Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly
Identifieur interne : 000781 ( Istex/Corpus ); précédent : 000780; suivant : 000782Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly
Auteurs : Sujatha Narayanan Kutty ; Thomas Pape ; Brian M. Wiegmann ; Rudolf MeierSource :
- Systematic Entomology [ 0307-6970 ] ; 2010-10.
Abstract
The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).
Url:
DOI: 10.1111/j.1365-3113.2010.00536.x
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<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title><author><name sortKey="Kutty, Sujatha Narayanan" sort="Kutty, Sujatha Narayanan" uniqKey="Kutty S" first="Sujatha Narayanan" last="Kutty">Sujatha Narayanan Kutty</name><affiliation><mods:affiliation>Department of Biological Sciences, National University of Singapore, Singapore</mods:affiliation></affiliation></author><author><name sortKey="Pape, Thomas" sort="Pape, Thomas" uniqKey="Pape T" first="Thomas" last="Pape">Thomas Pape</name><affiliation><mods:affiliation>Natural History Museum of Denmark, University of Copenhagen, Denmark</mods:affiliation></affiliation></author><author><name sortKey="Wiegmann, Brian M" sort="Wiegmann, Brian M" uniqKey="Wiegmann B" first="Brian M." last="Wiegmann">Brian M. 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Wiegmann</name><affiliation><mods:affiliation>Department of Entomology, North Carolina State University, Raleigh, NC, U.S.A.</mods:affiliation></affiliation></author><author><name sortKey="Meier, Rudolf" sort="Meier, Rudolf" uniqKey="Meier R" first="Rudolf" last="Meier">Rudolf Meier</name><affiliation><mods:affiliation>Department of Biological Sciences, National University of Singapore, Singapore</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Systematic Entomology</title><idno type="ISSN">0307-6970</idno><idno type="eISSN">1365-3113</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2010-10">2010-10</date><biblScope unit="volume">35</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="614">614</biblScope><biblScope unit="page" to="635">635</biblScope></imprint><idno type="ISSN">0307-6970</idno></series><idno type="istex">877E7D8EFEF3470CE03D43DBC6B67587891E789C</idno><idno type="DOI">10.1111/j.1365-3113.2010.00536.x</idno><idno type="ArticleID">SYEN536</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0307-6970</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>SUJATHA NARAYANAN KUTTY</name><affiliations><json:string>Department of Biological Sciences, National University of Singapore, Singapore</json:string></affiliations></json:item><json:item><name>THOMAS PAPE</name><affiliations><json:string>Natural History Museum of Denmark, University of Copenhagen, Denmark</json:string></affiliations></json:item><json:item><name>BRIAN M. WIEGMANN</name><affiliations><json:string>Department of Entomology, North Carolina State University, Raleigh, NC, U.S.A.</json:string></affiliations></json:item><json:item><name>RUDOLF MEIER</name><affiliations><json:string>Department of Biological Sciences, National University of Singapore, Singapore</json:string></affiliations></json:item></author><articleId><json:string>SYEN536</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).</abstract><qualityIndicators><score>8</score><pdfVersion>1.3</pdfVersion><pdfPageSize>595.276 x 790.866 pts</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>0</keywordCount><abstractCharCount>2409</abstractCharCount><pdfWordCount>12809</pdfWordCount><pdfCharCount>91848</pdfCharCount><pdfPageCount>22</pdfPageCount><abstractWordCount>339</abstractWordCount></qualityIndicators><title>Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title><genre><json:string>article</json:string></genre><host><volume>35</volume><publisherId><json:string>SYEN</json:string></publisherId><pages><total>22</total><last>635</last><first>614</first></pages><issn><json:string>0307-6970</json:string></issn><issue>4</issue><genre><json:string>journal</json:string></genre><language><json:string>unknown</json:string></language><eissn><json:string>1365-3113</json:string></eissn><title>Systematic Entomology</title><doi><json:string>10.1111/(ISSN)1365-3113</json:string></doi></host><publicationDate>2010</publicationDate><copyrightDate>2010</copyrightDate><doi><json:string>10.1111/j.1365-3113.2010.00536.x</json:string></doi><id>877E7D8EFEF3470CE03D43DBC6B67587891E789C</id><score>0.06991698</score><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/877E7D8EFEF3470CE03D43DBC6B67587891E789C/fulltext/pdf</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/877E7D8EFEF3470CE03D43DBC6B67587891E789C/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/877E7D8EFEF3470CE03D43DBC6B67587891E789C/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><availability><p>© 2010 The Authors. Systematic Entomology © 2010 The Royal Entomological Society</p></availability><date>2010</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title><author xml:id="author-1"><persName><forename type="first">SUJATHA NARAYANAN</forename><surname>KUTTY</surname></persName><affiliation>Department of Biological Sciences, National University of Singapore, Singapore</affiliation></author><author xml:id="author-2"><persName><forename type="first">THOMAS</forename><surname>PAPE</surname></persName><affiliation>Natural History Museum of Denmark, University of Copenhagen, Denmark</affiliation></author><author xml:id="author-3"><persName><forename type="first">BRIAN M.