Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)
Identifieur interne : 000111 ( Pmc/Corpus ); précédent : 000110; suivant : 000112Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)
Auteurs : Dong Zhang ; Liping Yan ; Ming Zhang ; Hongjun Chu ; Jie Cao ; Kai Li ; Defu Hu ; Thomas PapeSource :
- International Journal of Biological Sciences [ 1449-2288 ] ; 2016.
Abstract
The complete mitogenome of the horse stomach bot fly
Url:
DOI: 10.7150/ijbs.12148
PubMed: 27019632
PubMed Central: 4807417
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)</title><author><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Yan, Liping" sort="Yan, Liping" uniqKey="Yan L" first="Liping" last="Yan">Liping Yan</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Zhang, Ming" sort="Zhang, Ming" uniqKey="Zhang M" first="Ming" last="Zhang">Ming Zhang</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Chu, Hongjun" sort="Chu, Hongjun" uniqKey="Chu H" first="Hongjun" last="Chu">Hongjun Chu</name><affiliation><nlm:aff id="A3">3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China.</nlm:aff></affiliation></author><author><name sortKey="Cao, Jie" sort="Cao, Jie" uniqKey="Cao J" first="Jie" last="Cao">Jie Cao</name><affiliation><nlm:aff id="A4">4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China.</nlm:aff></affiliation></author><author><name sortKey="Li, Kai" sort="Li, Kai" uniqKey="Li K" first="Kai" last="Li">Kai Li</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Hu, Defu" sort="Hu, Defu" uniqKey="Hu D" first="Defu" last="Hu">Defu Hu</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Pape, Thomas" sort="Pape, Thomas" uniqKey="Pape T" first="Thomas" last="Pape">Thomas Pape</name><affiliation><nlm:aff id="A2">2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27019632</idno><idno type="pmc">4807417</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807417</idno><idno type="RBID">PMC:4807417</idno><idno type="doi">10.7150/ijbs.12148</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000111</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)</title><author><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Yan, Liping" sort="Yan, Liping" uniqKey="Yan L" first="Liping" last="Yan">Liping Yan</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Zhang, Ming" sort="Zhang, Ming" uniqKey="Zhang M" first="Ming" last="Zhang">Ming Zhang</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Chu, Hongjun" sort="Chu, Hongjun" uniqKey="Chu H" first="Hongjun" last="Chu">Hongjun Chu</name><affiliation><nlm:aff id="A3">3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China.</nlm:aff></affiliation></author><author><name sortKey="Cao, Jie" sort="Cao, Jie" uniqKey="Cao J" first="Jie" last="Cao">Jie Cao</name><affiliation><nlm:aff id="A4">4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China.</nlm:aff></affiliation></author><author><name sortKey="Li, Kai" sort="Li, Kai" uniqKey="Li K" first="Kai" last="Li">Kai Li</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Hu, Defu" sort="Hu, Defu" uniqKey="Hu D" first="Defu" last="Hu">Defu Hu</name><affiliation><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff></affiliation></author><author><name sortKey="Pape, Thomas" sort="Pape, Thomas" uniqKey="Pape T" first="Thomas" last="Pape">Thomas Pape</name><affiliation><nlm:aff id="A2">2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:aff></affiliation></author></analytic><series><title level="j">International Journal of Biological Sciences</title><idno type="eISSN">1449-2288</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The complete mitogenome of the horse stomach bot fly <italic>Gasterophilus pecorum</italic> (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly <italic>Wohlfahrtia magnifica</italic> (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, <italic>Pollenia</italic> + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Simon, C" uniqKey="Simon C">C Simon</name></author><author><name sortKey="Frati, F" uniqKey="Frati F">F Frati</name></author><author><name sortKey="Beckenbach, A" uniqKey="Beckenbach A">A Beckenbach</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Trautwein, Md" uniqKey="Trautwein M">MD Trautwein</name></author><author><name sortKey="Wiegmann, Bm" uniqKey="Wiegmann B">BM Wiegmann</name></author><author><name sortKey="Beutel, R" uniqKey="Beutel R">R Beutel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burger, G" uniqKey="Burger G">G 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Int J Biol Sci</journal-id><journal-id journal-id-type="iso-abbrev">Int. J. Biol. Sci</journal-id><journal-id journal-id-type="publisher-id">ijbs</journal-id><journal-title-group><journal-title>International Journal of Biological Sciences</journal-title></journal-title-group><issn pub-type="epub">1449-2288</issn><publisher><publisher-name>Ivyspring International Publisher</publisher-name><publisher-loc>Sydney</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27019632</article-id><article-id pub-id-type="pmc">4807417</article-id><article-id pub-id-type="doi">10.7150/ijbs.12148</article-id><article-id pub-id-type="publisher-id">ijbsv12p0489</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Paper</subject></subj-group></article-categories><title-group><article-title>Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Dong</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="corresp" rid="FNA_envelop">✉</xref><xref ref-type="author-notes" rid="FNA_star">*</xref></contrib><contrib contrib-type="author"><name><surname>Yan</surname><given-names>Liping</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="author-notes" rid="FNA_star">*</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Ming</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Chu</surname><given-names>Hongjun</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Cao</surname><given-names>Jie</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Kai</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Defu</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Pape</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib></contrib-group><aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</aff><aff id="A2">2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</aff><aff id="A3">3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China.</aff><aff id="A4">4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China.</aff><author-notes><corresp id="FNA_envelop">✉ Corresponding author: Dong Zhang, Tel: +86 10 62336801; Email: <email>ernest8445@163.com</email>.</corresp><fn fn-type="equal" id="FNA_star"><p>* These authors contributed equally to this study.</p></fn><fn fn-type="conflict"><p>Competing Interests: The authors have declared that no competing interest exists.</p></fn></author-notes><pub-date pub-type="collection"><year>2016</year></pub-date><pub-date pub-type="epub"><day>20</day><month>2</month><year>2016</year></pub-date><volume>12</volume><issue>5</issue><fpage>489</fpage><lpage>504</lpage><history><date date-type="received"><day>16</day><month>3</month><year>2015</year></date><date date-type="accepted"><day>22</day><month>12</month><year>2015</year></date></history><permissions><copyright-statement>© Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions.</copyright-statement><copyright-year>2016</copyright-year></permissions><abstract><p>The complete mitogenome of the horse stomach bot fly <italic>Gasterophilus pecorum</italic> (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly <italic>Wohlfahrtia magnifica</italic> (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, <italic>Pollenia</italic> + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.</p></abstract><kwd-group><kwd>mitogenome</kwd><kwd>gene contribution</kwd><kwd>taxon sampling</kwd><kwd>long-branch attraction</kwd><kwd>phylogeny</kwd><kwd>Oestroidea</kwd><kwd>Calyptratae.