1
|
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.
Collapse
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
| |
Collapse
|
2
|
Kurina O. A contribution towards checklist of fungus gnats (Diptera, Diadocidiidae, Ditomyiidae, Bolitophilidae, Keroplatidae, Mycetophilidae) in Georgia, Transcaucasia. Zookeys 2021; 1026:69-142. [PMID: 33850419 PMCID: PMC8018941 DOI: 10.3897/zookeys.1026.63749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/03/2022] Open
Abstract
The fungus gnats of Georgia are studied based on 2682 specimens collected from 57 localities during 2011–2019. Altogether, 245 species are recorded including four species of Bolitophilidae, three species of Diadocidiidae, two species of Ditomyiidae, 34 species of Keroplatidae and 202 species of Mycetophilidae. 230 and 188 species are recorded from Georgia and the whole of Transcaucasia for the first time, respectively. Three new species – Sciophilageorgei sp. nov., Leiakatae sp. nov. and Anatellametae sp. nov. – are described including detailed illustrations of the male terminalia. Photographs are provided for an additional 38 species to highlight a variability of their general facies. Combined with earlier published data, the number of fungus gnat species in Georgia is set at 246. The estimated diversity of fungus gnats in Georgia is calculated using non-parametric methods and discussed with respect to other Western Palaearctic regions.
Collapse
Affiliation(s)
- Olavi Kurina
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi st 5 D, 51006 Tartu, Estonia Estonian University of Life Sciences Tartu Estonia
| |
Collapse
|
3
|
Tummeleht L, Jürison M, Kurina O, Kirik H, Jeremejeva J, Viltrop A. Diversity of Diptera Species in Estonian Pig Farms. Vet Sci 2020; 7:E13. [PMID: 31979423 PMCID: PMC7157211 DOI: 10.3390/vetsci7010013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/25/2022] Open
Abstract
In light of the African swine fever outbreaks in Estonian pig farms during the past few years, the question of the vector potential of Diptera in the pig farm environment has risen. However, the arthropod fauna of the pig farm environment is currently not well established. Hence, the aim of this study was to clarify the species diversity in pig farms. In total, 22 Diptera species or species groups were found in Estonian pig farms. There were altogether 186,701 individual arthropods collected, from which 96.6% (180,444) belonged to the order of true flies (Insecta: Diptera). The remaining 3.4% were from other insect orders, arachnids, or just damaged and unidentifiable specimens. The activity density and diversity of dipterans differed significantly between 12 sampled farms but not throughout the sampling period. The present study is amongst the few to provide a large-scale overview of pig-farm-associated Diptera in the temperate climate zone.
Collapse
Affiliation(s)
- Lea Tummeleht
- Institute of Veterinary Medicine & Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.J.); (A.V.)
| | - Margret Jürison
- Institute of Agriculture & Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, EE-51006 Tartu, Estonia; (M.J.); (O.K.); (H.K.)
| | - Olavi Kurina
- Institute of Agriculture & Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, EE-51006 Tartu, Estonia; (M.J.); (O.K.); (H.K.)
| | - Heli Kirik
- Institute of Agriculture & Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, EE-51006 Tartu, Estonia; (M.J.); (O.K.); (H.K.)
| | - Julia Jeremejeva
- Institute of Veterinary Medicine & Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.J.); (A.V.)
| | - Arvo Viltrop
- Institute of Veterinary Medicine & Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.J.); (A.V.)
| |
Collapse
|
4
|
Lu J, Zhang Y, Chen H. Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species. PeerJ 2018; 6:e5160. [PMID: 30202640 PMCID: PMC6129143 DOI: 10.7717/peerj.5160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022] Open
Abstract
The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.
Collapse
Affiliation(s)
- Jinming Lu
- Department of Entomology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuan Zhang
- Department of Entomology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hongwei Chen
- Department of Entomology, South China Agricultural University, Guangzhou, Guangdong, China
| |
Collapse
|
5
|
Koskinen J, Roslin T, Nyman T, Abrego N, Michell C, Vesterinen EJ. Finding flies in the mushroom soup: Host specificity of fungus-associated communities revisited with a novel molecular method. Mol Ecol 2018; 28:190-202. [PMID: 30040155 DOI: 10.1111/mec.14810] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 12/24/2022]
Abstract
Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities. Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.
