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Kjærandsen J. Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library. INSECTS 2022; 13:insects13020147. [PMID: 35206721 PMCID: PMC8879535 DOI: 10.3390/insects13020147] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022]
Abstract
Simple Summary DNA barcoding is a method by which a specific region of the mitochondrial genome is used to quantify genetic distances within and between animal species. Most DNA barcodes of the world are assembled on the Barcode of Life online database BoldSystems (BOLD). There, machine-generated barcode index numbers (BINs) are automatically assigned to clusters of specimens thought to represent species. I review the current state of DNA barcoding of the superfamily Sciaroidea, a diverse insect group consisting of close to 16,000 described fly species in eight families. To date, over 1.2 million specimens of Sciaroidea have been barcoded and the 56,648 assigned BINs on BOLD already represent 3.5 times the number of described species. Still, 95% of the BINs have currently no associated scientific name and very little effort has been put into building a quality-checked reference library where named species are linked to the BINs on BOLD. In the Nordic region, however, substantial progress is made towards building a complete reference library. While DNA barcoding has tremendous potential for advancing the knowledge for many diverse groups of insects, its potential will never be fully reached absent more engagement of trained taxonomists to build voucher collections, curate the reference libraries, and describe new species. Abstract DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.
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Affiliation(s)
- Jostein Kjærandsen
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, P.O. Box 6050 Langnes, NO-9037 Tromsø, Norway
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Okuyama Y, Okamoto T, Kjaerandsen J, Kato M. Bryophytes facilitate outcrossing of Mitella by functioning as larval food for pollinating fungus gnats. Ecology 2018; 99:1890-1893. [PMID: 29889299 DOI: 10.1002/ecy.2364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Yudai Okuyama
- Tsukuba Botanical Garden, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, 305-0005, Japan
| | - Tomoko Okamoto
- Laboratory of Insect Ecology, Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Jostein Kjaerandsen
- Tromsø University Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Makoto Kato
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo, Kyoto, 606-8501, Japan
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Salmela J, Suuronen A, Kaunisto KM. New and poorly known Holarctic species of Boletina Staeger, 1840 (Diptera, Mycetophilidae). Biodivers Data J 2016:e7218. [PMID: 26929712 PMCID: PMC4759439 DOI: 10.3897/bdj.4.e7218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/15/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The genus Boletina is a species rich group of fungus gnats. Members of the genus are mainly known from temperate, boreal and arctic biomes. Phylogeny of the genus is still poorly resolved, dozens of species are insufficiently described and undescribed species are often discovered, especially from samples taken from the boreal zone. NEW INFORMATION Four new species are described. Boletina valteri Salmela sp.n. (Finland), Boletina kullervoi Salmela sp.n. (Finland), B. hyperborea Salmela sp.n. (Finland, Norway, Sweden, Canada) and B. nuortti Salmela sp.n. (Finland). Boletina arctica Holmgren is redescribed and reported for the first time from the Canadian high arctic zone. Boletina borealis Zetterstedt and B. birulai Lundström are reported for the first time from Canada. Boletina subnitidula Sasakawa (syn. n.) is proposed as a junior synonym of B. pallidula Edwards.
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Affiliation(s)
- Jukka Salmela
- Natural Heritage Services (Metsähallitus), Rovaniemi, Finland; Zoological Museum, Department of Biology, University of Turku, Finland
| | - Anna Suuronen
- University of Jyväskylä, Dept. of Biological and Environmental Sciences, Jyväskylä, Finland; Jyväskylä University Museum, University of Jyväskylä, Jyväskylä, Finland
| | - Kari M Kaunisto
- Zoological Museum, Department of Biology, University of Turku, Turku, Finland
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Jürgenstein S, Kurina O, Põldmaa K. The Mycetophilaruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data. Zookeys 2015:15-51. [PMID: 26167119 PMCID: PMC4492204 DOI: 10.3897/zookeys.508.9814] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/27/2015] [Indexed: 11/12/2022] Open
Abstract
European species of the Mycetophilaruficollis group are compared on the basis of morphology and sequences of mitochondrial cytochrome oxidase subunit one (COI) and the ITS2 region of nuclear ribosomal DNA. The study represents the first evaluation of morphology-based species delimitation of closely related fungus gnat species by applying molecular information. Detailed descriptions and illustrations of the male terminalia are presented along with a key for the identification of all nine European species of the group. Phylogenetic analyses of molecular data generally supported the morphological species discrimination. The barcoding region of COI superseded ITS2 rDNA in resolving species. In the COI barcoding region interspecific differences ranged from 2.9 to 10.6% and the intraspecific distance from 0.08 to 0.8%. Only COI data distinguished between the similar and closely related Mycetophilaichneumonea and Mycetophilauninotata of which the latter was observed to include cryptic species. The host range of some species is suggested to be narrower than previously considered and to depend on the forest type. Presented evidence indicates the importance of analysing sequence data of morphologically very similar mycetophages reared from identified host fungi for elucidating species delimitation as well as their geographic and host ranges. New country records, viz. Estonia for Mycetophilaevanida, Georgia for Mycetophilaichneumonea, Mycetophilaidonea and Mycetophilaruficollis, and Norway for Mycetophilastrobli, widen the known distribution ranges of these species.
