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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.


Mitochondrial maps of two muscoid flies.Circular maps were drawn with GCView [53] with the unsequenced portion of each genome indicated. Gene arrangement is shown on the outermost circle with arrows indicating the orientation of gene transcription. tRNAs are are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). GC content was plotted (in black) using a sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted (positive skew in green, negative skew in purple) as the deviation from the average GC-skew of the entire sequence. The innermost cycle indicates size.
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pone.0134170.g001: Mitochondrial maps of two muscoid flies.Circular maps were drawn with GCView [53] with the unsequenced portion of each genome indicated. Gene arrangement is shown on the outermost circle with arrows indicating the orientation of gene transcription. tRNAs are are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). GC content was plotted (in black) using a sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted (positive skew in green, negative skew in purple) as the deviation from the average GC-skew of the entire sequence. The innermost cycle indicates size.

Mentions: The near complete mt genomes of Euryomma sp. (Fannidae) and Delia platura (Anthomyiidae) were sequenced. The lengths of mt genomes among Diptera, range from 14,922 bp in Sarcophaga peregrine (Sarcophagidae, Zhong et al., unpublished; control region is 123 bp in length) to 19,517 bp in Drosophila melanogaster (Drosophilidae [29]; CR 4601 bp long), with both newly sequenced species in the middle of this range. The mt genomes of muscoid flies have the typical circular, double-stranded molecule (GenBank accession number: KP01268, KP01269; Fig 1) with length of about 16000 bp, and contain 37 genes including 13 PCGs, 22 tRNA genes, 2 rRNA genes and a control region, found in almost all bilaterian animals [22]. The gene order in both species is the same as that of the ancestral insect mt genome (as in almost all Diptera), with 23 genes encoded on the majority strand (J-strand), while the minority strand (N-strand) encodes the remaining 14 genes. Some general characteristics of the genomes are given in S4 Table and S5 Table. The near complete mt genomes of Euryomma and Delia are 15315 bp and 14858 bp in length respectively (Fig 1), however we failed to complete sequencing of their control regions. Genome annotation statistics are listed in S4 and S5 Tables.


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)

Mitochondrial maps of two muscoid flies.Circular maps were drawn with GCView [53] with the unsequenced portion of each genome indicated. Gene arrangement is shown on the outermost circle with arrows indicating the orientation of gene transcription. tRNAs are are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). GC content was plotted (in black) using a sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted (positive skew in green, negative skew in purple) as the deviation from the average GC-skew of the entire sequence. The innermost cycle indicates size.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520480&req=5

pone.0134170.g001: Mitochondrial maps of two muscoid flies.Circular maps were drawn with GCView [53] with the unsequenced portion of each genome indicated. Gene arrangement is shown on the outermost circle with arrows indicating the orientation of gene transcription. tRNAs are are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). GC content was plotted (in black) using a sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted (positive skew in green, negative skew in purple) as the deviation from the average GC-skew of the entire sequence. The innermost cycle indicates size.
Mentions: The near complete mt genomes of Euryomma sp. (Fannidae) and Delia platura (Anthomyiidae) were sequenced. The lengths of mt genomes among Diptera, range from 14,922 bp in Sarcophaga peregrine (Sarcophagidae, Zhong et al., unpublished; control region is 123 bp in length) to 19,517 bp in Drosophila melanogaster (Drosophilidae [29]; CR 4601 bp long), with both newly sequenced species in the middle of this range. The mt genomes of muscoid flies have the typical circular, double-stranded molecule (GenBank accession number: KP01268, KP01269; Fig 1) with length of about 16000 bp, and contain 37 genes including 13 PCGs, 22 tRNA genes, 2 rRNA genes and a control region, found in almost all bilaterian animals [22]. The gene order in both species is the same as that of the ancestral insect mt genome (as in almost all Diptera), with 23 genes encoded on the majority strand (J-strand), while the minority strand (N-strand) encodes the remaining 14 genes. Some general characteristics of the genomes are given in S4 Table and S5 Table. The near complete mt genomes of Euryomma and Delia are 15315 bp and 14858 bp in length respectively (Fig 1), however we failed to complete sequencing of their control regions. Genome annotation statistics are listed in S4 and S5 Tables.

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.