</kwd></kwd-group></article-meta></front><body><sec sec-type="intro"><title>Introduction</title><p>During the last decade, phylogeny reconstruction of extant life forms has shifted from being mainly morphology-based to currently relying primarily on evidence from molecular data. Just as for morphological data, it is imperative that we acquire an in-depth understanding of the information content and suitability of the sequence data used in the analysis. The mitochondrial genome, with its multiple copies in each cell, as well as the design of conserved primers for broad-scale amplification <xref rid="B1" ref-type="bibr">1</xref>, has been dominating until the advent of next generation sequencing <xref rid="B2" ref-type="bibr">2</xref>. Still, as the mitochondrial genome appears to evolve faster than the nuclear genome <xref rid="B3" ref-type="bibr">3</xref>-<xref rid="B5" ref-type="bibr">5</xref>, it should have the potential for a finer phylogenetic resolution (or higher branch support values) in fast-evolving groups. Mitogenomes are thought to be reliable markers for reconstructing phylogenies <xref rid="B5" ref-type="bibr">5</xref>, but the use of mitochondrial data in deep phylogeny analyses has been criticized because of biases in nucleotide frequencies, high substitution rates of nucleotides, and different phylogenetic information content among genes <xref rid="B6" ref-type="bibr">6</xref>-<xref rid="B12" ref-type="bibr">12</xref>. Further, although complete mitogenomes provide high phylogenetic resolution and the most accurate dating estimates, phylogenetic estimates based on complete and incomplete mitogenomes have yielded inconsistent phylogenies for insects <xref rid="B13" ref-type="bibr">13</xref>, <xref rid="B14" ref-type="bibr">14</xref>, and vertebrates as well <xref rid="B8" ref-type="bibr">8</xref>, <xref rid="B15" ref-type="bibr">15</xref>, indicating conflicts between the phylogenetic signals provided by the different mitochondrial genes. Mitogenomes are therefore of considerable interest in evolutionary studies, and the aim of the present paper is to investigate the phylogenetic signal contained in the mitogenome for members of the large subradiation of the schizophoran flies termed Calyptratae.</p><p>The nearly 20 000 described species of calyptrate flies comprise the largest and ecologically most diverse clade within the schizophoran super-radiation <xref rid="B11" ref-type="bibr">11</xref>, <xref rid="B16" ref-type="bibr">16</xref>, <xref rid="B17" ref-type="bibr">17</xref>. Several phylogenetic studies, utilizing morphological and molecular data, have been conducted at different taxonomic levels within this group, but the phylogenetic relationships within major parts of this fly radiation are still controversial <xref rid="B17" ref-type="bibr">17</xref>-<xref rid="B39" ref-type="bibr">39</xref>. Inferring a robust phylogeny of the Calyptratae will require the combination of a sufficiently informative dataset with carefully selected terminal taxa <xref rid="B6" ref-type="bibr">6</xref>, <xref rid="B40" ref-type="bibr">40</xref>, <xref rid="B41" ref-type="bibr">41</xref>.</p><p>At present, there are 36 complete or near-complete mitogenome sequences of calyptrate species in GenBank, representing the muscoid families Anthomyiidae, Fanniidae, Muscidae, and Scathophagidae, as well as several families of the Oestroidea. We sequenced the complete mtDNA of the stomach bot fly <italic>Gasterophilus pecorum</italic> (Fabricius), as the first representative of the bot fly subfamily Gasterophilinae (Oestridae), and provide a near-complete mitogenome of <italic>Wohlfahrtia magnifica</italic> (Schiner) as the first representative of the subfamily Paramacronychiinae (Sarcophagidae). We use these data to reconstruct calyptrate phylogeny and discuss mitogenomic performance.</p></sec><sec sec-type="methods"><title>Materials and methods</title><sec><title>Taxon sampling</title><p>Complete (or near-complete) mitogenomes from a total of 38 calyptrate taxa and 2 non-calyptrate taxa were obtained by downloading existing data from GenBank and adding two mitogenomes (Table <xref ref-type="table" rid="T1">1</xref>). All four families of the muscoid grade are represented, but the Hippoboscoidea are not represented because no mitogenomes are available for that clade. The family-level classification of the Oestroidea is not yet settled, primarily because of the long-standing issue of resolving the non-monophyletic status of the blow flies <xref rid="B17" ref-type="bibr">17</xref>, <xref rid="B33" ref-type="bibr">33</xref>. We include representatives from the traditional Calliphoridae, the Tachinidae, the Sarcophagidae (adding the first species from subfamily Paramacronychiinae) and the Oestridae (adding the first species from subfamily Gasterophilinae). We include one representative from each of the tachinid subfamilies Exoristinae and Phasiinae but exclude <italic>Exorista sorbillans</italic> (Wiedemann) (Tachinidae) <xref rid="B66" ref-type="bibr">66</xref> because a BLAST search places it close to <italic>Drosophila</italic> and widely removed from other species of the family. No mitogenome is available for the small family Rhinophoridae. Two non-calyptrate outgroup taxa are chosen to root the tree: the lower brachyceran species <italic>Cydistomyia duplonotata</italic> (Ricardo) (Tabanidae) and the acalyptrate species <italic>Drosophila melanogaster</italic> (Meigen) (Drosophilidae).</p></sec><sec><title>DNA extraction, amplification, sequencing, and annotation</title><p>A single larva of <italic>G</italic>.<italic> pecorum</italic>, collected in 99.5% ethanol in Kalamaili, Xinjiang Province, China, in 2013, and a dry specimen of male <italic>W</italic>. <italic>magnifica</italic>, hatched from a larva collected in Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China, in 2014, served as sources of mitogenomic DNA. Muscular tissue was transferred to an Eppendorf tube, incubated in splitting solution with proteinase K (Beijing Cowin Biosciencee Co., Ltd., China) at 56℃ for three hours, and DNA was isolated with phenol-chloroform (MYM Biological Technology Ltd., India). After extraction in ethanol, genomic DNA was dissolved in Tris-EDTA buffer and stored at -20℃ until use.</p><p>The mitochondrial genomes were amplified by Polymerase Chain Reaction (PCR) using 16 primer pairs (Table <xref ref-type="supplementary-material" rid="SM1">S1</xref>) synthesized by Beijing Genomics Institute. Genomic DNA (1 μL) was added to the PCR reaction mix (24 μL), which contained 17.2 μL sterilized distilled water, 2.5 μL of 10× Es Taq PCR Buffer (Beijing Cowin Biosciencee Co., Ltd., China), 2 μL of dNTPs mixture (2.5 mM each) (Beijing Cowin Biosciencee Co., Ltd., China), 1 μL of each primer (10 μM), and 0.3 μL of Es Taq DNA Polymerase (1.5 U) (Beijing Cowin Biosciencee Co., Ltd., China). The PCR was performed in a thermal cycler, using the cycling protocols reported in Table <xref ref-type="supplementary-material" rid="SM1">S1</xref> for each primer combination. The polymerase activation (95℃, 10 min), the denaturation (95℃, 1 min), the final extension (72℃, 7 min) and the number of cycles (<italic>n </italic>= 35) were identical in all of the protocols <xref rid="B60" ref-type="bibr">60</xref>. The PCR products were detected via electrophoresis in 0.5% agarose gels and sized by comparison with markers (Beijing Cowin Biosciencee Co., Ltd., China). Gels were photographed using a gel documentation system. Amplicons were sequenced bidirectionally using the BigDye<sup>®</sup> Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Inc., USA), and then purified using BigDye XTerminator<sup>®</sup> Purification Kit (Applied Biosystems, Inc., USA). Sequences were read with Chromas (Technelysium, Ltd., Australia), after running an ABI 3730xl DNA analyzer (Applied Biosystems, Inc., USA.).</p><p>The software BioEdit version v7.0.9.0 <xref rid="B69" ref-type="bibr">69</xref> and SeqMan (DNAStar, Steve ShearDown, 1998-2001 version, DNASTAR Inc., USA) were used for assembly of raw sequences. Gene boundaries and genomic positions of protein-coding genes (PCGs), ribosomal RNA genes, and transfer RNA genes were identified by BLAST search <xref rid="B70" ref-type="bibr">70</xref>, MITOS search <xref rid="B71" ref-type="bibr">71</xref>, and by comparing with other calyptrates using DNAMAN software (version 8, Lynnon Corp., Canada). Nucleotide composition and codon usage were calculated using MEGA 5.2 <xref rid="B72" ref-type="bibr">72</xref>.