Part of the Bayesian tree of dataset PCG Phylogenetic relationships among the Muscoidea and Oestroidea remains controversial [ 67 ]. Michelsen et al. Based on four mitochondrial and four nuclear genes sequenced from exemplar species, Kutty et al.
These relationships were subsequently supported by Kutty et al. The robust inference of relationships within the Muscoidea and Oestroidea still needs further investigation, so we tested the phylogenetic position of each of the four families in the Muscoidea. This result is different from most previous studies which found Oestroidea to be monophyletic, and Muscoidea as a paraphyletic grade at the base of Oestroidea [ 1 , 4 , 5 , 7 ]. In all analyses Scathophagidae is sister to Anthomyiidae and relative derived within the muscoidea i.
These results contradict previous conclusions based on morphological characters that Scathophagidae retained a more plesiomorphic conditions than any other group [ 68 ]. The different topologies in our study may be due to the compositional bias of mt genome data, particularly at third codon positions as has been proposed for other insect mt genome phylogenies [ 28 , 32 , 54 , 69 ]. In this study, however, removal of third codon positions did not stabilize the topology as all three recovered topologies were found in the subset of 4 analyses that omitted third codon positions.
Further studies with more sampling species are crucial for better understanding relationships within the Cyclorrhapha. Of the 4 alignment datasets used to estimate muscoid phylogeny, PCG was used to estimate divergence times as it had the highest node support in initial phylogenetic assessment and the topology of this dataset was the most representative one the main tree among all of datasets.
This result is consistent with the evidence from a number of amber specimens of Acalyptrata and Calyptratae [ 70 ]. Our estimation of interfamilial divergences of Muscoidea shows broad confidence intervals, suggesting possible limitations in the use of mt genomic data for divergence time estimation. First, broad confidence intervals may reflect difficulties in modeling the inherently heterogeneous patterns of mutation of various PCGs in the mt genome [ 71 — 72 ].
Alternatively, when using all the three sites of PCGs to estimate the divergence time, the saturated nucleotide sites may overestimate the branching times [ 73 ]. In general, the phylogeny inferred from mt genomes indicated that both the superfamily Muscoidea and Oestroidea were polyphyletic, and that interfamily relationships among Muscoidea and Oestroidea are still unresolved. It is worth noting that mt genes are physically linked, and they act as a single locus, so they may alternatively simply illustrate the evolution of mt genomes within this clade, the analysis of additional taxa and nuclear gene data would be helpful for better understanding the relationships of Calyptratae.
We express our sincere thanks to Ms. Jinying Yang and Ms. Lei Zhang Beijing for collecting the specimens. SLC was funded by an Australian Research Council Future Fellowship FT The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
National Center for Biotechnology Information , U. PLoS One. Published online Jul Stephen L. Bi-Song Yue, Editor. Author information Article notes Copyright and License information Disclaimer. Competing Interests: The authors have declared that no competing interests exist. Received Mar 12; Accepted Jul 6. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
This article has been cited by other articles in PMC. S1 Table: Primers used in this study. S2 Table: The best partitioning scheme selected by PartitionFinder for different dataset. S3 Table: Organization of the mt genome of Euryomma sp. S4 Table: Organization of the mt genome of Delia platura.
S5 Table: Codon usage of the Euryomma sp. S6 Table: Codon usage of the Delia platura mt genome. Abstract Muscoidea is a significant dipteran clade that includes house flies Family Muscidae , latrine flies F. Material and Methods Ethics statement No specific permits were required for the insects collected for this study. Phylogenetic Analysis Phylogenetic analysis was conducted on a taxon set of 17 species of Brachycera, including 15 cyclorrhaphans and 2 outgroup species from the families Tabanidae and Nemestrinidae, which belong to the basal Brachycera and non-heteroneuran muscomorphs respectively.
Table 1 Taxon sampling and availability. Open in a separate window. Results and Discussion General features of Fanniidae and Anthomyiidae mt genomes The near complete mt genomes of Euryomma sp. Fig 1. Mitochondrial maps of two muscoid flies.
Diptera: Cyclorrhapha. - PDF Drive
Table 2 Mitochondrial nucleotide composition in six muscoid flies. Region Delia Euryomma. Fig 2. Predicted secondary structure of the lrRNA gene in muscoid flies. Fig 3. Predicted secondary structure of the srRNA gene in muscoid flies. Fig 4. Phylogenetic tree based on mt genome data. Fig 5. Evolutionary timescale for Calyptratae inferred from a mitochondrial PCG dataset. TIF Click here for additional data file. S1 Table Primers used in this study. DOCX Click here for additional data file. S2 Table The best partitioning scheme selected by PartitionFinder for different dataset.
S3 Table Organization of the mt genome of Euryomma sp. S4 Table Organization of the mt genome of Delia platura. S5 Table Codon usage of the Euryomma sp. S6 Table Codon usage of the Delia platura mt genome. Acknowledgments We express our sincere thanks to Ms. References 1. The Muscoidea Diptera: Calyptratae are paraphyletic: evidence from four mitochondrial and four nuclear genes.
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