Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)
Identifieur interne : 000111 ( Pmc/Curation ); précédent : 000110; suivant : 000112Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)
Auteurs : Dong Zhang [République populaire de Chine] ; Liping Yan [République populaire de Chine] ; Ming Zhang [République populaire de Chine] ; Hongjun Chu [République populaire de Chine] ; Jie Cao [République populaire de Chine] ; Kai Li [République populaire de Chine] ; Defu Hu [République populaire de Chine] ; Thomas Pape [Danemark]Source :
- 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 wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Yan, Liping" sort="Yan, Liping" uniqKey="Yan L" first="Liping" last="Yan">Liping Yan</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Ming" sort="Zhang, Ming" uniqKey="Zhang M" first="Ming" last="Zhang">Ming Zhang</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Chu, Hongjun" sort="Chu, Hongjun" uniqKey="Chu H" first="Hongjun" last="Chu">Hongjun Chu</name><affiliation wicri:level="1"><nlm:aff id="A3">3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang</wicri:regionArea></affiliation></author><author><name sortKey="Cao, Jie" sort="Cao, Jie" uniqKey="Cao J" first="Jie" last="Cao">Jie Cao</name><affiliation wicri:level="1"><nlm:aff id="A4">4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang</wicri:regionArea></affiliation></author><author><name sortKey="Li, Kai" sort="Li, Kai" uniqKey="Li K" first="Kai" last="Li">Kai Li</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Hu, Defu" sort="Hu, Defu" uniqKey="Hu D" first="Defu" last="Hu">Defu Hu</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Pape, Thomas" sort="Pape, Thomas" uniqKey="Pape T" first="Thomas" last="Pape">Thomas Pape</name><affiliation wicri:level="1"><nlm:aff id="A2">2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Danemark</country><wicri:regionArea>2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen</wicri:regionArea></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><idno type="wicri:Area/Pmc/Curation">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 wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Yan, Liping" sort="Yan, Liping" uniqKey="Yan L" first="Liping" last="Yan">Liping Yan</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Ming" sort="Zhang, Ming" uniqKey="Zhang M" first="Ming" last="Zhang">Ming Zhang</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Chu, Hongjun" sort="Chu, Hongjun" uniqKey="Chu H" first="Hongjun" last="Chu">Hongjun Chu</name><affiliation wicri:level="1"><nlm:aff id="A3">3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang</wicri:regionArea></affiliation></author><author><name sortKey="Cao, Jie" sort="Cao, Jie" uniqKey="Cao J" first="Jie" last="Cao">Jie Cao</name><affiliation wicri:level="1"><nlm:aff id="A4">4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang</wicri:regionArea></affiliation></author><author><name sortKey="Li, Kai" sort="Li, Kai" uniqKey="Li K" first="Kai" last="Li">Kai Li</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Hu, Defu" sort="Hu, Defu" uniqKey="Hu D" first="Defu" last="Hu">Defu Hu</name><affiliation wicri:level="1"><nlm:aff id="A1">1. School of Nature Conservation, Beijing Forestry University, Beijing, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>1. School of Nature Conservation, Beijing Forestry University, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Pape, Thomas" sort="Pape, Thomas" uniqKey="Pape T" first="Thomas" last="Pape">Thomas Pape</name><affiliation wicri:level="1"><nlm:aff id="A2">2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Danemark</country><wicri:regionArea>2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen</wicri:regionArea></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><floats-group><fig id="F1" position="float"><label>Figure 1</label><caption><p>Mitochondrial genome maps of <italic>Gasterophilus pecorum</italic> (Fabricius) and <italic>Wohlfahrtia magnifica</italic> (Schiner). Gene names without underline indicate that these genes are coded on (+) strand, while those with underline are on the (-) strand. Transfer RNA (tRNA) genes are designated by single-letter amino acid codes. White colored regions indicate those failed to sequence.</p></caption><graphic xlink:href="ijbsv12p0489g001"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><p>Comparisons of average mitochondrial gene <italic>p</italic>-distances at different taxonomic levels in 38 species of Calyptratae. 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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