</p></sec><sec><title>Estimates of genetic divergence of mitochondrial genes</title><p>Genetic divergence was evaluated by calculating the mean evolutionary distances of each of the PCGs, rRNA genes, and concatenation of 13 PCGs, 2 rRNA genes, and 22 tRNA genes respectively from MEGA 5.2 under an uncorrected <italic>p</italic>-distance model. Uncorrected <italic>p</italic>-distances were calculated in MEGA 5.2 and obtained between species and averaged for each gene or combination of genes at three levels: within subfamily, within family, and within superfamily.</p><p>The percentage of gaps and percentage of conserved positions for each of the 13 PCGs were calculated following Nardi <italic>et al</italic>. <xref rid="B73" ref-type="bibr">73</xref>.</p></sec><sec><title>Nucleotide substitution saturation</title><p>Nucleotide substitution saturation analyses were performed for each of the 13 PCGs, for the 1st & 2nd codon positions combined, and for the 3rd codon positions, using MEGA 5.2 following Huang <xref rid="B74" ref-type="bibr">74</xref>.</p></sec><sec><title>Phylogenetic analysis</title><p>Phylogenetic analyses were conducted with (subgroup_1) or without (subgroup_2) the non-calyptrate outgroups (Table <xref ref-type="table" rid="T2">2</xref>).</p><p>For both subgroups, two phylogenetic analyses were conducted: (1) using PCGs and rRNA genes, (2) using PCGs, rRNA genes and the concatenated tRNA genes. Phylogenetic trees were constructed using three partitioning approaches: (1) not partitioned; (2) partitioned by gene, and; (3) excluding 3rd codon positions of PCGs, not partitioned.</p><p>Each of the mitochondrial genes were aligned separately using MUSCLE <xref rid="B75" ref-type="bibr">75</xref>, as implemented in MEGA 5.2. For protein-coding genes, nucleotide sequences were aligned after translation into amino acid sequences by reference, and then back-translated for analysis as nucleotide sequences. The 22 tRNA genes were aligned separately and then concatenated as a combined partition, as all individual tRNA genes are very short. Amino acid and nucleotide sequences were aligned using default settings. Individually aligned genes were then concatenated using SequenceMatrix <xref rid="B76" ref-type="bibr">76</xref> for phylogenetic analyses.</p><p>MrModeltest 2.3 <xref rid="B77" ref-type="bibr">77</xref> was used to select the best model for the non-partitioned data set, and for the data set that excluded the 3rd codon position of PCGs. PartitionFinder v1.1.1 <xref rid="B78" ref-type="bibr">78</xref> was used to evaluate the best partitioning scheme for the partitioned datasets (Table <xref ref-type="table" rid="T2">2</xref>), after using the “greedy” algorithm with branch lengths estimated as ''unlinked”, following the Bayesian Information Criterion (BIC).</p><p>Phylogenetic trees were inferred using Bayesian, and Maximum Likelihood (ML) methods. Bayesian analyses were performed with MrBayes v3.2.1 <xref rid="B79" ref-type="bibr">79</xref> on CIPRES (Cyberinfrastructure for Phylogenetic Research) Science Gateway <xref rid="B80" ref-type="bibr">80</xref>. Two independent runs were conducted, each with four chains (one cold and three hot chains), for 10 million generations and samples were drawn every 1000 generations. The first 25% of steps were discarded as burn-in. For both partitioned and unpartitioned data, the Maximum Likelihood analyses were performed with the RaxML <xref rid="B81" ref-type="bibr">81</xref>, using the rapid hill-climbing algorithm starting from 100 randomized maximum parsimony trees. Node supports were evaluated via bootstrap tests with 1000 iterations.</p></sec><sec><title>Phylogenetic examination of separate genes</title><p>The Ktreedist program <xref rid="B82" ref-type="bibr">82</xref> was used to evaluate the relative contribution of each single mitochondrial gene to the construction of the phylogenetic tree. Bayesian analyses were performed using each of the 13 PCGs and the two rRNA genes as described above, and k-scores were calculated by comparing each of these trees with a reference tree obtained by a Bayesian analysis of the non-partitioned dataset of 13 PCGs and two rRNA genes for subgroup_2.</p></sec></sec><sec sec-type="results"><title>Results</title><sec><title>General features of the <italic>Gasterophilus pecorum</italic> and <italic>Wohlfahrtia magnifica</italic> mitogenomes</title><p>The complete mitogenome of <italic>G</italic>.<italic> pecorum</italic> (15 750 bp) and near-complete mitogenome of <italic>W</italic>. <italic>magnifica</italic> (14 705 bp) were sequenced (GenBank accession numbers KU578262-KU578263). The control region of <italic>W</italic>. <italic>magnifica</italic> could not be amplified, resulting in the failure to sequence tRNA<sup>Ile</sup>.</p><p>Both sequences are similar to all known calyptrates, both in the order and orientation of genes. They are circular molecules containing all 37 genes usually present in bilaterians: 13 PCGs, 22 tRNA genes, and 2 rRNA genes (Fig. <xref ref-type="fig" rid="F1">1</xref>, Table <xref ref-type="supplementary-material" rid="SM1">S2</xref>). The control regions are located at the same site (between srRNA and tRNA<sup>Ile</sup> genes) as found in other calyptrate flies for which the complete mtDNA sequences are available <xref rid="B44" ref-type="bibr">44</xref>, <xref rid="B45" ref-type="bibr">45</xref>, <xref rid="B47" ref-type="bibr">47</xref>, <xref rid="B49" ref-type="bibr">49</xref>, <xref rid="B58" ref-type="bibr">58</xref>-<xref rid="B60" ref-type="bibr">60</xref>, <xref rid="B62" ref-type="bibr">62</xref>.</p><p>The start codons of all protein-coding genes were compared with data available from other dipterans. All protein-coding genes, except COI, have one of the common start codons for mitochondrial DNA: ATG, ATA, or ATT (Table <xref ref-type="supplementary-material" rid="SM1">S2</xref>). The start codon of COI was identified as TCG. COI has been reported using a nonstandard start codon in species belonging to the Calyptratae <xref rid="B43" ref-type="bibr">43</xref>-<xref rid="B65" ref-type="bibr">65</xref>. TAA, TAG and T stop codons were found (Table <xref ref-type="supplementary-material" rid="SM1">S2</xref>), and further details about the mitogenome of <italic>G</italic>. <italic>pecorum </italic>and <italic>W</italic>. <italic>magnifica</italic> are presented in Table <xref ref-type="table" rid="T3">3</xref>, Table <xref ref-type="supplementary-material" rid="SM1">S2</xref>, and Fig. <xref ref-type="supplementary-material" rid="SM1">S1</xref>a, S1b. Specifically for <italic>G</italic>. <italic>pecorum</italic>, the AT content of the complete genome, lrRNA gene, srRNA gene and control region, 70.7%, 75.4%, 72.3% and 80.8% respectively, are the lowest when compared with other species of the Calyptratae (Table <xref ref-type="table" rid="T3">3</xref>, Table <xref ref-type="supplementary-material" rid="SM1">S3</xref>).</p></sec><sec><title>Genetic divergence</title><p>The average <italic>p</italic>-distances of PCGs show greater variation than that of rRNA genes, and ND6 and ATP8 genes show the largest distance and standard deviation respectively (Fig. <xref ref-type="fig" rid="F2">2</xref>, Table <xref ref-type="supplementary-material" rid="SM1">S4</xref>). Percentages of gaps in each protein-coding gene alignment are below 10%, while percentages of conserved positions range from 39.96% to 60.04% (Fig. <xref ref-type="fig" rid="F3">3</xref>, Table <xref ref-type="supplementary-material" rid="SM1">S5</xref>).</p></sec><sec><title>Nucleotide substitution saturation</title><p>The nucleotide substitution is estimated (Fig. <xref ref-type="fig" rid="F4">4</xref>) and there is no or little sign of saturation. The number of transversions and transitions of the 13 PCGs increases with increasing evolutionary distance. For different codon positions, transversions and transitions increase with the <italic>p</italic>-distance for 1st & 2nd codon positions, while for 3rd codon positions the numbers of transitions show a plateau for <italic>p</italic>-distance values around 0.15-0.20, but increase after that.