Molecular phylogeny of the megadiverse insect infraorder Bibionomorpha sensu lato (Diptera)
Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
27781163
PubMed Central
PMC5075709
DOI
10.7717/peerj.2563
PII: 2563
Knihovny.cz E-zdroje
- Klíčová slova
- Lower Diptera, Molecular markers, Phylogenetic analysis, Sciaroidea, Systematics,
- Publikační typ
- časopisecké články MeSH
The phylogeny of the insect infraorder Bibionomorpha (Diptera) is reconstructed based on the combined analysis of three nuclear (18S, 28S, CAD) and three mitochondrial (12S, 16S, COI) gene markers. All the analyses strongly support the monophyly of Bibionomorpha in both the narrow (sensu stricto) and the broader (sensu lato) concepts. The major lineages of Bibionomorpha sensu lato (Sciaroidea, Bibionoidea, Anisopodoidea, and Scatopsoidea) and most of the included families are supported as monophyletic groups. Axymyiidae was not found to be part of Bibionomorpha nor was it found to be its sister group. Bibionidae was paraphyletic with respect to Hesperinidae and Keroplatidae was paraphyletic with respect to Lygistorrhinidae. The included Sciaroidea incertae sedis (except Ohakunea Edwards) were found to belong to one clade, but the relationships within this group and its position within Sciaroidea require further study.
Faculty of Science Department of Biology and Ecology University of Ostrava Ostrava Czech Republic
Faculty of Science Department of Botany and Zoology Masaryk University Brno Czech Republic
Pacific Northwest Diptera Research Lab Corvallis OR United States of America
Zobrazit více v PubMed
Amorim DS. A phylogenetic analysis of the basal groups of Bibionomorpha, with a critical reanalysis of the wing vein homology. Revista Brasileira de Biologia. 1993;52:379–399.
Amorim DS, Grimaldi DA. Valeseguyidae, a new family of Diptera in the Scatopsoidea, with a new genus in Cretaceous amber from Myanmar. Systematic Entomology. 2006;31:508–516. doi: 10.1111/j.1365-3113.2006.00326.x. DOI
Amorim DS, Rindal E. Phylogeny of the Mycetophiliformia, with proposal of the subfamilies Heterotrichinae, Ohakuneinae, and Chiletrichinae for the Rangomaramidae (Diptera, Bibionomorpha) Zootaxa. 2007;1535:1–92.
Amorim DS, Tozoni SHS. Phylogenetic and biogeographic analysis of the Anisopodoidea (Diptera, Bibionomorpha), with an area cladogram for intercontinental relationships. Revista Brasileira de Entomologia. 1994;38:517–543.
Amorim DS, Yeates D. Pesky gnats: ridding dipteran classification of the “Nematocera”. Studia Dipterologica. 2006;13:3–9.
Beckenbach AT. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly. Genome Biology and Evolution. 2012;4:89–101. doi: 10.1093/gbe/evr131. PubMed DOI PMC
Belshaw R, Lopez-Vaamonde C, Degerli N, Quicke DLJ. Paraphyletic taxa and taxonomic chaining: evaluating the classification of braconine wasps (Hymenoptera: Braconidae) using 28S D2-3 rDNA sequences and morphological characters. Biological Journal of the Linnean Society. 2001;73:411–424. doi: 10.1006/bijl.2001.0539. DOI
Bertone MA, Courtney GW, Wiegmann BM. Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes. Systematic Entomology. 2008;33:668–687. doi: 10.1111/j.1365-3113.2008.00437.x. DOI
Blagoderov V, Grimaldi D. Fossil Sciaroidea (Diptera) in Cretaceous ambers, exclusive of Cecidomyiidae, Sciaridae, and Keroplatidae. American Museum Novitates. 2004;3433:1–76.
