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Macko P, Derka T, Čiamporová-Zaťovičová Z, Grabowski M, Čiampor F. Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries. Mol Ecol Resour 2024; 24:e13954. [PMID: 38520175 DOI: 10.1111/1755-0998.13954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
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Affiliation(s)
- Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Tomáš Derka
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
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2
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Ferreira S, Corley MFV, Nunes J, Rosete J, Vasconcelos S, Mata VA, Veríssimo J, Silva TL, Sousa P, Andrade R, Grosso-Silva JM, Pinho CJ, Chaves C, Martins FMS, Pinto J, Puppo P, Muñoz-Mérida A, Archer J, Pauperio J, Beja P. The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths. Biodivers Data J 2024; 12:e117169. [PMID: 38903959 PMCID: PMC11188589 DOI: 10.3897/bdj.12.e117169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/19/2024] [Indexed: 06/22/2024] Open
Abstract
Background The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. New information The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).
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Affiliation(s)
- Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões,
Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
| | - Martin F. V. Corley
- Pucketty Farm Cottage, Faringdon, Oxfordshire SN7 8JP,
U.K, Oxfordshire, United KingdomPucketty Farm Cottage, Faringdon, Oxfordshire SN7 8JP, U.KOxfordshireUnited Kingdom
| | - João Nunes
- Rua Eduardo Joaquim Reis Figueira, 1104 RC AR, 4440-647,
Valongo, PortugalRua Eduardo Joaquim Reis Figueira, 1104 RC AR, 4440-647ValongoPortugal
| | - Jorge Rosete
- Urbanização Lourisol, Rua Manuel Cerqueira Nobrega, Lote
16, 2. frente, P-3105-165 Louriçal, Pombal, PortugalUrbanização Lourisol, Rua Manuel Cerqueira Nobrega, Lote 16, 2. frente,
P-3105-165 LouriçalPombalPortugal
| | - Sasha Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia,
Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Instituto Superior de Agronomia, Universidade de
LisboaLisboaPortugal
- Department of Ecology, Swedish University of Agricultural
Sciences, PO Box 7044, 750 07, Uppsala, SwedenDepartment of Ecology, Swedish University of Agricultural Sciences, PO Box
7044, 750 07UppsalaSweden
| | - Vanessa A. Mata
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências,
Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto,
4169-007PortoPortugal
| | - Teresa L Silva
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pedro Sousa
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- International Union for Conservation of Nature (IUCN),
Species Survival Commission (SSC), Spider and Scorpion Specialist Group, Gland,
SwitzerlandInternational Union for Conservation of Nature (IUCN), Species Survival
Commission (SSC), Spider and Scorpion Specialist GroupGlandSwitzerland
| | - Rui Andrade
- Rua Calouste Gulbenkian 237 4H3, 4050-145, Porto,
PortugalRua Calouste Gulbenkian 237 4H3, 4050-145PortoPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do
Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Catarina J. Pinho
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências,
Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto,
4169-007PortoPortugal
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Filipa MS Martins
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pamela Puppo
- Marshall University, Department of Biological Sciences,
Huntington, West Virginia, United States of AmericaMarshall University, Department of Biological SciencesHuntington, West VirginiaUnited States of America
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Pauperio
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto,,
4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairão, Universidade do Porto,4485–661 Vairão, Vila do CondePortugal
- European Molecular Biology Laboratory, European
Bioinformatics Institute, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics
InstituteHinxton, CambridgeUnited Kingdom
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia,
Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Instituto Superior de Agronomia, Universidade de
LisboaLisboaPortugal
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3
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Schattanek-Wiesmair B, Huemer P, Wieser C, Stark W, Hausmann A, Koblmüller S, Sefc KM. A DNA barcode library of Austrian geometridae (Lepidoptera) reveals high potential for DNA-based species identification. PLoS One 2024; 19:e0298025. [PMID: 38466749 PMCID: PMC10927147 DOI: 10.1371/journal.pone.0298025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/12/2024] [Indexed: 03/13/2024] Open
Abstract
Situated in the Eastern section of the European Alps, Austria encompasses a great diversity of different habitat types, ranging from alpine to lowland Pannonian ecosystems, and a correspondingly high level of species diversity, some of which has been addressed in various DNA barcoding projects. Here, we report a DNA barcode library of all the 476 species of Geometridae (Lepidoptera) that have been recorded in Austria. As far as possible, species were sampled from different Austrian regions in order to capture intraspecific genetic variation. In total, 2500 DNA barcode sequences, representing 438 species, were generated in this study. For complete coverage of Austrian geometrid species in the subsequent analyses, the dataset was supplemented with DNA barcodes from specimens of non-Austrian origin. Species delimitations by ASAP, BIN and bPTP methods yielded 465, 510 and 948 molecular operational taxonomic units, respectively. Congruency of BIN and ASAP partitions with morphospecies assignments was reasonably high (85% of morphospecies in unique partitions), whereas bPTP appeared to overestimate the number of taxonomic units. The study furthermore identified taxonomically relevant cases of morphospecies splitting and sharing in the molecular partitions. We conclude that DNA barcoding and sequence analysis revealed a high potential for accurate DNA-based identification of the Austrian Geometridae species. Additionally, the study provides an updated checklist of the geometrid moths of Austria.