</p></sec><sec><title>Phylogenetic analysis</title><p>Four parallel analyses are performed: subgroup_1 with all genes (i.e., 13 PCGs, 2 rRNA genes, and concatenation of 22 tRNA genes) (subgroup_1_ALL); subgroup_1 with all but tRNA genes (subgroup_1_PCG&rRNA); subgroup_2 with all genes (subgroup_2_ALL), and; subgroup_2 with all but tRNA genes (subgroup_2_PCG&rRNA).</p><p>For subgroup_1, all analyses place <italic>G</italic>. <italic>pecorum</italic> at the basal split of the Calyptratae with strong support (Figs. <xref ref-type="fig" rid="F5">5</xref>, <xref ref-type="fig" rid="F6">6</xref>). Topologies of the remaining calyptrates of most datasets show a consistent relationship of (Fanniidae-Muscidae ((Anthomyiidae + Scathophagidae) (remaining Calliphoridae (Sarcophagidae (Oestridae (<italic>Pollenia</italic> + Tachinidae)))))), except for the unpartitioned Bayesian tree of subgroup_1_PCG&rRNA, and ML tree of subgroup_1 excluding 3rd codon positions of PCGs, which are inferred with the clade of muscoid grade or (Anthomyiidae + Scathophagidae) nested within the Oestroidea.</p><p>For subgroup_2, all analyses infer an identical oestroid family-level topology of (remaining Calliphoridae (Sarcophagidae (Oestridae (<italic>Pollenia</italic> + Tachinidae)))), except for the Bayesian tree of subgroup_2_PCG&rRNA without 3rd codon positions of PCGs, which places <italic>Pollenia</italic> together with Oestridae rather than Tachinidae (Figs. <xref ref-type="fig" rid="F7">7</xref>, <xref ref-type="fig" rid="F8">8</xref>). At intrafamilial level, relationships within Sarcophagidae (within <italic>Sarcophaga</italic>) present small changes when the data are partitioned. When the 3rd codon positions of PCGs are excluded, the Muscidae emerge as monophyletic and relationships within Sarcophagidae (within <italic>Sarcophaga</italic>), Calliphoridae (within subfamily Chrysomyinae), and within Oestridae are different from relationships inferred from datasets with this position included. Each family is moderately or well supported, except for the Oestridae, and Bayesian and ML inference fail to reach an agreement on the relationships within this family, with either <italic>Dermatobia</italic> or <italic>Gasterophilus</italic> at the base.</p></sec><sec><title>Phylogenetic examination of separate genes</title><p>The set of k-scores calculated by Ktreedist program is shown in Fig. <xref ref-type="fig" rid="F9">9</xref>. High scores indicate a poor match between the comparison and reference tree. For the PCGs, ND2 and ND5 produce trees that match well with the topology of the reference tree. ND6 and ATP8 genes show the most deviant topologies.</p></sec></sec><sec sec-type="discussion"><title>Discussion</title><sec><title>Taxon sampling</title><p>Inferred topologies can be recognized as being of two types: (1) for analyses with the two non-calyptrate outgroups, the muscoid families are nested within a paraphyletic Oestroidea in the Bayesian trees based on the unpartitioned dataset with all codon sites, and <italic>G</italic>.<italic> pecorum</italic> takes part in the basal split of the Calyptratae; (2) for analyses without the two non-calyptrate outgroups, the Oestroidea are inferred as monophyletic, which is in agreement with previous studies <xref rid="B11" ref-type="bibr">11</xref>, <xref rid="B17" ref-type="bibr">17</xref>. When tRNA genes are included in the matrix in the present study, some node supports decrease (Figs. <xref ref-type="fig" rid="F7">7</xref>, <xref ref-type="fig" rid="F8">8</xref>), and relationships within Oestridae vary when data are partitioned (Figs. <xref ref-type="fig" rid="F7">7</xref>B1, 7B2). Besides, in the analyses without the two non-calyptrate outgroups, topologies within the Calliphoridae change noticeably at genus level when the 3rd codon positions of PCGs are omitted. Taken together, the trees of subgroup_2 excluding tRNA genes but including all codon sites of PCGs are thought to be the most reliable in the present study.</p><p>Our analyses highlight the importance of taxon sampling in phylogeny reconstruction. Appropriate taxon sampling is very important for accurate phylogenetic estimation <xref rid="B6" ref-type="bibr">6</xref>, but there are some disagreements whether phylogenies are improved by increased taxon sampling. Some have argued that adding taxa would decrease accuracy <xref rid="B83" ref-type="bibr">83</xref>, <xref rid="B84" ref-type="bibr">84</xref>, or at least does not help resolve conflicts <xref rid="B40" ref-type="bibr">40</xref>, while others believe that increased sampling improves accuracy [e.g., 85-89]. The present analysis includes many more species than previous mitogenomic studies of calyptrate flies (e.g., Nelson et al. <xref rid="B44" ref-type="bibr">44</xref>, with 20 species, 13 of which are calliphorids; Zhao et al. <xref rid="B58" ref-type="bibr">58</xref>, with 9 calyptrate species; Ding et al. <xref rid="B61" ref-type="bibr">61</xref>, with 10 calyptrate species) and also includes all available mitogenomes. Our research strongly supports monophyly of Oestroidea, as well as relationships within Sarcophagidae and within Calliphoridae (excluding <italic>Pollenia</italic>). Although we cannot resolve relationships within Oestridae, bot fly monophyly is well supported in the Bayesian analyses. The different results among the previous studies most likely reflect different coverage of taxa. Our approach, which includes more taxa, yields a better supported topology.</p><p>It is interesting that all three bot flies have remarkably long branches, with <italic>G</italic>. <italic>pecorum</italic> showing the longest terminal branch of any calyptrate in our analyses and <italic>H. lineatum</italic> the next longest. For all analyses of subgroup_1, <italic>G</italic>. <italic>pecorum</italic> is separated from the remaining bot flies and located at the base of the Calyptratae (Figs. <xref ref-type="fig" rid="F5">5</xref>, <xref ref-type="fig" rid="F6">6</xref>). With both morphology and biology providing very strong support for bot fly monophyly <xref rid="B29" ref-type="bibr">29</xref>, this placement is very likely an artefact, which is here considered to be caused by long-branch attraction <xref rid="B90" ref-type="bibr">90</xref>, <xref rid="B91" ref-type="bibr">91</xref> between <italic>G</italic>. <italic>pecorum</italic> and the long branches of both outgroups. Improved taxon sampling can help minimise this effect <xref rid="B74" ref-type="bibr">74</xref>, <xref rid="B92" ref-type="bibr">92</xref>, either by a denser taxon sampling <xref rid="B88" ref-type="bibr">88</xref>, <xref rid="B89" ref-type="bibr">89</xref>, <xref rid="B91" ref-type="bibr">91</xref>, or by optimization of outgroup selection <xref rid="B74" ref-type="bibr">74</xref>. We optimized outgroup selection by omitting the non-calyptrate outgroups (subgroup_2) and instead rooted the tree at <italic>Euryomma</italic> from Fanniidae, as this family has been found to be the sister group to the non-hippoboscoid calyptrates in other studies <xref rid="B11" ref-type="bibr">11</xref>, <xref rid="B17" ref-type="bibr">17</xref>. Following the exclusion of non-calyptrate outgroups, <italic>G</italic>.<italic> pecorum</italic> is pulled into the Oestroidea, where it clusters together with the remaining oestrids, and the monophyletic Oestroidea is nested within the muscoid grade, consistent with the widely accepted relationships <xref rid="B11" ref-type="bibr">11</xref>, <xref rid="B17" ref-type="bibr">17</xref>, <xref rid="B19" ref-type="bibr">19</xref>. These results indicate that the overall phylogeny, and in particular the placement of <italic>G</italic>.<italic> pecorum</italic>, is influenced by the long branches of the two non-calyptrate outgroups. Similarly, the non-monophyletic Oestroidea inferred by Ding <italic>et al</italic>. <xref rid="B61" ref-type="bibr">61</xref> may be an artefact caused by the use of distant outgroups (Tabanidae, Nemestrinidae). Clearly, close attention should be paid to the selection of outgroups, as inappropriate (e.g., very distant) outgroups may cause long-branch attraction and result in erroneous phylogeny reconstructions.