Blagoderov V, Hippa H, Ševčík J. Asiorrhina, a new Oriental genus of Lygistorrhinidae (Diptera: Sciaroidea) and its phylogenetic position. Zootaxa. 2009;2295:31–45.
Blaschke-Berthold U. Bonner zoologische Monographien 34. Zoologisches Forschungsinstitut und Museum Alexander Koenig; Bonn: 1994. Anatomie und Phylogenie der Bibionomorpha (Insecta: Diptera)
Brown BV, Borkent A, Cumming JM, Wood DM, Woodley NE, Zumbado M. Manual of central american diptera: volume 1. National Research Council Research Press; Ottawa, Ontario: 2009.
Campbell BC, Ross GF, Woodward TE. Paraphyly of Homoptera and Auchenorrhyncha inferred from 18S rDNA nucleotide sequence. Systematic Entomology. 1995;20:175–194. doi: 10.1111/j.1365-3113.1995.tb00090.x. DOI
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution. 2000;17:540–552. PubMed
Chandler P. Heterotricha Loew and allied genera (Diptera: Sciaroidea): offshoots of the stem group of Mycetophilidae and/or Sciaridae? Annales de la Société Entomologique de France (Nouvelle série) 2002;38:101–144.
Cook CE, Austin JJ, Disney RHL. A mitochondrial 12S and 16S rRNA phylogeny of critical genera of Phoridae (Diptera) and related families of Aschiza. Zootaxa. 2004;593:1–11.
Edwards FW. A note on the “New Zealand glow-worm” (Diptera, Mycetophilidae) Annals and Magazine of Natural History. 1924;14:175–179.
Evenhuis NL. Catalogue of the fossil flies of the world (Insecta: Diptera) Backhuys Publishers; Leiden: 1994.
Fitzgerald SJ. D. Phil. Thesis. 2004. Evolution and classification of Bibionidae (Diptera: Bibionomorpha)
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology. 1994;3:294–297. PubMed
Gadagkar SR, Kumar S. Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Molecular Biology and Evolution. 2005;22:2139–2141. doi: 10.1093/molbev/msi212. PubMed DOI
Gagné RJ. The plant-feeding gall midges of North America. Cornell University Press; Ithaca and London: 1989.
Gagné RJ, Jaschhof M. A Catalog of the Cecidomyiidae (Diptera) of the world. 2014. Third edition. Digital version 2. http://www.ars.usda.gov/SP2UserFiles/Place/12454900/Gagne_2014_World_Cecidomyiidae_Catalog_3rd_Edition.pdf . PubMed
Gagné RJ, Moser JC. The North American gall midges (Diptera: Cecidomyiidae) of hackberries (Cannabaceae: Celtis spp.) Memoirs of the American Entomological Institute. 2013;49:1–103.
Grimaldi DA, Engel NS, Nascimbene PC. Fossiliferous Cretaceous amber from Myanmar (Burma): its rediscovery, biotic diversity, and paleontological significance. American Museum Novitates. 2002;3361:1–71.
Hebert PDN, Ratnasingham S, Zakharov EV, Telfer AC, Levesque-Beaudin V, Milton MA, Pedersen S, Jannetta P, DeWaard JR. Counting animal species with DNA barcodes: Canadian insects. Philosophical Transactions of the Royal Society B. 2016;371:20150333. doi: 10.1098/rstb.2015.0333. PubMed DOI PMC
Hennig W. Flügelgeäder und System der Dipteren unter Berücksichtigung der aus dem Mesozoikum beschriebenen Fossilien. Beiträge zur Entomologie. 1954;4:245–388.
Hennig W. Ordnung Diptera (Zweiflügler) Handbuch der Zoologie. 1973;4(2)/1(Lfg. 20):1–227.
Hippa H, Mattsson I, Vilkamaa P. New taxa of the Lygistorrhinidae (Diptera: Sciaroidea) and their implications for a phylogenetic analysis of the family. Zootaxa. 2005;960:1–34.