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Affiliation(s)
- Siiri Jürgenstein
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi st 5D, 51014 Tartu, ESTONIA
| | - Olavi Kurina
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi st 5D, 51014 Tartu, ESTONIA
| | - Kadri Põldmaa
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Ravila 14a, 50411 Tartu, ESTONIA
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Kurina O, Õunap E, Põldmaa K. Two new Neuratelia Rondani (Diptera, Mycetophilidae) species from Western Palaearctic: a case of limited congruence between morphology and DNA sequence data. Zookeys 2015:105-29. [PMID: 25931957 PMCID: PMC4410159 DOI: 10.3897/zookeys.496.9315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/31/2015] [Indexed: 11/12/2022] Open
Abstract
Two new Mycetophilidae species, Neurateliajabalmoussae sp. n. and Neurateliasalmelai sp. n. are described on the basis of material collected from Lebanon, Estonia and Finland. Detailed figures of male terminalia and photographs of general facies are provided along with discussions of their morphological distinction from sibling species. For the first time molecular characters are used to distinguish new fungus gnat species. Molecular analysis relies on cytochrome oxidase subunit one (COI) but has additionally been corroborated by information from the 28S and ITS2 regions of nuclear ribosomal DNA. Situations where morphological and molecular data provide conflicting evidence for species delimitation are discussed. A new country record from Georgia is provided for Neurateliacaucasica.
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Affiliation(s)
- Olavi Kurina
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi st 5D, 51014 Tartu, ESTONIA
| | - Erki Õunap
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi st 5D, 51014 Tartu, ESTONIA ; Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, ESTONIA
| | - Kadri Põldmaa
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Ravila 14a, 50411 Tartu, ESTONIA
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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. Mol Phylogenet Evol 2012; 66:833-46. [PMID: 23159893 DOI: 10.1016/j.ympev.2012.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/18/2022]
Abstract
The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group+Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated "new subfamily"); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter+rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats.
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Affiliation(s)
- Seunggwan Shin
- Insect Biosystematics Laboratory, Seoul National University, Seoul 151-921, Republic of Korea.
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Martinsson S, Kjærandsen J. Katatopygia gen. n., a monophyletic branch segregated from Boletina (Diptera, Mycetophilidae). Zookeys 2012; 175:37-67. [PMID: 22451790 PMCID: PMC3307347 DOI: 10.3897/zookeys.175.2388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/01/2012] [Indexed: 11/24/2022] Open
Abstract
The genus Katatopygiagen. n. is proposed for the Boletina erythropyga/punctus-group that was first introduced by Garrett (1924, 1925) and currently comprises eight described species. Molecular studies have strongly indicated that this group forms a monophyletic sister-group to a clade consisting of all other Boletina, Coelosia and Gnoriste, and its monophyly is supported by morphological data as well. The new genus includes the following species: Katatopygia antoma (Garrett, 1924), comb. n., Katatopygia antica (Garrett, 1924), comb. n., Katatopygia erythropyga (Holmgren, 1883), comb. n.,Katatopygia hissarica (Zaitzev & Polevoi, 2002), comb. n., Katatopygia magna (Garrett, 1925), comb. n., Katatopygia laticauda (Saigusa, 1968), comb. n., Katatopygia neoerythropyga (Zaitzev & Polevoi, 2002), comb. n. andKatatopygia sahlbergi (Lundström, 1906), comb. n., all transferred from Boletina. Katatopygia sahlbergi is found to be a senior synonym of Boletina punctus Garrett, 1925, syn. n. A phylogeny based on morphological data and using parsimony analysis yielded four most parsimonious trees where the new genus is retrieved as monophyletic with high support. Katatopygia neoerythropyga is found to be the sister-taxon to all other species that form two clades, one with Katatopygia sahlbergi-like species and one with Katatopygia erythropyga-like species. A key to males of Katatopygia is provided.
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Affiliation(s)
- Svante Martinsson
- Department of Zoology, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden
| | - Jostein Kjærandsen
- Museum of Zoology, Department of Biology, Lund University, Helgonavägen 3, SE-223 62 Lund, Sweden
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