</p></sec><sec><title>Reliability of single mitochondrial genes</title><p>We document two new mitogenomes in the subfamilies Gasterophilinae (of Oestridae) and Paramacronychiinae (of Sarcophagidae), thereby providing an opportunity to reanalyse phylogeny of the Calyptratae in the light of recent results <xref rid="B44" ref-type="bibr">44</xref>, <xref rid="B58" ref-type="bibr">58</xref> and with a focus on mitogenomic performance.</p><p>The contribution of each mitochondrial gene to the calyptrate mitogenome phylogeny is estimated by calculating the k-score <xref rid="B82" ref-type="bibr">82</xref> for each gene. Phylogenetic resolution varies with the contribution of different genes: for rRNA, the lrRNA provides relatively more topological resolution than srRNA; for the protein-coding genes, according to their k-score, trees based on ND2 and ND5 are closest to the reference tree, followed by trees based on ND1, COIII, COI, and ND4L, while trees based on ATP8 and ND6 are farthest from the reference tree. Surprisingly, the widely used CYTB provides relatively little topological resolution. Furthermore, our different analyses for each protein-coding gene suggest that ATP8 and ND6 are faster evolving genes (see Figs. <xref ref-type="fig" rid="F3">3</xref>, <xref ref-type="fig" rid="F4">4</xref>). The evidence suggests that ATP8 and ND6 may contribute least in calyptrate phylogeny reconstruction, and that lrRNA, ND2, ND5, ND1, COIII, and COI perform better than other mitochondrial genes. Similar conclusions were reached in other phylogenetic analyses <xref rid="B15" ref-type="bibr">15</xref>, <xref rid="B73" ref-type="bibr">73</xref>. In contrast, the most conservative genes (i.e., concatenation of tRNA genes) decrease some node supports in the present study (Figs. <xref ref-type="fig" rid="F7">7</xref>A1, 7A2, 7B1, 7B2, Figs. <xref ref-type="fig" rid="F8">8</xref>A1, 8A2, 8B1, 8B2). Salichos & Rokas <xref rid="B41" ref-type="bibr">41</xref> similarly concluded that selecting genes with strong phylogenetic signal are very important in accurate reconstruction of ancient divergences.</p></sec><sec><title>Data partitioning</title><p>The effects of data partitioning and partition schemes on phylogeny reconstruction have been widely investigated [e.g., 93, 94]. Different partitioning schemes may have no effect at a certain level, but can result in strong nodal support for otherwise conflicting topologies at more inclusive levels <xref rid="B14" ref-type="bibr">14</xref>, <xref rid="B93" ref-type="bibr">93</xref>-<xref rid="B96" ref-type="bibr">96</xref>, suggesting that partitioning has most effect at deeper phylogenetic levels <xref rid="B5" ref-type="bibr">5</xref>. In this study, data partition has little influence except for minor changes in node supports.</p></sec><sec><title>Excluding 3rd codon position of protein-coding genes</title><p>The 3rd codon positions are sometimes excluded in phylogeny reconstruction, generally because this codon site can be highly saturated and therefore is considered less informative <xref rid="B58" ref-type="bibr">58</xref>, <xref rid="B93" ref-type="bibr">93</xref>, <xref rid="B97" ref-type="bibr">97</xref>. In the present study, only small topological differences resulted from excluding the 3rd codon positions of PCGs, the major ones being <italic>Pollenia</italic> clustering together with Oestridae rather than with the Tachinidae, and the Muscidae being monophyletic in the Bayesian tree (Fig. <xref ref-type="fig" rid="F7">7</xref>A3, Fig. <xref ref-type="fig" rid="F8">8</xref>A3). However, phylogenetic relationships within families vary, depending upon whether the 3rd codon positions are pruned. Testing nucleotide substitution saturation of PCGs revealed that 3rd codon positions of PCGs in the present study are not saturated, or at most showing partly saturation for transversions (Fig. <xref ref-type="fig" rid="F4">4</xref>). Interestingly, Caravas et al. <xref rid="B98" ref-type="bibr">98</xref> estimated the performance of 3rd codon positions of Diptera and found that they still resolved some recent clades within the Calyptratae. Taken together, these results indicate that the 3rd codon positions of PCGs are informative in calyptrate phylogeny reconstruction and should not be pruned.</p></sec><sec><title>tRNA genes</title><p>Calyptrate phylogenies based on datasets with and without tRNA genes are almost identical, except for slight differences in some node supports and branch lengths, irrespective of the analytic methods (i.e., with or without 3rd codon positions of PCGs, partitioned or not). Genetic divergence analysis also shows that tRNA genes are more conserved than other mitochondrial genes. Kumazawa et al. <xref rid="B99" ref-type="bibr">99</xref> proposed that tRNA genes may be useful for resolving deep splits that occurred some hundreds of millions of years ago. Since calyptrates are estimated to have appeared 70-55 million years ago <xref rid="B11" ref-type="bibr">11</xref>, <xref rid="B16" ref-type="bibr">16</xref>, <xref rid="B100" ref-type="bibr">100</xref>, the phylogenetic signal of tRNA genes in this group is not strong enough to help resolve calyptrate phylogeny.</p></sec><sec><title>Phylogenetic topology</title><p>The Calyptratae are considered “one of the most surely grounded monophyletic groups within the Schizophora” (<xref rid="B101" ref-type="bibr">101</xref>, see also <xref rid="B27" ref-type="bibr">27</xref>, <xref rid="B102" ref-type="bibr">102</xref>) based on morphological data, and phylogenies from molecular data have been in strong agreement <xref rid="B11" ref-type="bibr">11</xref>. The group has been subject to very extensive phylogenetic analyses, using both morphological and variable amounts of molecular data, e.g., <xref rid="B17" ref-type="bibr">17</xref>-<xref rid="B22" ref-type="bibr">22</xref>, <xref rid="B26" ref-type="bibr">26</xref>, <xref rid="B27" ref-type="bibr">27</xref>, <xref rid="B29" ref-type="bibr">29</xref>, <xref rid="B31" ref-type="bibr">31</xref>, <xref rid="B33" ref-type="bibr">33</xref>, <xref rid="B34" ref-type="bibr">34</xref>, <xref rid="B37" ref-type="bibr">37</xref>, <xref rid="B38" ref-type="bibr">38</xref>, <xref rid="B44" ref-type="bibr">44</xref>, <xref rid="B58" ref-type="bibr">58</xref>, <xref rid="B61" ref-type="bibr">61</xref>, <xref rid="B103" ref-type="bibr">103</xref>-<xref rid="B115" ref-type="bibr">115</xref>. However, some relationships within the Calyptratae remain controversial, primarily through differences in the selection of molecular markers, and the sample of taxa used for phylogeny reconstruction.</p><p>The favoured tree topologies in the present study (Figs. <xref ref-type="fig" rid="F7">7</xref>, <xref ref-type="fig" rid="F8">8</xref>) differ in some important respects from the previous study also obtained using whole mitogenomes <xref rid="B44" ref-type="bibr">44</xref>, and that obtained using a small data set of two mitochondrial and two nuclear genes <xref rid="B26" ref-type="bibr">26</xref>. The relationships at the family level are almost identical across all three studies, except for the placement of Sarcophagidae in the analysis using whole mitogenomes. In the present study, Sarcophagidae is sister group to the clade (Oestridae (Tachinidae + <italic>Pollenia</italic>)), while Nelson et al. <xref rid="B44" ref-type="bibr">44</xref> place the Sarcophagidae and Calliphoridae (except for <italic>Pollenia</italic>) as sister groups. This difference may be due to the limited representation of taxa from the Sarcophagidae: Nelson et al. <xref rid="B44" ref-type="bibr">44</xref> focus on the phylogeny within the Calliphoridae, and so the Sarcophagidae are represented by a single species, compared with 9 species representing two subfamilies in the present study.</p><p>A noticeable difference of these studies lies at the subfamily level within the Calliphoridae. With 11 subfamilies <xref rid="B33" ref-type="bibr">33</xref>, the non-monophyletic Calliphoridae represent a considerable challenge for calyptrate phylogeny reconstruction <xref rid="B26" ref-type="bibr">26</xref>, <xref rid="B33" ref-type="bibr">33</xref>, <xref rid="B44" ref-type="bibr">44</xref>. Calliphoridae are non-monophyletic in the present study, like in previous studies <xref rid="B11" ref-type="bibr">11</xref>, <xref rid="B17" ref-type="bibr">17</xref>, <xref rid="B26" ref-type="bibr">26</xref>, <xref rid="B44" ref-type="bibr">44</xref>, and combining these results the clade (Chrysomyinae, (Calliphorinae + Luciliinae)) appears to form a robust relationship, and both Mesembrinellinae and Polleninae are phylogenetically closer to the Tachinidae than to other calliphorids and would as such warrant separate status as valid families. The placement of Sarcophagidae and Rhiniidae (formerly Calliphoridae: Rhiniinae) by Kutty et al. <xref rid="B17" ref-type="bibr">17</xref> was not well supported in Marinho et al. <xref rid="B26" ref-type="bibr">26</xref>, highlighting how increasing the number of molecular markers helps produce more robust phylogenies.</p></sec></sec><sec sec-type="conclusions"><title>Conclusion</title><p>The mitogenome in general provides informative molecular markers in calyptrate phylogenetic research. Partitioning data by genes does not change the phylogenetic topology at the family level but improves some node supports. Similarly, the topology is hardly changed by including conservative tRNA genes, except for some slightly reduced node supports. Taxon sampling plays an important role in calyptrate phylogeny reconstruction, and more stable family-level relationships can be inferred by increased coverage. More taxa and nuclear genes should be selected in calyptrate phylogeny reconstruction in the future, in order to break long branches and improve resolution.</p><p>Family-level relationships within the Oestroidea are poorly understood and difficult to resolve. One of the more challenging aspects of resolving oestroid relationships is the non-monophyly of the traditional Calliphoridae <xref rid="B33" ref-type="bibr">33</xref>. Another is the position of the Oestridae, which is a small family of less than 200 species <xref rid="B116" ref-type="bibr">116</xref>, <xref rid="B117" ref-type="bibr">117</xref>, the larvae of which are obligate parasites of mammals. Solving the issue of bot fly ancestry is closely connected to establishing the phylogenetic relationships for the subgroups of the traditional Calliphoridae.</p></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="SM1"><caption><p>Supplementary Tables and Figures.</p></caption><media xlink:href="ijbsv12p0489s1.pdf"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec></body><back><ack><p>We are grateful to Drs. Jie Liu (Institute of Zoology, Chinese Academy of Sciences) and Eliana Buenaventura (Natural History Museum of Denmark, University of Copenhagen), Prof. Aibing Zhang and Miss Jie Qin (Capital Normal University) who gave us invaluable help during this study. We wish to extend our sincerest thanks to Mr. Zhe Zhao (Institute of Zoology, Chinese Academy of Sciences), Mr. Yuan Wang (Institute of Zoology, Chinese Academy of Sciences), and Dr. Xingyi Li (Third Military Medical University of Chinese P.L.A) for giving useful suggestions of phylogenetic analyses, and to Drs Kelly A. Meiklejohn (University of Florida, Gainesville, USA), Thomas J. Simonsen (Natural History Museum, London, UK) and Mark Eglar (University of Melbourne, Australia) for kindly providing valuable comments to the manuscript. We would also like to express our gratitude to the online information providers Diptera info (<ext-link ext-link-type="uri" xlink:href="http://mail.diptera.info/news.php">http://mail.diptera.info/news.php</ext-link>) and Discover Life (<ext-link ext-link-type="uri" xlink:href="http://www.discoverlife.org">http://www.discoverlife.org</ext-link>) for specimen pictures in our graphical abstract. This study was supported by the Fundamental Research Funds for the Central Universities (No. JC2015-04), the Program for New Century Excellent Talents in University (No. NCET-12-0783), Beijing Higher Education Young Elite Teacher Project (No. YETP0771), and the National Science Foundation of China (No. 31201741), all to DZ, and the Carlsberg Foundation (No. 2012_01_0433) to TP.</p></ack><glossary><title>Abbreviations</title><def-list><def-item><term id="GL1">ATP6</term><def><p>ATP synthase subunit 6 gene</p></def></def-item><def-item><term id="GL2">ATP8</term><def><p>ATP synthase subunit 8 gene</p></def></def-item><def-item><term id="GL3">COI</term><def><p>cytochrome c oxidase subunit I gene</p></def></def-item><def-item><term id="GL4">COII</term><def><p>cytochrome c oxidase subunit II gene</p></def></def-item><def-item><term id="GL5">COIII</term><def><p>cytochrome c oxidase subunit III gene</p></def></def-item><def-item><term id="GL6">CYTB</term><def><p>cytochrome b gene</p></def></def-item><def-item><term id="GL7">ML</term><def><p>Maximum Likelihood</p></def></def-item><def-item><term id="GL8">ND1</term><def><p>NADH dehydrogenase subunit 1 gene</p></def></def-item><def-item><term id="GL9">ND2</term><def><p>NADH dehydrogenase subunit 2 gene</p></def></def-item><def-item><term id="GL10">ND3</term><def><p>NADH dehydrogenase subunit 3 gene</p></def></def-item><def-item><term id="GL11">ND4</term><def><p>NADH dehydrogenase subunit 4 gene</p></def></def-item><def-item><term id="GL12">ND4L</term><def><p>NADH dehydrogenase subunit 4L gene</p></def></def-item><def-item><term id="GL13">ND5</term><def><p>NADH dehydrogenase subunit 5 gene</p></def></def-item><def-item><term id="GL14">ND6</term><def><p>NADH dehydrogenase subunit 6 gene</p></def></def-item><def-item><term id="GL15">PCGs</term><def><p>protein-coding genes</p></def></def-item><def-item><term id="GL16">lrRNA</term><def><p>large ribosomal RNA</p></def></def-item><def-item><term 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Black bars indicate the standard deviation.</p></caption><graphic xlink:href="ijbsv12p0489g002"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><p>Percentage of conserved sites (%cons) and percentage of positions experiencing gaps (%gaps) in the alignments of the 13 protein-coding genes.</p></caption><graphic xlink:href="ijbsv12p0489g003"></graphic></fig><fig id="F4" position="float"><label>Figure 4</label><caption><p>Nucleotide substitution saturation of each 13 PCGs, 1st & 2nd codon positions of PCGs, and 3rd codon positions of PCGs.</p></caption><graphic xlink:href="ijbsv12p0489g004"></graphic></fig><fig id="F5" position="float"><label>Figure 5</label><caption><p>Phylogeny of subgroup_1, inferred from mitochondrial datasets comprising 13 protein-coding genes, 2 rRNA genes, and concatenation of tRNA genes. A1, Bayesian tree inferred from not partitioned data. A2, Bayesian tree inferred from partitioned data. A3, Bayesian tree inferred from data excluding 3rd codon positions of PCGs. B1, ML tree inferred from not partitioned data. B2, ML tree inferred from partitioned data. B3, ML tree inferred from data excluding 3rd codon positions of PCGs. Numbers at nodes are posterior probabilities (Bayesian trees), and Bootstrap values (ML trees).</p></caption><graphic xlink:href="ijbsv12p0489g005"></graphic></fig><fig id="F6" position="float"><label>Figure 6</label><caption><p>Phylogeny of subgroup_1, inferred from mitochondrial datasets comprising 13 protein-coding genes and 2 rRNA genes. A1, Bayesian tree inferred from not partitioned data. A2, Bayesian tree inferred from partitioned data. A3, Bayesian tree inferred from data excluding 3rd codon positions of PCGs. B1, ML tree inferred from not partitioned data. B2, ML tree inferred from partitioned data. B3, ML tree inferred from data excluding 3rd codon positions of PCGs. Numbers at nodes are posterior probabilities (Bayesian trees), and Bootstrap values (ML trees).</p></caption><graphic xlink:href="ijbsv12p0489g006"></graphic></fig><fig id="F7" position="float"><label>Figure 7</label><caption><p>Phylogeny of subgroup_2, inferred from mitochondrial datasets comprising 13 protein-coding genes, 2 rRNA genes, and concatenation of tRNA genes. A1, Bayesian tree inferred from non-partitioned data. A2, Bayesian tree inferred from partitioned data. A3, Bayesian tree inferred from data excluding 3rd codon position of PCGs. B1, ML tree inferred from not partitioned data. B2, ML tree inferred from partitioned data. B3, ML tree inferred from data excluding 3rd codon positions of PCGs. Numbers at nodes are posterior probabilities (Bayesian trees), and Bootstrap values (ML trees).