Hippa H, Ševčík J. Notes on Nepaletricha (Diptera: Sciaroidea incertae sedis), with description of three new species from India and Vietnam. Acta Entomologica Musei Nationalis Pragae. 2014;54:729–739.
Hippa H, Vilkamaa P. The genus Sciarotricha gen. n. (Sciaridae) and the phylogeny of recent and fossil Sciaroidea (Diptera) Insect Systematics, Evolution. 2005;36:121–144. doi: 10.1163/187631205788838492. DOI
Hippa H, Vilkamaa P. Phylogeny of the Sciaroidea (Diptera): the implication of additional taxa and character data. Zootaxa. 2006;1132:63–68.
Hoffeins C, Hoffeins HW. Diptera in Baltic amber—the most frequent order within arthropod inclusions. In: Dorchin N, Kotrba M, Mengual X, Menzel F, editors. 8th international congress of dipterology, Potsdam. 2014. p. 140 p.
Huelsenbeck JP, Ronquist FR. MrBayes: Bayesian inference of phylogeny. Biometrics. 2001;17:754–755. doi: 10.1093/bioinformatics/17.8.754. PubMed DOI
Jaschhof M. Catotrichinae subfam. n.: a re-examination of higher classification in gall midges (Diptera: Cecidomyiidae) Entomological Science. 2001;3:639–652.
Jaschhof M. Phylogeny classification of the Sciaroidea (Diptera: Bibionomorpha): Where do we stand after Amorim & Rindal (2007)? BeiträGe zur Entomologie. 2011;61:455–463.
Jaschhof M, Didham RK. Rangomaramidae fam. nov. from New Zealand and implications for the phylogeny of the Sciaroidea (Diptera: Bibionomorpha) Studia Dipterologica Supplement. 2002;11:1–60.
Jaschhof M, Hippa H. Sciaroid but not sciarid: a review of the genus Ohakunea Tonnoir, Edwards, with the description of two new species (Insecta: Diptera: Bibionomorpha) Entomologische Abhandlungen. 2003;60:23–44.
Jaschhof M, Jaschhof C. Catotrichinae (Diptera: Cecidomyiidae) in Tasmania, with the description of Trichotoca edentula gen. et sp. n. Zootaxa. 2008;1966:53–61.
Jaschhof M, Jaschhof C. The Wood Midges (Diptera: Cecidomyiidae: Lestremiinae) of Fennoscandia and Denmark. Studia Dipterologica Supplement. 2009;18:1–333.
Jaschhof M, Jaschhof C. The Porricondylinae (Diptera: Cecidomyiidae) of Sweden, with notes on extralimital species. Studia Dipterologica Supplement. 2013;20:1–392.
Jaschhof M, Jaschhof C, Viklund B, Kallweit U. On the morphology and systematic position of Sciarosoma borealis Chandler, based on new material from Fennoscandia (Diptera: Sciaroidea) Studia Dipterologica. 2006;12(2005):231–241.
Kallweit U. Lygistorrhina Skuse has branched from the Keroplatidae (Diptera: Sciaroidea)—a new perspective on the phylogenetic relationships in the keroplatid group of fungus gnats. In: Dorchin N, Kotrba M, Mengual X, Menzel F, editors. 8th international congress of dipterology, Potsdam. 2014. p. 156 p.
Katana A, Kwiatowski J, Spalik K, Zakryś B, Szalacha E, Szymańska H. Phylogenetic position of Koliella (Chlorophyta) as inferred from nuclear and chloroplast small subunit rDNA. Journal of Phycology. 2001;37:443–451. doi: 10.1046/j.1529-8817.2001.037003443.x. DOI
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution. 2013;30:772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC
Lambkin CL, Sinclair BJ, Pape T, Courtney GW, Skevington JH, Meier R, Yeates DK, Blagoderov V, Wiegmann BM. The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence. Systematic Entomology. 2013;38:164–179. doi: 10.1111/j.1365-3113.2012.00652.x. DOI
Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research. 2011;39:475–478. doi: 10.1093/nar/gkr201. PubMed DOI PMC
Matile L. Recherches sur la systématique et l’évolution des Keroplatidae (Diptera, Mycetophiloidea) Mémoires du Muséum National d’Histoire Naturelle Paris Sér A, Zoologie. 1990;148:1–654.
