Please use this identifier to cite or link to this item: https://doi.org/10.1186/s12915-020-00944-8
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dc.titleBeyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics
dc.contributor.authorBayless, Keith M
dc.contributor.authorTrautwein, Michelle D
dc.contributor.authorMeusemann, Karen
dc.contributor.authorShin, Seunggwan
dc.contributor.authorPetersen, Malte
dc.contributor.authorDonath, Alexander
dc.contributor.authorPodsiadlowski, Lars
dc.contributor.authorMayer, Christoph
dc.contributor.authorNiehuis, Oliver
dc.contributor.authorPeters, Ralph S
dc.contributor.authorMEIER,RUDOLF
dc.contributor.authorSUJATHA NARAYANAN KUTTY
dc.contributor.authorLiu, Shanlin
dc.contributor.authorZhou, Xin
dc.contributor.authorMisof, Bernhard
dc.contributor.authorYeates, David K
dc.contributor.authorWiegmann, Brian M
dc.date.accessioned2021-03-30T06:15:18Z
dc.date.available2021-03-30T06:15:18Z
dc.date.issued2021-02-08
dc.identifier.citationBayless, Keith M, Trautwein, Michelle D, Meusemann, Karen, Shin, Seunggwan, Petersen, Malte, Donath, Alexander, Podsiadlowski, Lars, Mayer, Christoph, Niehuis, Oliver, Peters, Ralph S, MEIER,RUDOLF, SUJATHA NARAYANAN KUTTY, Liu, Shanlin, Zhou, Xin, Misof, Bernhard, Yeates, David K, Wiegmann, Brian M (2021-02-08). Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics. BMC BIOLOGY 19 (1). ScholarBank@NUS Repository. https://doi.org/10.1186/s12915-020-00944-8
dc.identifier.issn1741-7007
dc.identifier.issn1741-7007
dc.identifier.urihttps://scholarbank.nus.edu.sg/handle/10635/187900
dc.description.abstractBackground: The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge. Results: Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila’s superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the ‘Modified Oviscapt Clade’ containing Tephritoidea, Nerioidea, and other families, and the ‘Cleft Pedicel Clade’ containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data. Conclusions: Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.
dc.language.isoen
dc.publisherBMC
dc.sourceElements
dc.subjectScience & Technology
dc.subjectLife Sciences & Biomedicine
dc.subjectBiology
dc.subjectLife Sciences & Biomedicine - Other Topics
dc.subjectDiptera
dc.subjectPhylogenomics
dc.subjectTranscriptomes
dc.subjectDrosophilidae
dc.subjectTephritidae
dc.subjectSEQUENCE ALIGNMENTS
dc.subjectHIERARCHICAL CATALOG
dc.subjectTREE
dc.subjectPHYLOGENY
dc.subjectDIPTERA
dc.subjectMODEL
dc.subjectTOOL
dc.subjectIMPACT
dc.subjectFLY
dc.subjectDIVERSIFICATION
dc.typeArticle
dc.date.updated2021-03-30T05:01:43Z
dc.contributor.departmentDEPT OF BIOLOGICAL SCIENCES
dc.contributor.departmentTROPICAL MARINE SCIENCE INSTITUTE
dc.description.doi10.1186/s12915-020-00944-8
dc.description.sourcetitleBMC BIOLOGY
dc.description.volume19
dc.description.issue1
dc.published.statePublished
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