Collapse
Affiliation(s)
- Janne Koskinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tommi Nyman
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Nerea Abrego
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Craig Michell
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Eero J Vesterinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Biodiversity Unit, University of Turku, Turku, Finland
| |
Collapse
|
6
|
Salmela J, Kolcsár LP. New and poorly known Palaearctic fungus gnats (Diptera, Sciaroidea). Biodivers Data J 2017:e11760. [PMID: 28325987 PMCID: PMC5345105 DOI: 10.3897/bdj.5.e11760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/01/2017] [Indexed: 01/23/2023] Open
Abstract
Background Fungus gnats (Sciaroidea) are a globally species rich group of lower Diptera. In Europe, Fennoscandian peninsula in particular holds a notable diversity, ca. 1000 species, of which 10 % are still unnamed. Fungus gnats are predominantly terrestrial insects, but some species dwell in wetland habitats. New information Eight new fungus gnat species, belonging to the families Keroplatidae (Orfeliaboreoalpina Salmela sp.n.) and Mycetophilidae (Sciophilaholopaineni Salmela sp.n., S.curvata Salmela sp.n., Boletinasasakawai Salmela & Kolcsár sp.n., B.norokorpii Salmela & Kolcsár sp.n., Phroniasompio Salmela sp.n., P.reducta Salmela sp.n., P.prolongata Salmela sp.n.), are described. Four of the species are known from Fennoscandia only whilst two are supposed to have boreo-alpine disjunct ranges, i.e. having populations in Fennoscandia and the Central European Alps. One of the species probably has a boreal range (Finnish Lapland and Central Siberia). Type material of Boletinacurta Sasakawa & Kimura from Japan was found to consist of two species, and a further species close to these taxa is described from Finland. Phroniaelegantula Hackman is redescribed and reported for the first time from Norway. DNA barcodes are provided for the first time for five species.
Collapse
Affiliation(s)
- Jukka Salmela
- Parks & Wildlife Finland (Metsähallitus), Rovaniemi, Finland; Biodiversity Unit, University of Turku, Turku, Finland
| | | |
Collapse
|
7
|
Põldmaa K, Kaasik A, Tammaru T, Kurina O, Jürgenstein S, Teder T. Polyphagy on unpredictable resources does not exclude host specialization: insects feeding on mushrooms. Ecology 2016; 97:2824-2833. [PMID: 27859105 DOI: 10.1002/ecy.1526] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 03/08/2016] [Accepted: 06/22/2016] [Indexed: 11/08/2022]
Abstract
The degree of ecological specialization plays a crucial role in shaping the structure and functioning of communities. However, comparing specialization within and among groups of organisms is complicated by both methodological issues and conceptual and terminological inconsistencies. Environmental predictability has been considered a key determinant of specialization though empirical evidence is still limited. Fungi and their insect consumers provide a poorly studied but promising system to measure host specialization and test the predictability hypothesis. In this study, we systematically sampled mushrooms in North European boreal forest, and reared total samples of fungivores colonizing the fruitbodies. Due to the unpredictable nature of mushrooms as a resource, low levels of host specialization can be predicted for these insects, which have indeed widely been considered polyphagous. Contrary to expectations, the majority of the studied fungus gnats were found not to exploit their host taxa indiscriminately. Not only were some mushroom taxa never colonized, the infestation rate of acceptable hosts also differed in most of these fungivores. Gnat species themselves formed continua with respect to the estimates of the degree of specialization, derived from parametric individual-based analyses of presence-absence data. In most cases, host use was best explained by models in which the hosts were classified at genus level, with limited support to specialization to particular host species, families, or orders. Indeed, most of the common fungivores appeared to preferentially use various species from one or a few mushroom genera while occasionally feeding on members of other host taxa. This pattern has likely evolved as a compromise between selective forces stemming from host unpredictability and taxon-specific chemical profiles of the mushrooms. Our study highlights the multidimensional nature of ecological specialization: a high number of acceptable hosts does not preclude considerable discrimination among members of the available resource pool. Such situations can only be revealed by individual-based analyses capable of capturing differences in partner-to-partner interaction intensities.
Collapse
Affiliation(s)
- Kadri Põldmaa
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Ravila 14a, Tartu, 50411, Estonia
| | - Ants Kaasik
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Toomas Tammaru
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Olavi Kurina
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu, 51014, Estonia
| | - Siiri Jürgenstein
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu, 51014, Estonia
| | - Tiit Teder
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| |
Collapse
|
8
|
Ševčík J, Kaspřák D, Rulik B. A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae). Zookeys 2016; 549:127-43. [PMID: 26843833 PMCID: PMC4727484 DOI: 10.3897/zookeys.549.6925] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 11/23/2015] [Indexed: 12/04/2022] Open
Abstract
A new species of Docosia Winnertz, Docosia dentata sp. n., is described and illustrated, based on a single male specimen collected in Muránska planina National Park in Central Slovakia. DNA sequences (COI, COII, CytB, and ITS2) are included and compared for 13 species of Docosia. There was found only little congruence between the molecular results and previous scarce data about interspecific relationships based on morphology. The COI and CytB gene markers showed the highest interspecific gene distances while ITS2 showed the lowest ones. An updated key to the 23 Central European species of Docosia is also presented.
Collapse
Affiliation(s)
- Jan Ševčík
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Chittussiho 10, CZ-710 00 Ostrava, Czech Republic; Silesian Museum, Nádražní okruh 31, CZ-746 01 Opava, Czech Republic
| | - David Kaspřák
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Chittussiho 10, CZ-710 00 Ostrava, Czech Republic
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitaetsforschung, Adenauerallee 160, D-53113 Bonn, Germany
| |
Collapse
|