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

Ding S, Li X, Wang N, Cameron SL, Mao M, Wang Y, Xi Y, Yang D - PLoS ONE (2015)

Bottom Line: Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F.Anthomyiidae).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, China Agricultural University, Beijing, China.

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.

No MeSH data available.


Phylogenetic tree based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG123 & PCG12RNA and ML analyses with datasets PCG12, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities≥ 0.90 or ML bootstrap≥ 70, white indicates posterior probabilities< 0.90 or ML bootstrap< 70, ‘ns’ = not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. The Bayesian tree of datasets PCG123 and PCG12RNA as well as ML tree of datasets PCG12 and PCG123. B. Part of the Bayesian tree of dataset PCG123RNA as well as ML tree of datasets PCG123RNA and PCG12RNA. C. Part of the Bayesian tree of dataset PCG12.
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pone.0134170.g004: Phylogenetic tree based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG123 & PCG12RNA and ML analyses with datasets PCG12, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities≥ 0.90 or ML bootstrap≥ 70, white indicates posterior probabilities< 0.90 or ML bootstrap< 70, ‘ns’ = not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. The Bayesian tree of datasets PCG123 and PCG12RNA as well as ML tree of datasets PCG12 and PCG123. B. Part of the Bayesian tree of dataset PCG123RNA as well as ML tree of datasets PCG123RNA and PCG12RNA. C. Part of the Bayesian tree of dataset PCG12.

Mentions: Phylogenetic trees were inferred using two approaches (BI and ML) for four datasets that differ by including or excluding third codon positions or RNA genes or both (PCG123, PCG123RNA, PCG12, and PCG12RNA) (Fig 4). All three topologies inferred from four datasets were exhibited in Fig 4. The topology of BI-P123, BI-12R, ML-P12, as well as ML-P123 were Fig 4A, the topology of BI-P123R, ML-P12R,and ML-P123R were Fig 4B, the Fig 4C represented BI-P12 only. The monophyly of the Schizophora and Calyptratae were consistently supported (posterior probability = 1.00, ML bootstrap = 100% in all four dataset). The Aschiza was paraphyletic, as is commonly accepted [5, 53, 61–66]. Phoridae was sister to the remaining Cyclorrhapha (PP 1.00, ML 100% in all four datasets). These results are same as recent wide-scale molecular [5] and morphological [7] studies regarding the branching order within the Aschiza.


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

Ding S, Li X, Wang N, Cameron SL, Mao M, Wang Y, Xi Y, Yang D - PLoS ONE (2015)

Phylogenetic tree based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG123 & PCG12RNA and ML analyses with datasets PCG12, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities≥ 0.90 or ML bootstrap≥ 70, white indicates posterior probabilities< 0.90 or ML bootstrap< 70, ‘ns’ = not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. The Bayesian tree of datasets PCG123 and PCG12RNA as well as ML tree of datasets PCG12 and PCG123. B. Part of the Bayesian tree of dataset PCG123RNA as well as ML tree of datasets PCG123RNA and PCG12RNA. C. Part of the Bayesian tree of dataset PCG12.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4520480&req=5

pone.0134170.g004: Phylogenetic tree based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG123 & PCG12RNA and ML analyses with datasets PCG12, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities≥ 0.90 or ML bootstrap≥ 70, white indicates posterior probabilities< 0.90 or ML bootstrap< 70, ‘ns’ = not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. The Bayesian tree of datasets PCG123 and PCG12RNA as well as ML tree of datasets PCG12 and PCG123. B. Part of the Bayesian tree of dataset PCG123RNA as well as ML tree of datasets PCG123RNA and PCG12RNA. C. Part of the Bayesian tree of dataset PCG12.
Mentions: Phylogenetic trees were inferred using two approaches (BI and ML) for four datasets that differ by including or excluding third codon positions or RNA genes or both (PCG123, PCG123RNA, PCG12, and PCG12RNA) (Fig 4). All three topologies inferred from four datasets were exhibited in Fig 4. The topology of BI-P123, BI-12R, ML-P12, as well as ML-P123 were Fig 4A, the topology of BI-P123R, ML-P12R,and ML-P123R were Fig 4B, the Fig 4C represented BI-P12 only. The monophyly of the Schizophora and Calyptratae were consistently supported (posterior probability = 1.00, ML bootstrap = 100% in all four dataset). The Aschiza was paraphyletic, as is commonly accepted [5, 53, 61–66]. Phoridae was sister to the remaining Cyclorrhapha (PP 1.00, ML 100% in all four datasets). These results are same as recent wide-scale molecular [5] and morphological [7] studies regarding the branching order within the Aschiza.

Bottom Line: Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F.Anthomyiidae).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, China Agricultural University, Beijing, China.

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.

No MeSH data available.