</forename><surname>WIEGMANN</surname></persName><affiliation>Department of Entomology, North Carolina State University, Raleigh, NC, U.S.A.</affiliation></author><author xml:id="author-4"><persName><forename type="first">RUDOLF</forename><surname>MEIER</surname></persName><note type="correspondence"><p>Correspondence: Rudolf Meier, Department of Biological Sciences, National University of Singapore, Singapore. E‐mail:</p></note><affiliation>Department of Biological Sciences, National University of Singapore, Singapore</affiliation></author></analytic><monogr><title level="j">Systematic Entomology</title><idno type="pISSN">0307-6970</idno><idno type="eISSN">1365-3113</idno><idno type="DOI">10.1111/(ISSN)1365-3113</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2010-10"></date><biblScope unit="volume">35</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="614">614</biblScope><biblScope unit="page" to="635">635</biblScope></imprint></monogr><idno type="istex">877E7D8EFEF3470CE03D43DBC6B67587891E789C</idno><idno type="DOI">10.1111/j.1365-3113.2010.00536.x</idno><idno type="ArticleID">SYEN536</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2010</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).</p></abstract></profileDesc><revisionDesc><change when="2010-10">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/877E7D8EFEF3470CE03D43DBC6B67587891E789C/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1365-3113</doi><issn type="print">0307-6970</issn><issn type="electronic">1365-3113</issn><idGroup><id type="product" value="SYEN"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="SYSTEMATIC ENTOMOLOGY">Systematic Entomology</title></titleGroup></publicationMeta><publicationMeta level="part" position="10104"><doi origin="wiley">10.1111/sen.2010.35.issue-4</doi><numberingGroup><numbering type="journalVolume" number="35">35</numbering><numbering type="journalIssue" number="4">4</numbering></numberingGroup><coverDate startDate="2010-10">October 2010</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="3" status="forIssue"><doi origin="wiley">10.1111/j.1365-3113.2010.00536.x</doi><idGroup><id type="unit" value="SYEN536"></id></idGroup><countGroup><count type="pageTotal" number="22"></count></countGroup><titleGroup><title type="tocHeading1">Original Articles</title></titleGroup><copyright>© 2010 The Authors. Systematic Entomology © 2010 The Royal Entomological Society</copyright><eventGroup><event type="firstOnline" date="2010-08-04"></event><event type="publishedOnlineAcceptedOrEarlyUnpaginated" date="2010-08-04"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:3.1.3 standalone mode:FullText" date="2012-04-16"></event><event type="publishedOnlineFinalForm" date="2010-09-15"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-02-10"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-11-04"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="614">614</numbering><numbering type="pageLast" number="635">635</numbering></numberingGroup><correspondenceTo>Rudolf Meier, Department of Biological Sciences, National University of Singapore, Singapore. E‐mail: <email>dbsmr@nus.edu.sg</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:SYEN.SYEN536.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Accepted 6 May 2010, First published online 4 August 2010</unparsedEditorialHistory><countGroup><count type="figureTotal" number="2"></count><count type="tableTotal" number="1"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="152"></count></countGroup><titleGroup><title type="main">Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title><title type="shortAuthors"><i>S. N. Kutty</i> et al.</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1"><personName><givenNames>SUJATHA NARAYANAN</givenNames><familyName>KUTTY</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2"><personName><givenNames>THOMAS</givenNames><familyName>PAPE</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a3"><personName><givenNames>BRIAN M.