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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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Vella A, Vella N. The First Report of Pennella (Crustacea: Copepoda) Infesting Stenella coeruleoalba Stranded in Malta: Morphological and Genetic Analyses. Animals (Basel) 2024; 14:1107. [PMID: 38612346 PMCID: PMC11010884 DOI: 10.3390/ani14071107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Here, we document the stranding of a striped dolphin Stenella coeruleoalba (Meyen, 1833) (Mammalia: Delphinidae), which was found dead in Maltese waters in July 2020. The stranded dolphin exhibited a severe infestation of the mesoparasitic copepod, Pennella balaenoptera Koren and Danielssen, 1877 (Copepoda: Pennelidae). Parasites of this genus represent the largest known mesoparasites to infest cetaceans. Under normal circumstances, cetaceans may have a few P. balaenoptera individuals attached to them, but cetaceans with compromised health are more prone to heavy infestations. The identification of the parasite was accomplished through morphological and genetic analyses. This incident highlights the significance of monitoring mesoparasitic infestations, offering valuable insights into the health of cetacean populations and emphasizing the potential implications for conservation efforts in the region.
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Affiliation(s)
- Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, MSD 2080 Msida, Malta
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Lees DC. The genome sequence of the Hoary Footman, Eilema caniola (Hübner, 1808). Wellcome Open Res 2024; 9:5. [PMID: 38779146 PMCID: PMC11109690 DOI: 10.12688/wellcomeopenres.20574.1] [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] [Accepted: 11/23/2023] [Indexed: 05/25/2024] Open
Abstract
We present a genome assembly from one female Eilema caniola (the Hoary Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 781.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.42 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,953 protein coding genes.
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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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DNA Barcoding of Lepidoptera Species from the Maltese Islands: New and Additional Records, with an Insight into Endemic Diversity. DIVERSITY 2022. [DOI: 10.3390/d14121090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and used to assess the ability of the local DNA barcodes to discriminate species. Results showed that each species occupies a different BOLD BIN; therefore, DNA barcoding was able to discriminate between the studied species. Our data led to the formation of 12 new BOLD BINs—that is, OTUs that were identified during this work—while nearly 46% of the barcodes generated during this study were never recorded on conspecifics, further indicating the uniqueness of genetic diversity on these central Mediterranean islands. The outcomes of this study highlight the integrative taxonomic approach, where molecular taxonomy plays an important role for biodiversity investigation in its entirety.
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DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest. PLoS One 2022; 17:e0267390. [PMID: 35482734 PMCID: PMC9049551 DOI: 10.1371/journal.pone.0267390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency to protect them, there is a compelling need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was deployed for 12 months in a semi-degraded area of the southern Upper Paraná ecoregion of the Atlantic Forest. All specimens were DNA barcoded and the Barcode Index Number (BIN) system was employed to assign each specimen to a species proxy. DNA barcodes were obtained from 75,500 arthropods that included representatives of 8,651 BINs. Nearly 81% of these BINs were first records, highlighting the high rates of endemism and lack of study of arthropods from the Atlantic Forest. Diptera was the most abundant order, followed by Hemiptera, Lepidoptera and Hymenoptera. Diptera was also the most species-rich order, followed by Hymenoptera, Lepidoptera, and Coleoptera, a result consistent with studies in other biogeographic regions. Insects were most abundant in winter and most diverse in autumn and winter. This pattern, however, was caused mainly by the dynamics of dipteran diversity as other orders differed in their seasonal variation. The BIN composition of the insect community varied sharply through the year and also differed between the two consecutive summers included in the sampling period. The study of the 38 commonest BINs showed that seasonal patterns of abundance were not order-specific. Temperature had the strongest impact on seasonal abundance variation. Our results highlight the striking and understudied arthropod diversity of the highly fragmented Atlantic Forest, the predominance of dipterans, and the fact that abundance and richness in this insect community peak in the coolest months. Standardized studies like this generate fast and reliable biodiversity inventories and unveil ecological patterns, thus providing valuable information for conservation programs.
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Ashfaq M, Khan AM, Rasool A, Akhtar S, Nazir N, Ahmed N, Manzoor F, Sones J, Perez K, Sarwar G, Khan AA, Akhter M, Saeed S, Sultana R, Tahir HM, Rafi MA, Iftikhar R, Naseem MT, Masood M, Tufail M, Kumar S, Afzal S, McKeown J, Samejo AA, Khaliq I, D’Souza ML, Mansoor S, Hebert PDN. A DNA barcode survey of insect biodiversity in Pakistan. PeerJ 2022; 10:e13267. [PMID: 35497186 PMCID: PMC9048642 DOI: 10.7717/peerj.13267] [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: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 01/15/2023] Open
Abstract
Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- Centre for Animal Sciences and Fisheries, University of Swat, Mingora, Pakistan
| | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Naila Nazir
- Department of Entomology, University of Poonch, Rawalakot, Azad Kashmir, Pakistan
| | - Nazeer Ahmed
- Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Farkhanda Manzoor
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Azhar A. Khan
- College of Agriculture, Bahauddin Zakariya University Bahadur Campus, Layyah, Pakistan
| | - Muhammad Akhter
- Pulses Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shafqat Saeed
- Faculty of Agriculture and Environmental Sciences, MNS University of Agriculture, Multan, Pakistan
| | - Riffat Sultana
- Department of Zoology, University of Sindh, Jamshoro, Pakistan
| | | | - Muhammad A. Rafi
- National Insect Museum, National Agricultural Research Center, Islamabad, Pakistan
| | - Romana Iftikhar
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Mariyam Masood
- Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Santosh Kumar
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Sabila Afzal
- Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | | | | | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
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Catzim VV, Elías-Gutiérrez M, Pérez-Lachaud G. Contribution to the lady beetle fauna of the Yucatan Peninsula and integrative taxonomy for species delimitation. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2017060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Vannesa V. Catzim
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| | - Manuel Elías-Gutiérrez
- Departamento de Ecología y Sistemática Acuática, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| | - Gabriela Pérez-Lachaud
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
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9
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DNA barcoding in Dorcadionini (Coleoptera, Cerambycidae) uncovers mitochondrial-morphological discordance and the hybridogenic origin of several subspecies. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00531-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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Murillo-Ramos L, Sihvonen P, Brehm G, Ríos-Malaver IC, Wahlberg N. A database and checklist of geometrid moths (Lepidoptera) from Colombia. Biodivers Data J 2021; 9:e68693. [PMID: 34566452 PMCID: PMC8433126 DOI: 10.3897/bdj.9.e68693] [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: 05/14/2021] [Accepted: 08/13/2021] [Indexed: 12/01/2022] Open
Abstract
Background Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs - Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015–2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only. New information We enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoología of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.
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Affiliation(s)
- Leidys Murillo-Ramos
- Universidad de Sucre, Sincelejo, Colombia Universidad de Sucre Sincelejo Colombia
| | - Pasi Sihvonen
- University of Helsinki, Helsinki, Finland University of Helsinki Helsinki Finland
| | - Gunnar Brehm
- Universität Jena, Jena, Germany Universität Jena Jena Germany
| | - Indiana C Ríos-Malaver
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Boyacá, Colombia Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Boyacá Colombia.,McGuire Center for Lepidoptera and Biodiversity, University of Florida, Florida Museum of Natural History, Gainesville, United States of America McGuire Center for Lepidoptera and Biodiversity, University of Florida, Florida Museum of Natural History Gainesville United States of America
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11
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Meier R, Blaimer BB, Buenaventura E, Hartop E, von Rintelen T, Srivathsan A, Yeo D. A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science. Cladistics 2021; 38:264-275. [PMID: 34487362 DOI: 10.1111/cla.12489] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.
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Affiliation(s)
- Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Eliana Buenaventura
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Emily Hartop
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
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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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Rewicz T, Móra A, Tończyk G, Szymczak A, Grabowski M, Calleja EJ, Pernecker B, Csabai Z. First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean. Genome 2020; 64:196-206. [PMID: 32502367 DOI: 10.1139/gen-2019-0226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.
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Affiliation(s)
- Tomasz Rewicz
- University of Lodz, Department of Invertebrate Zoology and Hydrobiology, Łódź, Poland.,University of Guelph, Centre for Biodiversity Genomics, Guelph, Ontario, Canada
| | - Arnold Móra
- University of Pécs, Department of Hydrobiology, Pécs, Hungary
| | - Grzegorz Tończyk
- University of Lodz, Department of Invertebrate Zoology and Hydrobiology, Łódź, Poland
| | - Ada Szymczak
- University of Lodz, Department of Invertebrate Zoology and Hydrobiology, Łódź, Poland
| | - Michal Grabowski
- University of Lodz, Department of Invertebrate Zoology and Hydrobiology, Łódź, Poland
| | - Eman J Calleja
- Malta College of Arts, Science and Technology, Paola, Malta
| | | | - Zoltán Csabai
- University of Pécs, Department of Hydrobiology, Pécs, Hungary.,Masaryk University, Department of Botany and Zoology, Brno, Czechia
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Naseem MT, Ashfaq M, Khan AM, Rasool A, Asif M, Hebert PDN. BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae). PLoS One 2019; 14:e0220426. [PMID: 31821347 PMCID: PMC6903727 DOI: 10.1371/journal.pone.0220426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.
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Affiliation(s)
- Muhammad Tayyib Naseem
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Arif Muhammad Khan
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Zoology, University of Swat, Swat, Pakistan
| | - