Molecular phylogeny of the megadiverse insect infraorder Bibionomorpha sensu lato (Diptera)

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Abstract

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.

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Most cited references 68

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The general stochastic model of nucleotide substitution.

F. Rodríguez, J L Oliver, A. Marin … (1990)

DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.

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Counting animal species with DNA barcodes: Canadian insects

Paul Hebert, Sujeevan Ratnasingham, Evgeny V. Zakharov … (2016)

Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy. This article is part of the themed issue ‘From DNA barcodes to biomes’.

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Evolution and phylogenetic utility of CAD (rudimentary) among Mesozoic-aged Eremoneuran Diptera (Insecta).

K Moulton, Brian M Wiegmann (2004)

We sequenced nearly the entire carbomoylphosphate synthase (CPS) domain of CAD, or rudimentary, (ca. 4 kb) from 29 species of flies representing all major clades within Eremoneura, or higher flies, and several orthorrhaphous brachyceran outgroups. We compared these sequences with orthologs from Anopheles gambiae and Drosophila melanogaster to assess structure, compositional bias, and phylogenetic utility. CAD is large (6.6+ kb), complex (comprised of three major and myriad minor functional domains) and relatively free of introns, extreme nucleotide bias (except third codon positions), and large hypervariable regions. The CPS domain possesses moderate levels of nonsynonymous divergence among taxa of intermediate evolutionary age and conveys considerable phylogenetic signal. Phylogenetic analysis of CPS sequences under varying methods and assumptions resulted in well-resolved, strongly supported trees concordant with many traditional ideas about higher dipteran phylogeny and with prior inferences from 28S rDNA. The most robustly supported major eremoneuran clades were Cyclorrhapha, Platypezoidea, Eumuscomorpha, Empidoidea, Atelestidae, Empidoidea exclusive of Atelestidae, Hybotidae s.l., Microphoridae+Dolichopodidae, and Empididae s. str. Because CAD is ubiquitous, apparently single copy (at least within holometabolous insects), readily obtained from several insect orders using primers described herein, and exhibits considerable phylogenetic utility, it should have wide applicability in insect molecular systematics.

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Author and article information

Contributors

Jan Ševčík

Journal

Journal ID (nlm-ta): PeerJ

Journal ID (iso-abbrev): PeerJ

Journal ID (publisher-id): peerj

Journal ID (pmc): peerj

Title: PeerJ

Publisher: PeerJ Inc. (San Francisco, USA )

ISSN (Electronic): 2167-8359

Publication date (Electronic): 18 October 2016

Publication date Collection: 2016

Volume: 4

Electronic Location Identifier: e2563

Affiliations

[1 ]Faculty of Science, Department of Biology and Ecology, University of Ostrava , Ostrava, Czech Republic

[2 ]Pacific Northwest Diptera Research Lab , Corvallis, OR, United States of America

[3 ]Faculty of Science, Department of Botany and Zoology, Masaryk University , Brno, Czech Republic

[4 ]Station Linné , Färjestaden, Sweden

Article

Publisher ID: 2563

DOI: 10.7717/peerj.2563

PMC ID: 5075709

PubMed ID: 27781163

SO-VID: f6181ebc-5201-4b15-8d4c-73646caa0c32

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

History

Date received : 11 July 2016

Date accepted : 13 September 2016

Funding

Funded by: Ministry of Education, Youth and Sports Life of the Czech Republic

Funded by: University of Ostrava

Award ID: SGS21/PřF/2013

Award ID: SGS28/PřF/2014

Award ID: SGS28/PřF/2015

Funded by: Structural Funds of the European Union

Award ID: CZ.1.05/2.1.00/03.0100

Funded by: National Feasibility Programme I of the Czech Republic

Award ID: LO1208

Funded by: US National Science Foundation

Award ID: DEB-0542864

Funded by: National Research Council of Thailand

Funded by: Department of National Parks, Wildlife and Plant Conservation

Funded by: Swedish Species Information Centre

Award ID: dha 2014-150 4.3

Funded by: Willi Hennig Society

This study was mostly supported by the Ministry of Education, Youth and Sports Life of the Czech Republic through the Institutional Support of research organisation (University of Ostrava). Various parts of our research activities were supported by the SGS21/PřF/2013, SGS28/PřF/2014 and SGS28/PřF/2015 projects of the University of Ostrava and by the projects CZ.1.05/2.1.00/03.0100 (IET) financed by the Structural Funds of the European Union and LO1208 of the National Feasibility Programme I of the Czech Republic. A part of the material examined was collected within the “Thailand Inventory Group for Entomological Research (TIGER) project” funded by US National Science Foundation grant DEB-0542864 to M Sharkey and B Brown, and supported by the National Research Council of Thailand and the Department of National Parks, Wildlife and Plant Conservation, Thailand, who gave permission for research and the collection of specimens. M Jaschhof is funded by the Swedish Species Information Centre within the framework of the Swedish Taxonomy Initiative (dha 2014-150 4.3). Sponsorship was provided by the Willi Hennig Society that made TNT v.2.0 available. CIPRES, an NSF-funded resource for phyloinformatics and computational phylogenetics, was used to conduct some of the analyses. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Molecular phylogeny of the megadiverse insect infraorder Bibionomorpha sensu lato (Diptera)

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Taxonomic intelligence

Most cited references 68

The general stochastic model of nucleotide substitution.

Counting animal species with DNA barcodes: Canadian insects

Evolution and phylogenetic utility of CAD (rudimentary) among Mesozoic-aged Eremoneuran Diptera (Insecta).

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