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Affiliation(s)
- Benjamin Schattanek-Wiesmair
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
- Institute of Biology, University of Graz, Universitätsplatz, Graz, Austria
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | | | - Wolfgang Stark
- Ökoplus Umweltforschung und Consulting GmbH, Trübensee, Austria
| | - Axel Hausmann
- Zoologische Staatssammlung München, München, Germany
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz, Graz, Austria
| | - Kristina M. Sefc
- Institute of Biology, University of Graz, Universitätsplatz, Graz, Austria
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4
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Huemer P, Karsholt O. Klimeschiopsis terroris auctt. from Spaina further case of cryptic diversity in European Lepidoptera (Lepidoptera, Gelechiidae, Gelechiinae). Zootaxa 2023; 5369:400-412. [PMID: 38220708 DOI: 10.11646/zootaxa.5369.3.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Indexed: 01/16/2024]
Abstract
A new species of Gnorimoschemini (Gelechiidae), Klimeschiopsis arnoldfransorum sp. nov., is described from specimens collected in Spain. The species is most closely related to Klimeschiopsis terroris (Hartig, 1938), with which it was hitherto mixed, but differs particularly by its small size with reduced yellowish-white forewing markings, the characters of the male and female genitalia, and the highly divergent DNA barcode (cytochrome c-oxidase subunit 1). Adult and genitalia of both sexes are figured. Finally, a checklist of the genus is provided.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H.; Natural History Collections; Krajnc-Str. 1; A-6060 Hall in Tirol; Austria.
| | - Ole Karsholt
- Natural History Museum of Denmark; Universitetsparken 15; DK-2100-Copenhagen; Denmark.
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5
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Bidzilya OV, Huemer P, Karsholt O. Thiotrichasumpichi sp. nov. - a new species of Thiotrichinae (Lepidoptera, Gelechiidae) from south-eastern Europe. Zookeys 2023; 1173:85-96. [PMID: 37564109 PMCID: PMC10410393 DOI: 10.3897/zookeys.1173.105037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/26/2023] [Indexed: 08/12/2023] Open
Abstract
Thiotrichasumpichisp. nov. is described from Greece and Croatia. The systematic position of the new species within Thiotricha is discussed based on external and genitalia characters and from DNA barcodes of the mitochondrial COI gene (cytochrome c oxidase 1). Adults, details of external morphology, and male and female genitalia of the new species are illustrated.
