123R analyses) (Figure 11A); this is in accordance with more recent mt genome phylogenies of the lower Brachycera [74].…”

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

“…Since it was specially analyzed by Ding et al [33] with two more muscoidean families than are included here (Anthomyiidae and Fanniidae), relationships within the Calyptratae will not be discussed here. While, contrary to some previous mt genome trees of the Diptera [7], the monophyly of the included 'orthorrhaphan' taxa (Nemestrinidae and Tabanidae) was not supported by most of our analyses (except the BI-P123, ML-P123and ML-P123R analyses) (Figures 11A), this is in accordance with more recent mt genome phylogenies of the lower Brachycera [74].…”

Molecular phylogeny and timing of evolution ofAnthomyzaand related genera (Diptera: Anthomyzidae)

“…We defined two calibration points: (a) root, as the common ancestor of all genera, derived from the time of origin of families of the Acalyptrata group, based on Wiegmann, Yeates, Thorne, & Kishino (), Wiegmann et al (), Grimaldi & Engel () & Ding et al (, fig. 5) (48–66–86 MYA; mean 3.25, SD 0.3, offset 40) and (b) Anthomyza umbrosa group stem (two species endemic to Madeira, associated with grasses in laurel forest), derived from the presupposed origin of laurel forests in Madeira, based on Góis‐Marques, Madeira, & Menezes de Sequeira () (1.2–1.5–1.8 MYA; mean 0.01, SD 0.15, offset 0.5).…”