</p></caption><graphic xlink:href="ijbsv12p0489g007"></graphic></fig><fig id="F8" position="float"><label>Figure 8</label><caption><p>Phylogeny of subgroup_2, inferred from mitochondrial datasets comprising 13 protein-coding genes and 2 rRNA genes. A1, Bayesian tree inferred from not partitioned data. A2, Bayesian tree inferred from partitioned data. A3, Bayesian tree inferred from data excluding 3rd codon positions of PCGs. B1, ML tree inferred from not partitioned data. B2, ML tree inferred from partitioned data. B3, ML tree inferred from data excluding 3rd codon positions of PCGs. Numbers at nodes are posterior probabilities (Bayesian trees), and Bootstrap values (ML trees).</p></caption><graphic xlink:href="ijbsv12p0489g008"></graphic></fig><fig id="F9" position="float"><label>Figure 9</label><caption><p>Calyptrate mitochondrial gene k-scores calculated by Ktreedist, measuring overall differences in the relative branch length and topology of the phylogenetic trees generated by single protein-coding genes compared to the combined dataset.</p></caption><graphic xlink:href="ijbsv12p0489g009"></graphic></fig><table-wrap id="T1" position="float"><label>Table 1</label><caption><p>Summary of mitogenomes from Calyptratae, and two outgroup species.</p></caption><table frame="hsides" rules="groups"><thead valign="top"><tr><th rowspan="1" colspan="1">Superfamily</th><th rowspan="1" colspan="1">Family</th><th rowspan="1" colspan="1">Subfamily</th><th rowspan="1" colspan="1">Species</th><th rowspan="1" colspan="1">Locus</th><th rowspan="1" colspan="1">Reference</th></tr></thead><tbody valign="top"><tr><td rowspan="1" colspan="1">Tabanoidea</td><td rowspan="1" colspan="1">Tabanidae</td><td rowspan="1" colspan="1">Tabanidae</td><td rowspan="1" colspan="1"><italic>Cydistomyia duplonotata </italic><sup>*</sup></td><td rowspan="1" colspan="1">NC_008756</td><td rowspan="1" colspan="1">[14]</td></tr><tr><td rowspan="1" colspan="1">Ephydroidea</td><td rowspan="1" colspan="1">Drosophilidae</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"><italic>Drosophila melanogaster </italic><sup>*</sup></td><td rowspan="1" colspan="1">NC_024511</td><td rowspan="1" colspan="1">[42]</td></tr><tr><td rowspan="1" colspan="1">Oestroidea</td><td rowspan="1" colspan="1">Calliphoridae</td><td rowspan="1" colspan="1">Calliphorinae</td><td rowspan="1" colspan="1"><italic>Aldrichina grahami</italic></td><td rowspan="1" colspan="1">KP872701</td><td rowspan="1" colspan="1">[43]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Calliphorinae</td><td rowspan="1" colspan="1"><italic>Calliphora vicina</italic></td><td rowspan="1" colspan="1">NC_019639</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Cochliomyia hominivorax</italic></td><td rowspan="1" colspan="1">NC_002660</td><td rowspan="1" colspan="1">[45]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya albiceps</italic></td><td rowspan="1" colspan="1">NC_019631</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya bezziana</italic></td><td rowspan="1" colspan="1">NC_019632</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya megacephala</italic></td><td rowspan="1" colspan="1">NC_019633</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya pinguis</italic></td><td rowspan="1" colspan="1">NC_025338</td><td rowspan="1" colspan="1">[46]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya putoria</italic></td><td rowspan="1" colspan="1">NC_002697</td><td rowspan="1" colspan="1">[47]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya rufifacies</italic></td><td rowspan="1" colspan="1">NC_019634</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Chrysomya saffranea</italic></td><td rowspan="1" colspan="1">NC_019635</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Phormia regina</italic></td><td rowspan="1" colspan="1">NC_026668</td><td rowspan="1" colspan="1">[48]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Chrysomyinae</td><td rowspan="1" colspan="1"><italic>Protophormia terraenovae</italic></td><td rowspan="1" colspan="1">NC_019636</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Luciliinae</td><td rowspan="1" colspan="1"><italic>Hemipyrellia ligurriens</italic></td><td rowspan="1" colspan="1">NC_019638</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Luciliinae</td><td rowspan="1" colspan="1"><italic>Lucilia cuprina</italic></td><td rowspan="1" colspan="1">NC_019573</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Luciliinae</td><td rowspan="1" colspan="1"><italic>Lucilia porphyrina</italic></td><td rowspan="1" colspan="1">NC_019637</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Luciliinae</td><td rowspan="1" colspan="1"><italic>Lucilia sericata</italic></td><td rowspan="1" colspan="1">NC_009733</td><td rowspan="1" colspan="1">[49]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Polleniinae</td><td rowspan="1" colspan="1"><italic>Pollenia rudis</italic></td><td rowspan="1" colspan="1">JX913761</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophagidae</td><td rowspan="1" colspan="1">Paramacronychiinae</td><td rowspan="1" colspan="1"><italic>Wohlfahrtia magnifica</italic></td><td rowspan="1" colspan="1">—</td><td rowspan="1" colspan="1">Present study</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Ravinia pernix</italic></td><td rowspan="1" colspan="1">NC_026196</td><td rowspan="1" colspan="1">[50]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga africa</italic></td><td rowspan="1" colspan="1">NC_025944</td><td rowspan="1" colspan="1">[51]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga crassipalpis</italic></td><td rowspan="1" colspan="1">NC_026667</td><td rowspan="1" colspan="1">[52]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga impatiens</italic></td><td rowspan="1" colspan="1">NC_017605</td><td rowspan="1" colspan="1">[53]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga melanura</italic></td><td rowspan="1" colspan="1">NC_026112</td><td rowspan="1" colspan="1">[54]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga peregrina</italic></td><td rowspan="1" colspan="1">NC_023532</td><td rowspan="1" colspan="1">[55]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga portschinskyi</italic></td><td rowspan="1" colspan="1">NC_025574</td><td rowspan="1" colspan="1">[56]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Sarcophaginae</td><td rowspan="1" colspan="1"><italic>Sarcophaga similis</italic></td><td rowspan="1" colspan="1">NC_025573</td><td rowspan="1" colspan="1">[57]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Tachinidae</td><td rowspan="1" colspan="1">Exoristinae</td><td rowspan="1" colspan="1"><italic>Elodia flavipalpis</italic></td><td rowspan="1" colspan="1">NC_018118</td><td rowspan="1" colspan="1">[58]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Dexiinae</td><td rowspan="1" colspan="1"><italic>Rutilia goerlingiana</italic></td><td rowspan="1" colspan="1">NC_019640</td><td rowspan="1" colspan="1">[44]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Oestridae</td><td rowspan="1" colspan="1">Cuterebrinae</td><td rowspan="1" colspan="1"><italic>Dermatobia hominis</italic></td><td rowspan="1" colspan="1">NC_006378</td><td rowspan="1" colspan="1">[59]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Gasterophilinae</td><td rowspan="1" colspan="1"><italic>Gasterophilus pecorum</italic></td><td rowspan="1" colspan="1">—</td><td rowspan="1" colspan="1">Present study</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Hypodermatinae</td><td rowspan="1" colspan="1"><italic>Hypoderma lineatum</italic></td><td rowspan="1" colspan="1">NC_013932</td><td rowspan="1" colspan="1">[60]</td></tr><tr><td rowspan="1" colspan="1">Muscoid grade</td><td rowspan="1" colspan="1">Anthomyiidae</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"><italic>Delia platura</italic></td><td rowspan="1" colspan="1">KP901268</td><td rowspan="1" colspan="1">[61]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Fanniidae</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"><italic>Euryomma </italic>sp.