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Affiliation(s)
- Oleksiy V. Bidzilya
- Institute for Evolutionary Ecology of the National Academy of Sciences of Ukraine, 37 Academician Lebedev str., 03143, Kyiv, UkraineInstitute for Evolutionary Ecology of the National Academy of Sciences of UkraineKyivUkraine
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Natural History Collections, Krajnc-Str. 1, A-6060 Hall in Tirol, Innsbruck, AustriaTiroler Landesmuseen Betriebsges.m.b.H., Natural History CollectionsInnsbruckAustria
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen, DenmarkNatural History Museum of DenmarkCopenhagenDenmark
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6
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DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity. DIVERSITY 2023. [DOI: 10.3390/d15020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete inventory of the megadiverse insect order Lepidoptera in a protected area in the Alps (Cottian Alps, Italy) was intended to test the possibilities and reliability of DNA-based identifications. From voucher material collected between 2019 and 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas DNA barcoding failed for another 18 species. A total of 35 species shared a BIN with one or more taxa, but a majority of 19 species could still be discriminated by divergent sequences. A total of 12 morphospecies split into two BINs. These species and a further 22 taxa with unique BINs and barcode divergences >2% to the nearest neighbor require taxonomic re-assessment. Two additional cryptic species from the study area were described recently. Finally, 16 species are newly recorded for Italy. Our study, therefore, demonstrates the importance of DNA barcoding for both faunistics and the discovery of cryptic diversity, even in apparently well-studied protected areas.
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7
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Chromosomal-level genome assembly of potato tuberworm, Phthorimaea operculella: a pest of solanaceous crops. Sci Data 2022; 9:748. [PMID: 36463249 PMCID: PMC9719551 DOI: 10.1038/s41597-022-01859-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
The potato tuberworm, Phthorimaea operculella Zeller, is an oligophagous pest feeding on crops mainly belonging to the family Solanaceae. It is one of the most destructive pests of potato worldwide and attacks foliage and tubers in the field and in storage. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis. Here, we report on the genome assembly of P. operculella at the chromosomal level. Using Illumina, Nanopore and Hi-C sequencing, a 648.2 Mb genome was generated from 665 contigs, with an N50 length of 3.2 Mb, and 92.0% (596/648.2 Mb) of the assembly was anchored to 29 chromosomes. In total, 16619 genes were annotated, and 92.4% of BUSCO genes were fully represented. The chromosome-level genome of P. operculella will provide a significant resource for understanding the genetic basis for the biological study of this insect, and for promoting the integrative management of this pest in future.
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8
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Zhao Y, Wang H, Huang H, Zhou Z. A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China. Zookeys 2022; 1123:147-171. [PMID: 36762040 PMCID: PMC9836636 DOI: 10.3897/zookeys.1123.86704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (I max > DNN) failed to be recovered as monophyletic clades (i.e., Elimaeaterminalis, Phyllomimusklapperichi, Sinochloraszechwanensis and Xizicushowardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.
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Affiliation(s)
- Yizheng Zhao
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Hui Wang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Huimin Huang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
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9
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Motyka M, Kusy D, Bilkova R, Bocak L. Analysis of the Holarctic Dictyoptera aurora Complex (Coleoptera, Lycidae) Reveals Hidden Diversity and Geographic Structure in Müllerian Mimicry Ring. INSECTS 2022; 13:817. [PMID: 36135518 PMCID: PMC9502218 DOI: 10.3390/insects13090817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The elateroid family Lycidae is known for limited dispersal propensity and high species-level endemism. The red net-winged beetle, Dictyoptera aurora (Herbst, 1874), differs from all relatives by the range comprising almost the entire Holarctic region. Based on a five-marker phylogeny and 67 barcode entries (cox1-5' mtDNA) from the whole range, we recovered two genetically distinct species within traditionally defined D. aurora and resurrected the name D. coccinata (Say, 1835) as the oldest available synonym for Nearctic populations. Yet, no reliable morphological trait distinguishes these species except for minute differences in the male genitalia. D. coccinata is a monophylum resulting from a single Miocene dispersal event, ~15.8 million years ago, and genetic divergence implies long-term isolation by the Bering Strait. Far East Asian and west European populations are also genetically distinct, although to a lower extent. Two independent colonization events established the Fennoscandian populations after the last glacial maximum. Besides intrinsic factors, the high morphological similarity might result from stabilizing selection for shared aposematic signals. The rapidly accumulating barcode data provide valuable information on the evolutionary history and the origins of regional faunas.