Matile L. Phylogeny and evolution of the larval diet in the Sciaroidea (Diptera, Bibionomorpha) since the Mesozoic. The origin of biodiversity in insects: phylogenetic tests of evolutionary scenarios. Mémoires du Muséum National d’Histoire Naturelle Paris Sér A, Zoologie. 1997;173:273–303.
Michelsen V. Neodiptera: new insights into the adult morphology and higher level phylogeny of Diptera (Insecta) Zoological Journal of the Linnean Society. 1996;117:71–102. doi: 10.1111/j.1096-3642.1996.tb02149.x. DOI
Michelsen V. Wood gnats of the genus Sylvicola (Diptera, Anisopodidae): taxonomic status, family assignment, and review of nominal species described by J. C. Fabricius. Tijdschrift voor Entomologie. 1999;142:69–75.
Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010; 2010. pp. 1–8.
Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, Von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TKF, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X. Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014;346:763–767. doi: 10.1126/science.1257570. PubMed DOI
Moulton JK, Wiegmann BM. Evolution and phylogenetic utility of CAD (rudimentary) among Mesozoic-aged Eremoneuran Diptera (Insecta) Molecular Phylogenetics and Evolution. 2004;31:363–378. doi: 10.1016/S1055-7903(03)00284-7. PubMed DOI
Nylander JAA. MrModeltest v2.2 [online] 2004. Program distributed by the author, Evolutionary Biology Centre, Uppsala University.
Oosterbroek P, Courtney G. Phylogeny of the nematocerous families of Diptera (Insecta) Zoological Journal of the Linnean Society. 1995;115:267–311. doi: 10.1006/zjls.1995.0080. DOI
Pape T, Bickel D, Meier R, editors. Diptera diversity: status, challenges and tools. Koninklijke Brill; Leiden: 2009.
Papp L, Ševčík J. Sciarokeroplatinae, a new subfamily of Keroplatidae (Diptera) Acta Zoologica Academiae Scientiarum Hungaricae. 2005;51:113–123.
Pinto LG, Amorim D. Morfologia e análise filogenética. Ribeirão Preto: Holos; 2000. Bibionidae (Diptera: Bibionomorpha) (in Portuguese)
Rindal E, Søli GEE, Bachmann L. Molecular phylogeny of the fungus gnat family Mycetophilidae (Diptera, Mycetophiliformia) Systematic Entomology. 2009;34:524–532. doi: 10.1111/j.1365-3113.2009.00474.x. DOI
Rodriguez F, Oliver JL, Marin A, Medina JR. The general stochastic model of nucleotide substitution. Journal of Theoretical Biology. 1990;142:485–501. doi: 10.1016/S0022-5193(05)80104-3. PubMed DOI
Roháček J, Tóthová A, Vaňhara J. Phylogeny and affiliation of European Anthomyzidae (Diptera) based on mitochondrial 12S and 16S rRNA. Zootaxa. 2009;2054:49–58.
Rohdendorf BB. The historical development of two-winged insects. Trudy Paleontologiceskogo Instituta. 1964;100:1–311. (in Russian)
Rohdendorf BB. In: The historical development of Diptera [transl. from Russian] Hocking B, Oldroyd H, Ball GE, editors. University of Alberta Press; Edmonton: 1974.
