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1. A molecular-based identification resource for the arthropods of Finland

Author

Roslin, T. (Tomas), Somervuo, P. (Panu), Pentinsaari, M. (Mikko), Hebert, P. D. (Paul D. N.), Agda, J. (Jireh), Ahlroth, P. (Petri), Anttonen, P. (Perttu), Aspi, J. (Jouni), Blagoev, G. (Gergin), Blanco, S. (Santiago), Chan, D. (Dean), Clayhills, T. (Tom), deWaard, J. (Jeremy), deWaard, S. (Stephanie), Elliot, T. (Tyler), Elo, R. (Riikka), Haapala, S. (Sami), Helve, E. (Eero), Ilmonen, J. (Jari), Hirvonen, P. (Petri), Ho, C. (Chris), Itämies, J. (Juhani), Ivanov, V. (Vladislav), Jakovlev, J. (Jevgeni), Juslen, A. (Aino), Jussila, R. (Reijo), Kahanpää, J. (Jere), Kaila, L. (Lauri), Kaitila, J.-P. (Jari-Pekka), Kakko, A. (Ari), Kakko, I. (Iiro), Karhu, A. (Ali), Karjalainen, S. (Sami), Kjaerandsen, J. (Jostein), Koskinen, J. (Janne), Laasonen, E. M. (Erkki M.), Laasonen, L. (Leena), Laine, E. (Erkka), Lampila, P. (Petri), Levesque-Beaudin, V. (Valerie), Lu, L. (Liuqiong), Lähteenaro, M. (Meri), Majuri, P. (Pekka), Malmberg, S. (Sampsa), Manjunath, R. (Ramya), Martikainen, P. (Petri), Mattila, J. (Jaakko), McKeown, J. (Jaclyn), Metsälä, P. (Petri), Miklasevskaja, M. (Margarita), Miller, M. (Meredith), Miskie, R. (Renee), Muinonen, A. (Arto), Mukkala, V.-M. (Veli-Matti), Naik, S. (Suresh), Nikolova, N. (Nadia), Nupponen, K. (Kari), Ovaskainen, O. (Otso), Österblad, I. (Ika), Paasivirta, L. (Lauri), Pajunen, T. (Timo), Parkko, P. (Petri), Paukkunen, J. (Juho), Penttinen, R. (Ritva), Perez, K. (Kate), Pohjoismäki, J. (Jaakko), Prosser, S. (Sean), Raekunnas, M. (Martti), Rahulan, M. (Miduna), Rannisto, M. (Meeri), Ratnasingham, S. (Sujeevan), Raukko, P. (Pekka), Rinne, A. (Aki), Rintala, T. (Teemu), Miranda Romo, S. (Susana), Salmela, J. (Jukka), Salokannel, J. (Juha), Savolainen, R. (Riitta), Schulman, L. (Leif), Sihvonen, P. (Pasi), Soliman, D. (Dina), Sones, J. (Jayme), Steinke, C. (Claudia), Stahls, G. (Gunilla), Tabell, J. (Jukka), Tiusanen, M. (Mikko), Varkonyi, G. (Gergely), Vesterinen, E. J. (Eero J.), Viitanen, E. (Esko), Vikberg, V. (Veli), Viitasaari, M. (Matti), Vilen, J. (Jussi), Warne, C. (Connor), Wei, C. (Catherine), Winqvist, K. (Kaj), Zakharov, E. (Evgeny), Mutanen, M. (Marko), Roslin, T. (Tomas), Somervuo, P. (Panu), Pentinsaari, M. (Mikko), Hebert, P. D. (Paul D. N.), Agda, J. (Jireh), Ahlroth, P. (Petri), Anttonen, P. (Perttu), Aspi, J. (Jouni), Blagoev, G. (Gergin), Blanco, S. (Santiago), Chan, D. (Dean), Clayhills, T. (Tom), deWaard, J. (Jeremy), deWaard, S. (Stephanie), Elliot, T. (Tyler), Elo, R. (Riikka), Haapala, S. (Sami), Helve, E. (Eero), Ilmonen, J. (Jari), Hirvonen, P. (Petri), Ho, C. (Chris), Itämies, J. (Juhani), Ivanov, V. (Vladislav), Jakovlev, J. (Jevgeni), Juslen, A. (Aino), Jussila, R. (Reijo), Kahanpää, J. (Jere), Kaila, L. (Lauri), Kaitila, J.-P. (Jari-Pekka), Kakko, A. (Ari), Kakko, I. (Iiro), Karhu, A. (Ali), Karjalainen, S. (Sami), Kjaerandsen, J. (Jostein), Koskinen, J. (Janne), Laasonen, E. M. (Erkki M.), Laasonen, L. (Leena), Laine, E. (Erkka), Lampila, P. (Petri), Levesque-Beaudin, V. (Valerie), Lu, L. (Liuqiong), Lähteenaro, M. (Meri), Majuri, P. (Pekka), Malmberg, S. (Sampsa), Manjunath, R. (Ramya), Martikainen, P. (Petri), Mattila, J. (Jaakko), McKeown, J. (Jaclyn), Metsälä, P. (Petri), Miklasevskaja, M. (Margarita), Miller, M. (Meredith), Miskie, R. (Renee), Muinonen, A. (Arto), Mukkala, V.-M. (Veli-Matti), Naik, S. (Suresh), Nikolova, N. (Nadia), Nupponen, K. (Kari), Ovaskainen, O. (Otso), Österblad, I. (Ika), Paasivirta, L. (Lauri), Pajunen, T. (Timo), Parkko, P. (Petri), Paukkunen, J. (Juho), Penttinen, R. (Ritva), Perez, K. (Kate), Pohjoismäki, J. (Jaakko), Prosser, S. (Sean), Raekunnas, M. (Martti), Rahulan, M. (Miduna), Rannisto, M. (Meeri), Ratnasingham, S. (Sujeevan), Raukko, P. (Pekka), Rinne, A. (Aki), Rintala, T. (Teemu), Miranda Romo, S. (Susana), Salmela, J. (Jukka), Salokannel, J. (Juha), Savolainen, R. (Riitta), Schulman, L. (Leif), Sihvonen, P. (Pasi), Soliman, D. (Dina), Sones, J. (Jayme), Steinke, C. (Claudia), Stahls, G. (Gunilla), Tabell, J. (Jukka), Tiusanen, M. (Mikko), Varkonyi, G. (Gergely), Vesterinen, E. J. (Eero J.), Viitanen, E. (Esko), Vikberg, V. (Veli), Viitasaari, M. (Matti), Vilen, J. (Jussi), Warne, C. (Connor), Wei, C. (Catherine), Winqvist, K. (Kaj), Zakharov, E. (Evgeny), and Mutanen, M. (Marko)

Abstract

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

Published
2022

2. Establishing a community-wide DNA barcode library as a new tool for arctic research

Author

Wirta, H., Várkonyi, G., Rasmussen, C., Kaartinen, R., Schmidt, N. M., Hebert, P. D. N., Barták, M., Blagoev, G., Disney, H., Ertl, S., Gjelstrup, Peter, Gwiazdowicz, D. J., Huldén, L., Ilmonen, J., Jakovlev, J., Jaschhof, M., Kahanpää, J., Kankaanpää, T., Krogh, P. H., Labbee, R., Lettner, C., Michelsen, Verner, Nielsen, S. A., Nielsen, T. R., Paasivirta, L., Pedersen, S., Pohjoismäki, J., Salmela, J., Vilkamaa, P., Väre, H., von Tschirnhaus, M., Roslin, T., Wirta, H., Várkonyi, G., Rasmussen, C., Kaartinen, R., Schmidt, N. M., Hebert, P. D. N., Barták, M., Blagoev, G., Disney, H., Ertl, S., Gjelstrup, Peter, Gwiazdowicz, D. J., Huldén, L., Ilmonen, J., Jakovlev, J., Jaschhof, M., Kahanpää, J., Kankaanpää, T., Krogh, P. H., Labbee, R., Lettner, C., Michelsen, Verner, Nielsen, S. A., Nielsen, T. R., Paasivirta, L., Pedersen, S., Pohjoismäki, J., Salmela, J., Vilkamaa, P., Väre, H., von Tschirnhaus, M., and Roslin, T.

Abstract

DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.

Published
2016

3. Establishing a community-wide DNA barcode library as a new tool for arctic research

Author

Wirta, H., primary, Várkonyi, G., additional, Rasmussen, C., additional, Kaartinen, R., additional, Schmidt, N. M., additional, Hebert, P. D. N., additional, Barták, M., additional, Blagoev, G., additional, Disney, H., additional, Ertl, S., additional, Gjelstrup, P., additional, Gwiazdowicz, D. J., additional, Huldén, L., additional, Ilmonen, J., additional, Jakovlev, J., additional, Jaschhof, M., additional, Kahanpää, J., additional, Kankaanpää, T., additional, Krogh, P. H., additional, Labbee, R., additional, Lettner, C., additional, Michelsen, V., additional, Nielsen, S. A., additional, Nielsen, T. R., additional, Paasivirta, L., additional, Pedersen, S., additional, Pohjoismäki, J., additional, Salmela, J., additional, Vilkamaa, P., additional, Väre, H., additional, von Tschirnhaus, M., additional, and Roslin, T., additional

Published
2015
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4. A molecular-based identification resource for the arthropods of Finland.

Author

Roslin T, Somervuo P, Pentinsaari M, Hebert PDN, Agda J, Ahlroth P, Anttonen P, Aspi J, Blagoev G, Blanco S, Chan D, Clayhills T, deWaard J, deWaard S, Elliot T, Elo R, Haapala S, Helve E, Ilmonen J, Hirvonen P, Ho C, Itämies J, Ivanov V, Jakovlev J, Juslén A, Jussila R, Kahanpää J, Kaila L, Jari-PekkaKaitila, Kakko A, Kakko I, Karhu A, Karjalainen S, Kjaerandsen J, Koskinen J, Laasonen EM, Laasonen L, Laine E, Lampila P, Levesque-Beaudin V, Lu L, Lähteenaro M, Majuri P, Malmberg S, Manjunath R, Martikainen P, Mattila J, McKeown J, Metsälä P, Miklasevskaja M, Miller M, Miskie R, Muinonen A, Veli-MattiMukkala, Naik S, Nikolova N, Nupponen K, Ovaskainen O, Österblad I, Paasivirta L, Pajunen T, Parkko P, Paukkunen J, Penttinen R, Perez K, Pohjoismäki J, Prosser S, Raekunnas M, Rahulan M, Rannisto M, Ratnasingham S, Raukko P, Rinne A, Rintala T, Miranda Romo S, Salmela J, Salokannel J, Savolainen R, Schulman L, Sihvonen P, Soliman D, Sones J, Steinke C, Ståhls G, Tabell J, Tiusanen M, Várkonyi G, Vesterinen EJ, Viitanen E, Vikberg V, Viitasaari M, Vilen J, Warne C, Wei C, Winqvist K, Zakharov E, and Mutanen M

Subjects
Animals, Biodiversity, DNA Barcoding, Taxonomic, Finland, Gene Library, Arthropods classification
Abstract

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society., (© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Published
2022
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5. DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae).

Author

Pohjoismäki JL, Kahanpää J, and Mutanen M

Subjects
Animals, Biodiversity, Cluster Analysis, Coleoptera genetics, DNA Barcoding, Taxonomic methods, Lepidoptera genetics, Parasites genetics, DNA genetics, Diptera genetics
Abstract

This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera., Competing Interests: The authors have declared that no competing interests exist.

Published
2016
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6. Notes on Shore Flies (Diptera: Ephydridae) from Finland and north-western Russia.

Author

Kahanpää J and Zatwarnicki T

Abstract

The recent checklist of the Ephydridae of Finland by Zatwarnicki and Kahanpää (2014) mentioned 13 ephydrid species as new for Finland without further details. This paper presents detailed records for those species and a few other species of interest. Four species are recorded for the first time from Russia. Trimerinaindistincta Krivosheina, 2004 is herein considered as a new junior synonym of Trimerinamicrochaeta Hendel, 1932, syn. nov.

Published
2015
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