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Affiliation(s)
| | | | | | - Ladislav Bocak
- Biodiversity & Molecular Evolution, Czech Advanced Technology and Research Institute, Center of the Region Hana, Slechtitelu 27, 779 00 Olomouc, Czech Republic
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10
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Solovyev VI, Dubatolov VV, Vavilova VY, Kosterin OE. Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Huemer P. Underestimated cryptic diversity in the Caryocolumtricolorella species complex (Lepidoptera, Gelechiidae). Zookeys 2022; 1103:189-209. [PMID: 36761790 PMCID: PMC9848873 DOI: 10.3897/zookeys.1103.83952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 11/12/2022] Open
Abstract
The taxonomy of the Caryocolumtricolorella species complex, an informal subsection of the diverse Caryocoluminteralbicella species group, is revised and four species are separated from DNA barcodes of the mitochondrial COI (cytochrome c oxidase subunit 1) gene and adult morphology: C.tricolorella (Haworth, 1812), C.fibigerium Huemer, 1988, C.herwigvanstaai sp. nov., and C.olekarsholti sp. nov. These species show a vicariant distribution pattern, with C.tricolorella widely distributed in Central and Northern Europe, C.fibigerium restricted to the Iberian Peninsula and southern France, C.herwigvanstaai sp. nov. to the Italian Peninsula, and C.olekarsholti sp. nov. to the Balkans. All species are described in detail, and the adults and genitalia of both sexes are illustrated.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebgsges.m.b.H., Sammlungs- und Forschungszentrum, Naturwissenschaftliche Sammlungen, Krajnc-Str. 1, A-6060 Hall in Tirol, Innsbruck, AustriaTiroler Landesmuseen Betriebgsges.m.b.H., Sammlungs- und ForschungszentrumInnsbruckAustria
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12
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Berggren K, Aarvik L, Huemer P, Lee KM, Mutanen M. Integrative taxonomy reveals overlooked cryptic diversity in the conifer feeding Batrachedra pinicolella (Zeller, 1839) (Lepidoptera, Batrachedridae). Zookeys 2022; 1085:165-182. [PMID: 35210909 PMCID: PMC8847276 DOI: 10.3897/zookeys.1085.76853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/20/2022] [Indexed: 11/14/2022] Open
Abstract
During efforts to generate DNA barcodes for all European Lepidoptera, Batrachedrapinicolella (Zeller, 1839) was found to comprise two genetically distinct clusters. Morphological investigation and results from two nuclear markers and ddRAD sequencing furthermore support the existence of two distinct taxa which we treat as two separate species, B.pinicolella and B.confusellasp. nov. A lectotype for B.pinicolella is designated. Available data indicate that the biology of both species also differs, with Piceaabies (L.) Karsten as a proved host-plant for B.pinicolella and Pinussylvestris L. for B.confusellasp. nov. Both species are mainly distributed on the European continent with B.pinicolella occurring in boreal parts of North and Central Europe and introduced to Canada, reflecting a boreo-montane distribution pattern. Batrachedraconfusellasp. nov. is more widely distributed in temperate Northern and Central Europe.
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13
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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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14
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DNA barcoding of insects from India: Current status and future perspectives. Mol Biol Rep 2022; 49:10617-10626. [PMID: 35716293 PMCID: PMC9206398 DOI: 10.1007/s11033-022-07628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/01/2022]
Abstract
Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.
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15
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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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16
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Prieto C, Faynel C, Robbins R, Hausmann A. Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae). PeerJ 2021; 9:e11843. [PMID: 34430077 PMCID: PMC8349518 DOI: 10.7717/peerj.11843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/01/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species. METHODS We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera. RESULTS We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily lowland species show higher percentages of local barcode gaps and congruence between BINs and morphology than genera that contain exclusively high montane species. The divergence values to the nearest neighbors were significantly lower in high Andean species while the intra-specific divergence values were significantly lower in the lowland species. These results raise questions regarding the causes of observed low inter and high intraspecific genetic variation. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the montane species concerned are relatively young and hybridization is probable. The release of our data set represents an essential baseline for a reference library for biological assessment studies of butterflies in mega diverse countries using modern high-throughput technologies an highlights the necessity of taxonomic revisions for various genera combining both molecular and morphological data.