</td><td rowspan="1" colspan="1">KP901269</td><td rowspan="1" colspan="1">[61]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Muscidae</td><td rowspan="1" colspan="1">Muscinae</td><td rowspan="1" colspan="1"><italic>Haematobia irritans</italic></td><td rowspan="1" colspan="1">NC_007102</td><td rowspan="1" colspan="1">[62]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Muscinae</td><td rowspan="1" colspan="1"><italic>Musca domestica</italic></td><td rowspan="1" colspan="1">NC_024855</td><td rowspan="1" colspan="1">[63]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Muscinae</td><td rowspan="1" colspan="1"><italic>Stomoxys calcitrans</italic></td><td rowspan="1" colspan="1">DQ533708</td><td rowspan="1" colspan="1">[62]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Reinwardtiinae</td><td rowspan="1" colspan="1"><italic>Muscina stabulans</italic></td><td rowspan="1" colspan="1">NC_026292</td><td rowspan="1" colspan="1">[64]</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">Scathophagidae</td><td rowspan="1" colspan="1">Scathophaginae</td><td rowspan="1" colspan="1"><italic>Scathophaga stercoraria</italic></td><td rowspan="1" colspan="1">NC_024856</td><td rowspan="1" colspan="1">[65]</td></tr></tbody></table><table-wrap-foot><fn><p><sup>*</sup> Species used as outgroups in subgroup_1.</p></fn></table-wrap-foot></table-wrap><table-wrap id="T2" position="float"><label>Table 2</label><caption><p>Summary of datasets used to perform phylogenetic analyses.</p></caption><table frame="hsides" rules="groups"><thead valign="top"><tr><th rowspan="1" colspan="1">Taxa</th><th rowspan="1" colspan="1">Dataset</th><th rowspan="1" colspan="1">Subanalyses</th><th rowspan="1" colspan="1">Models</th></tr></thead><tbody valign="top"><tr><td rowspan="6" colspan="1">subgroup_1 (40 species, 2 outgroups)</td><td rowspan="3" colspan="1">ALL: PCGs, rRNA genes, and a concatenation of tRNA genes.</td><td rowspan="1" colspan="1">Not partitioned</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Partitioned by genes</td><td rowspan="1" colspan="1">P1 (ND2, COI, COII, ATP8, ATP6, COIII, ND3, ND6, CYTB) GTR + I + G<break></break>P2 (ND5, ND4, ND4L, ND1) GTR + I + G<break></break>P3 (lrRNA, srRNA, tRNA) GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Without 3rd codon positions of PCGs</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="3" colspan="1">PCG&rRNA: PCGs, rRNA genes.</td><td rowspan="1" colspan="1">Not partitioned</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Partitioned by genes</td><td rowspan="1" colspan="1">P1 (ND2, COI, COII, ATP8, ATP6, COIII, ND3, ND6, CYTB) GTR + I + G<break></break>P2 (ND5, ND4, ND4L, ND1) GTR + I + G<break></break>P3 (lrRNA, srRNA) GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Without 3rd codon positions of PCGs</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="6" colspan="1">subgroup_2 (38 species, rooted using <italic>Euryomma</italic> as outgroup)</td><td rowspan="3" colspan="1">ALL: PCGs, rRNA genes, and a concatenation of tRNA genes.</td><td rowspan="1" colspan="1">Not partitioned</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Partitioned by genes</td><td rowspan="1" colspan="1">P1 (ND2, COI, COII, ATP8, ATP6, COIII, ND3, ND6, CYTB) GTR + I + G<break></break>P2 (ND5, ND4, ND4L, ND1) GTR + I + G<break></break>P3 (lrRNA, srRNA, tRNA) GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Without 3rd codon positions of PCGs</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="3" colspan="1">PCG&rRNA: PCGs, rRNA genes.</td><td rowspan="1" colspan="1">Not partitioned</td><td rowspan="1" colspan="1">GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Partitioned by genes</td><td rowspan="1" colspan="1">P1 (ND2, COI, COII, ATP8, ATP6, COIII, ND3, ND6, CYTB) GTR + I + G<break></break>P2 (ND5, ND4, ND4L, ND1) GTR + I + G<break></break>P3 (lrRNA, srRNA) GTR + I + G</td></tr><tr><td rowspan="1" colspan="1">Without 3rd codon positions of PCGs</td><td rowspan="1" colspan="1">GTR + I + G</td></tr></tbody></table></table-wrap><table-wrap id="T3" position="float"><label>Table 3</label><caption><p>Nucleotide composition of <italic>Gasterophilus pecorum </italic>(Fabricius) / <italic>Wohlfahrtia magnifica</italic> (Schiner).</p></caption><table frame="hsides" rules="groups"><thead valign="top"><tr><th rowspan="2" colspan="1">Region</th><th colspan="5" align="center" rowspan="1">Nucleotide composition (%)</th><th rowspan="2" colspan="1">AT-skew</th><th rowspan="2" colspan="1">GC-skew</th></tr><tr><th rowspan="1" colspan="1">T(U)</th><th rowspan="1" colspan="1">C</th><th rowspan="1" colspan="1">A</th><th rowspan="1" colspan="1">G</th><th rowspan="1" colspan="1">A+T</th></tr></thead><tbody valign="top"><tr><td rowspan="1" colspan="1">Whole genome</td><td rowspan="1" colspan="1">32.4 / N <sup>*</sup></td><td rowspan="1" colspan="1">18.9 / N</td><td rowspan="1" colspan="1">38.4 / N</td><td rowspan="1" colspan="1">10.3 / N</td><td rowspan="1" colspan="1">70.7 / N</td><td rowspan="1" colspan="1">0.08 / N</td><td rowspan="1" colspan="1">-0.29 / N</td></tr><tr><td rowspan="1" colspan="1">Protein-coding genes</td><td rowspan="1" colspan="1">39.5 / 43.3</td><td rowspan="1" colspan="1">16.2 / 12.8</td><td rowspan="1" colspan="1">29.0 / 31.3</td><td rowspan="1" colspan="1">15.3 / 12.6</td><td rowspan="1" colspan="1">68.5 / 74.6</td><td rowspan="1" colspan="1">-0.15 / -0.16</td><td rowspan="1" colspan="1">-0.03 / -0.01</td></tr><tr><td rowspan="1" colspan="1">1st codon position</td><td rowspan="1" colspan="1">33.9 / 36.6</td><td rowspan="1" colspan="1">14.6 / 12.3</td><td rowspan="1" colspan="1">30.1 / 31.6</td><td rowspan="1" colspan="1">21.3 / 19.5</td><td rowspan="1" colspan="1">64.0 / 68.2</td><td rowspan="1" colspan="1">-0.06 / -0.07</td><td rowspan="1" colspan="1">0.19 / 0.23</td></tr><tr><td rowspan="1" colspan="1">2nd codon position</td><td rowspan="1" colspan="1">45.9 / 46.3</td><td rowspan="1" colspan="1">20.2 / 19.5</td><td rowspan="1" colspan="1">19.4 / 20.1</td><td rowspan="1" colspan="1">14.5 / 14.0</td><td rowspan="1" colspan="1">65.3 / 66.4</td><td rowspan="1" colspan="1">-0.41 / -0.39</td><td rowspan="1" colspan="1">-0.16 / -0.16</td></tr><tr><td rowspan="1" colspan="1">3rd codon position</td><td rowspan="1" colspan="1">38.7 / 46.9</td><td rowspan="1" colspan="1">13.7 / 6.5</td><td rowspan="1" colspan="1">37.6 / 42.3</td><td rowspan="1" colspan="1">10.0 / 4.2</td><td rowspan="1" colspan="1">76.3 / 89.2</td><td rowspan="1" colspan="1">-0.01 / -0.05</td><td rowspan="1" colspan="1">-0.16 / -0.21</td></tr><tr><td rowspan="1" colspan="1">tRNA</td><td rowspan="1" colspan="1">38.1 / N</td><td rowspan="1" colspan="1">10.8 / N</td><td rowspan="1" colspan="1">37.4 / N</td><td rowspan="1" colspan="1">13.6 / N</td><td rowspan="1" colspan="1">75.5 / N</td><td rowspan="1" colspan="1">-0.01 / N</td><td rowspan="1" colspan="1">0.11 / N</td></tr><tr><td rowspan="1" colspan="1">lrRNA</td><td rowspan="1" colspan="1">42.1 / 41.5</td><td rowspan="1" colspan="1">6.9 / 6.4</td><td rowspan="1" colspan="1">33.3 / 38.8</td><td rowspan="1" colspan="1">17.6 / 13.3</td><td rowspan="1" colspan="1">75.4 / 80.3</td><td rowspan="1" colspan="1">-0.12 / -0.03</td><td rowspan="1" colspan="1">0.43 / 0.35</td></tr><tr><td rowspan="1" colspan="1">srRNA</td><td rowspan="1" colspan="1">38.2 / 37.5</td><td rowspan="1" colspan="1">9.3 / 8.5</td><td rowspan="1" colspan="1">34.1 / 37.7</td><td rowspan="1" colspan="1">18.4 / 16.3</td><td rowspan="1" colspan="1">72.3 / 75.2</td><td rowspan="1" colspan="1">-0.06 / 0.00</td><td rowspan="1" colspan="1">0.33 / 0.31</td></tr><tr><td rowspan="1" colspan="1">Control Region</td><td rowspan="1" colspan="1">45.1 / N</td><td rowspan="1" colspan="1">4.9 / N</td><td rowspan="1" colspan="1">35.8 / N</td><td rowspan="1" colspan="1">14.3 / N</td><td rowspan="1" colspan="1">80.8 / N</td><td rowspan="1" colspan="1">-0.12 / N</td><td rowspan="1" colspan="1">0.49 / 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