</givenNames><familyName>WIEGMANN</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a1" corresponding="yes"><personName><givenNames>RUDOLF</givenNames><familyName>MEIER</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="SG"><unparsedAffiliation>Department of Biological Sciences, National University of Singapore, Singapore</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="DK"><unparsedAffiliation>Natural History Museum of Denmark, University of Copenhagen, Denmark</unparsedAffiliation></affiliation><affiliation xml:id="a3" countryCode="US"><unparsedAffiliation>Department of Entomology, North Carolina State University, Raleigh, NC, U.S.A.</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p>Supporting Information</p><p>Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x.</p><p><b>Figure S1.</b> Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree.</p><p><b>Figure S2.</b> Likelihood tree from the maximum likelihood analysis using garli.</p><p><b>Figure S3.</b> Bayesian tree (mrbayes) with posterior probabilities.</p><p><b>Table S1.</b> List of species used in the study with author names.</p><p><b>Table S2.</b> Genetic data from earlier publications used for this study.</p><p><b>Table S3.</b> List of calyptrate species deleted from the dataset after using phyutility.</p><p>Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:03076970:media:syen536:SYEN_536_sm_FigS1-3"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:03076970:media:syen536:SYEN_536_sm_TableS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:03076970:media:syen536:SYEN_536_sm_TableS2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:03076970:media:syen536:SYEN_536_sm_TableS3"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><p>The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome <i>c</i> oxidase subunit I and cytochrome <i>b</i>) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly</title></titleInfo><name type="personal"><namePart type="given">SUJATHA NARAYANAN</namePart><namePart type="family">KUTTY</namePart><affiliation>Department of Biological Sciences, National University of Singapore, Singapore</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">THOMAS</namePart><namePart type="family">PAPE</namePart><affiliation>Natural History Museum of Denmark, University of Copenhagen, Denmark</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">BRIAN M.</namePart><namePart type="family">WIEGMANN</namePart><affiliation>Department of Entomology, North Carolina State University, Raleigh, NC, U.S.A.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">RUDOLF</namePart><namePart type="family">MEIER</namePart><affiliation>Department of Biological Sciences, National University of Singapore, Singapore</affiliation><description>Correspondence: Rudolf Meier, Department of Biological Sciences, National University of Singapore, Singapore. E‐mail: </description><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2010-10</dateIssued><edition>Accepted 6 May 2010, First published online 4 August 2010</edition><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">2</extent><extent unit="tables">1</extent><extent unit="references">152</extent></physicalDescription><abstract lang="en">The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).</abstract><relatedItem type="host"><titleInfo><title>Systematic Entomology</title></titleInfo><genre type="journal">journal</genre><note type="content"> Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Supporting Information Additional Supporting Information may be found in the online version of this article under the DOI reference: DOI: 10.1111/j.1365‐3113.2010.00536.x. Figure S1. Subtree illustrating topological differences within Oestroidea between the likelihood (left) and Bayesian (right) tree. Figure S2. Likelihood tree from the maximum likelihood analysis using garli. Figure S3. Bayesian tree (mrbayes) with posterior probabilities. Table S1. List of species used in the study with author names. Table S2. Genetic data from earlier publications used for this study. Table S3. List of calyptrate species deleted from the dataset after using phyutility. Please note: Neither the Editors nor Wiley‐Blackwell are responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.Supporting Info Item: Supporting info item - Supporting info item - Supporting info item - Supporting info item - </note><identifier type="ISSN">0307-6970</identifier><identifier type="eISSN">1365-3113</identifier><identifier type="DOI">10.1111/(ISSN)1365-3113</identifier><identifier type="PublisherID">SYEN</identifier><part><date>2010</date><detail type="volume"><caption>vol.</caption><number>35</number></detail><detail type="issue"><caption>no.</caption><number>4</number></detail><extent unit="pages"><start>614</start><end>635</end><total>22</total></extent></part></relatedItem><identifier type="istex">877E7D8EFEF3470CE03D43DBC6B67587891E789C</identifier><identifier type="DOI">10.1111/j.1365-3113.2010.00536.x</identifier><identifier type="ArticleID">SYEN536</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2010 The Authors. 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