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Affiliation(s)
- Carlos Prieto
- Departamento de Biología, Universidad del Atlántico, Barranquilla, Colombia
- Corporación Universitaria Autónoma del Cauca, Popayán, Colombia
| | | | - Robert Robbins
- Department of Entomology, Smithsonian Institution, Washington, USA
| | - Axel Hausmann
- SNSB-Bavarian State Collection of Zoology, Munich, Germany
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17
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Lopez-Vaamonde C, Kirichenko N, Cama A, Doorenweerd C, Godfray HCJ, Guiguet A, Gomboc S, Huemer P, Landry JF, Laštůvka A, Laštůvka Z, Lee KM, Lees DC, Mutanen M, van Nieukerken EJ, Segerer AH, Triberti P, Wieser C, Rougerie R. Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as “unassessed species splits” containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species.
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18
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Wöger R, Wöger R, Nuss M. DNA barcodes for Aotearoa New Zealand Pyraloidea (Lepidoptera). Biodivers Data J 2020; 8:e58841. [PMID: 33293886 PMCID: PMC7718215 DOI: 10.3897/bdj.8.e58841] [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: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 11/24/2022] Open
Abstract
Identification of pyraloid species is often hampered by highly similar external morphology requiring microscopic dissection of genitalia. This becomes especially obvious when mass samples from ecological studies or insect monitoring have to be analysed. DNA barcode sequences could accelerate identification, but are not available for most pyraloid species from New Zealand. Hence, we are presenting a first DNA-barcode library for this group, providing 440 COI barcodes (cytochrome C oxidase I sequences) for 73 morphologically-identified species, which is 29% of Pyraloidea known from New Zealand. Results are analysed using the Barcode Index Number system (BIN) of BOLD and the Automatic Barcode Gap Discovery method (ABGD). Using BIN, the 440 barcodes reveal 82 clusters. A perfect match between BIN assignment and morphological identification was found for 63 species (86.3%). Four species (5.5%) share BINs, each with two species in one BIN, of which Glaucocharis epiphaea and Glaucocharis harmonica even share the same barcode. In contrast, six species (8.2%) split into two or more BINs, with the highest number of five BINs for Orocrambus ramosellus. The interspecific variation of all collected specimens of New Zealand Pyraloidea averages 12.54%. There are deep intraspecific divergences (> 2%) in seven species, for instance Orocrambus vulgaris with up to 6.6% and Scoparia ustimacula with 5.5%. Using ABGD, the 440 barcodes reveal 71 or 88 operational taxonomic units (OTUs), depending on the preferred partition. A perfect match between OTU and morphological identification was found for 56 species (76.7%) or 62 species (84.9%). ABGD delivers four or seven species sharing OTUs and four or ten species split into more than one OTU. Morphological re-examination, as well as the analysis of a concatenated dataset of COI and the nuclear markers EF1α and GADPH for species split into more than one BIN or OTU, do not support a higher number of species. Likewise, there is no evidence for Wolbachia infection as a trigger for these sequence variations.
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Affiliation(s)
- Renate Wöger
- Senckenberg Museum of Zoology, Dresden, GermanySenckenberg Museum of ZoologyDresdenGermany
| | - Roland Wöger
- Senckenberg Museum of Zoology, Dresden, GermanySenckenberg Museum of ZoologyDresdenGermany
| | - Matthias Nuss
- Senckenberg Museum of Zoology, Dresden, GermanySenckenberg Museum of ZoologyDresdenGermany
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Mutanen M, Huemer P, Autto J, Karsholt O, Kaila L. Monopis jussii, a new species (Lepidoptera, Tineidae) inhabiting nests of the Boreal owl ( Aegolius funereus). Zookeys 2020; 992:157-181. [PMID: 33223909 PMCID: PMC7677292 DOI: 10.3897/zookeys.992.53975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/26/2020] [Indexed: 11/12/2022] Open
Abstract
Monopis jussii Kaila, Mutanen, Huemer, Karsholt & Autto, sp. nov. (Lepidoptera, Tineidae) is described as a new species. It is closely related to the widespread and common M. laevigella ([Denis & Schiffermüller], 1775), but differs in its distinct COI DNA barcode sequences, four examined nuclear loci as well as details in forewing coloration and pattern. Most reared specimens of M. jussii have emerged from the nest remnants of the Boreal owl (Aegolius funereus (Linnaeus, 1758)), but also nests of the Ural owl (Strix uralensis Pallas, 1771) and the Great tit (Parus major Linnaeus, 1758) have been observed as suitable habitats. Based on the present knowledge, the new species has a boreo-montane distribution as it is recorded only from northern Europe and the Alps. Several extensive rearing experiments from Strix spp. nest remnants from southern Finland did not produce any M. jussii, but thousands of M. laevigella, suggesting that the species is lacking in the area or, more unlikely, that the nest of these owl species do not serve as good habitat for the new species. This unexpected species discovery highlights, once again, the usefulness of DNA barcoding in revealing the cryptic layers of biodiversity. To serve stability we select a neotype for Tinea laevigella [Denis & Schiffermüller], 1775, and discuss the complicated synonymy and nomenclature of this species.
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Affiliation(s)
- Marko Mutanen
- Ecology and Genetics Research Unit, P.O.Box 3000, FI-90014 University of Oulu, Finland University of Oulu Oulu Finland
| | - Peter Huemer
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria Tiroler Landesmuseen-Betriebsgesellschaft m.b.H. Innsbruck Austria
| | - Jonna Autto
- Apajatie 11, FI-96800 Rovaniemi, Finland Unaffiliated Rovaniemi Finland
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen, Denmark Natural History Museum of Denmark Copenhagen Denmark
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, P.O.Box 17, FI-00014 University of Helsinki, Finland University of Helsinki Helsinki Finland
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Cryptic Diversity in the Monotypic Neotropical Micromoth Genus Angelabella (Lepidoptera: Gracillariidae) in the Peru-Chile Desert. INSECTS 2020; 11:insects11100677. [PMID: 33036122 PMCID: PMC7601689 DOI: 10.3390/insects11100677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022]
Abstract
Simple Summary The Neotropical Region harbors a highly diverse and poorly known fauna of leaf miners of the micromoth family Gracillariidae (Lepidoptera). Angelabella is a genus of Gracillariidae whose geographic range is restricted to a few valleys of the arid environments of the Peru-Chile desert. Only one species is currently included in this genus. The aims of this study were to explore the geographic range, determine the spatial distribution of mitochondrial lineages, and test lineage conspecificity hypotheses in Angelabella. The spatial distribution of genetic diversity indicated four spatial clusters, three of which are north of the previously known geographic range. These groups were defined as different species by four species delimitation methods. These results suggest that Angelabella harbors at least four morphologically cryptic species with restricted, not overlapping geographic ranges. This study shows that adequate single locus sequence analysis can be useful to discover surprising biodiversity patterns in underexplored environments, providing the base to plan further studies involving little-known organisms. Abstract Angelabella (Lepidoptera: Gracillariidae: Oecophyllembiinae) is considered a monotypic Neotropical genus of leaf miner micromoths known only from a few valleys of the arid environments of the Peru-Chile desert, particularly the southernmost part of Peru and northernmost part of Chile (type locality), where natural populations of its primary host plant occur. The geographic distribution of potential host plants provides a scenario for a wider range for this micromoth genus. The aims of this study were to explore the geographic range of Angelabella, determine the spatial distribution of mitochondrial lineages, and test lineage conspecificity hypotheses. The spatial distribution of genetic diversity indicated the presence of four spatial clusters, three of which are north of the previously known geographic range. Genetic distances were 0.2–0.8% and 3.6–8.3% (K2P) between haplotypes of the same and different spatial clusters, respectively. Phylogenetic relationships indicated reciprocal monophyly among the four spatial clusters, suggesting that allopatric differentiation processes have governed the recent history of Angelabella in these arid environments. These groups were defined as different species by four species delimitation methods, suggesting that Angelabella is not a monotypic genus, but harbors at least four morphologically cryptic allopatric species with restricted geographic ranges, including the type species and three candidate species.