Rohdendorf BB. The classification and phylogeny of the Diptera. In: Scarlato OA, Gorodkov KB, editors. Systematics and evolution of the Diptera (Insecta) Zoological Institute Russian Academy of Sciences; Leningrad: 1977. (A collection of scientific works). (in Russian)
Ševčík J, Kaspřák D, Mantič M, Ševčíková T, Tóthová A. Molecular phylogeny of the fungus gnat family Diadocidiidae and its position within the infraorder Bibionomorpha (Diptera) Zoologica Scripta. 2014;43:370–378. doi: 10.1111/zsc.12059. DOI
Ševčík J, Kaspřák D, Tóthová A. Molecular phylogeny of fungus gnats (Diptera: Mycetophilidae) revisited: position of Manotinae, Metanepsiini, and other enigmatic taxa as inferred from multigene analysis. Systematic Entomology. 2013;38:654–660. doi: 10.1111/syen.12023. DOI
Shin S, Jung S, Menzel F, Heller K, Lee H, Lee S. Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats. Molecular Phylogenetics and Evolution. 2013;66:833–846. doi: 10.1016/j.ympev.2012.11.008. PubMed DOI
Søli GEE. The adult morphology of Mycetophilidae (s.str.), with a tentative phylogeny of the family (Diptera, Sciaroidea) Entomologica Scandinavica Supplement. 1997;50:5–55.
Spencer M, Susko E, Roger AJ. Likelihood, parsimony, and heterogeneous evolution. Molecular Biology and Evolution. 2005;22:1161–1164. doi: 10.1093/molbev/msi123. PubMed DOI
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–2690. doi: 10.1093/bioinformatics/btl446. PubMed DOI
Thompson FC. Notes on the genus Lygistorrhina Skuse with the description of the first Nearctic species (Diptera: Mycetophiloidea) Proceedings of the Entomological Society of Washington. 1975;77:434–445.
Tuomikoski R. Systematic position of Lygistorrhina Skuse (Diptera, Mycetophiloidea) Annales Entomologici Fennici. 1966;32:254–260.
Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim J-W, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, Wheeler BM, Peterson KJ, Pape T, Sinclair BJ, Skevington JH, Blagoderov V, Caravas J, Kutty SN, Schmidt-Ott U, Kampmeier GE, Thompson FC, Grimaldi DA, Beckenbach AT, Courtney GW, Friedrich M, Meier R, Yeates DK. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences of the United States of America. 2011;108:5690–5695. doi: 10.1073/pnas.1012675108. PubMed DOI PMC
Winkler IS, Blaschke JD, Davis DJ, Stireman JO, O’Hara JE, Cerretti P, Moulton JK. Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae) Molecular Phylogenetics and Evolution. 2015;88:38–54. doi: 10.1016/j.ympev.2015.03.021. PubMed DOI
Wood DM, Borkent A. Phylogeny and Classification of the Nematocera. In: McAlpine JF, Peterson BV, Shewell GE, Teskey HJ, Vockeroth JR, Wood DM, editors. Manual of Nearctic Diptera. Vol. 3. Monograph No. 27. Research Branch, Agriculture Canada; Ottawa: 1989. pp. 1333–1370.
Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. Journal of Heredity. 2001;92:371–373. doi: 10.1093/jhered/92.4.371. PubMed DOI
Zaitzev A. Anatomia pischevaritelnogo trakta lichinok nizshich micetofiloidnych dvukrylych (Diptera, Mycetophiloidea) v sviazi s ich troficheskoi specializaciei. [Anatomy of the digestive system of the larvae of lower mycetophiloid flies (Diptera, Mycetophiloidea) in connection with their trophic specialisation.] Biologicheskie Nauki. 1983;4:38–43.
Zaitzev A. Osnovnye etapy specializacii rotovych aparatov lichinok micetofiloidnych dvukrylych (Diptera, Mycetophiloidea). [Main steps in specialisation of larval mouthparts of mycetophiloid flies (Diptera, Mycetophiloidea).] Biologicheskie Nauki. 1984;10:38–46.
Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems