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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, Mutanen M. A molecular-based identification resource for the arthropods of Finland. Mol Ecol Resour 2021; 22:803-822. [PMID: 34562055 DOI: 10.1111/1755-0998.13510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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.
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Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Petri Ahlroth
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Perttu Anttonen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Santiago Blanco
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Jeremy deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Stephanie deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler Elliot
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Riikka Elo
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Jari Ilmonen
- Metsähallitus, Parks & Wildlife Finland, Vantaa, Finland
| | | | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Aino Juslén
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Jere Kahanpää
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Iiro Kakko
- Forssa Museum of Natural History, Forssa, Finland
| | | | | | - Jostein Kjaerandsen
- The Arctic University Museum of Norway, UiT -The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Janne Koskinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | | | | | | | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meri Lähteenaro
- Division of Systematics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Meredith Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadia Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Timo Pajunen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Juho Paukkunen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ritva Penttinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sean Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meeri Rannisto
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Jukka Salmela
- Regional Museum of Lapland, Arktikum, Rovaniemi, Finland.,Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Riitta Savolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Leif Schulman
- Finnish Environment Institute (SYKE), Helsinki, Finland.,Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Pasi Sihvonen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Dina Soliman
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gunilla Ståhls
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Mikko Tiusanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gergely Várkonyi
- Biodiversity Centre, Finnish Environment Institute SYKE, Kuhmo, Finland
| | - Eero J Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | - Connor Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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Andrews KR, Gerritsen A, Rashed A, Crowder DW, Rondon SI, van Herk WG, Vernon R, Wanner KW, Wilson CM, New DD, Fagnan MW, Hohenlohe PA, Hunter SS. Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control. Commun Biol 2020; 3:489. [PMID: 32895437 PMCID: PMC7477237 DOI: 10.1038/s42003-020-01169-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 07/13/2020] [Indexed: 11/30/2022] Open
Abstract
The larvae of click beetles (Coleoptera: Elateridae), known as "wireworms," are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies.
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Affiliation(s)
- Kimberly R Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844, USA.
| | - Alida Gerritsen
- Computational Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Arash Rashed
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, 83844, USA
| | - David W Crowder
- Department of Entomology, Washington State University, Pullman, WA, 99164, USA
| | - Silvia I Rondon
- Oregon State University, Hermiston Agricultural Research and Extension Center, Hermiston, OR, 97838, USA
| | - Willem G van Herk
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, British Columbia, Canada, V0M 1A0
| | - Robert Vernon
- Sentinel IPM Services, Chilliwack, British Columbia, Canada, V2R 3B5
| | - Kevin W Wanner
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Daniel D New
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844, USA
| | - Matthew W Fagnan
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844, USA
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844, USA
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844, USA
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