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Huemer P, Karsholt O. Commented checklist of European Gelechiidae (Lepidoptera). Zookeys 2020; 921:65-140. [PMID: 32256151 PMCID: PMC7109147 DOI: 10.3897/zookeys.921.49197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/05/2020] [Indexed: 11/12/2022] Open
Abstract
The checklist of European Gelechiidae covers 865 species, belonging to 109 genera, with three species records which require confirmation. Further, it is the first checklist to include a complete coverage of proved synonyms of species and at generic level. The following taxonomic changes are introduced: Pseudosophronia constanti (Nel, 1998) syn. nov. of Pseudosophronia exustellus (Zeller, 1847), Metzneria expositoi Vives, 2001 syn. nov. of Metzneria aestivella (Zeller, 1839); Sophronia ascalis Gozmány, 1951 syn. nov. of Sophronia grandii Hering, 1933, Aproaerema incognitana (Gozmány, 1957) comb. nov., Aproaerema cinctelloides (Nel & Varenne, 2012) comb. nov., Aproaerema azosterella (Herrich-Schäffer, 1854) comb. nov., Aproaerema montanata (Gozmány, 1957) comb. nov., Aproaerema cincticulella (Bruand, 1851) comb. nov., Aproaerema buvati (Nel, 1995) comb. nov., Aproaerema linella (Chrétien, 1904) comb. nov., Aproaerema captivella (Herrich-Schäffer, 1854) comb. nov., Aproaerema semicostella (Staudinger, 1871) comb. nov., Aproaerema steppicola (Junnilainen, 2010) comb. nov., Aproaerema cottienella (Nel, 2012) comb. nov., Ptocheuusa cinerella (Chrétien, 1908) comb. nov., Pragmatodes melagonella (Constant, 1895) comb. nov., Pragmatodes albagonella (Varenne & Nel, 2010) comb. nov., Pragmatodes parvulata (Gozmány, 1953) comb. nov., Oxypteryx nigromaculella (Millière, 1872) comb. nov., Oxypteryx wilkella (Linnaeus, 1758) comb. nov., Oxypteryx ochricapilla (Rebel, 1903) comb. nov., Oxypteryx superbella (Zeller, 1839) comb. nov., Oxypteryx mirusella (Huemer & Karsholt, 2013) comb. nov., Oxypteryx baldizzonei (Karsholt & Huemer, 2013) comb. nov., Oxypteryx occidentella (Huemer & Karsholt, 2011) comb. nov., Oxypteryx libertinella (Zeller, 1872) comb. nov., Oxypteryx gemerensis (Elsner, 2013) comb. nov., Oxypteryx deserta (Piskunov, 1990) comb. nov., Oxypteryx unicolorella (Duponchel, 1843) comb. nov., Oxypteryx nigritella (Zeller, 1847) comb. nov., Oxypteryx plumbella (Heinemann, 1870) comb. nov., Oxypteryx isostacta (Meyrick, 1926) comb. nov., Oxypteryx helotella (Staudinger, 1859) comb. nov., Oxypteryx parahelotella (Nel, 1995) comb. nov., Oxypteryx graecatella (Šumpich & Skyva, 2012) comb. nov.; Aproaerema genistae (Walsingham, 1908) comb. rev., Aproaerema thaumalea (Walsingham, 1905) comb. rev.; Dichomeris neatodes Meyrick, 1923 sp. rev.; Caryocolum horoscopa (Meyrick, 1926) stat. rev.; Ivanauskiella occitanica (Nel & Varenne, 2013) sp. rev.; Apodia martinii Petry, 1911 sp. rev.; Caulastrocecis cryptoxena (Gozmány, 1952) sp. rev. Following Article 23.9.2 ICZN we propose Caryocolum blandella (Douglas, 1852) (Gelechia) nom. protectum and Caryocolum signatella (Eversmann, 1844) (Lita) nom. oblitum.
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Affiliation(s)
- Peter Huemer
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, AustriaNaturwissenschaftliche SammlungenInnsbruckAustria
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen, DenmarkZoological Museum, Natural History Museum of DenmarkCopenhagenDenmark
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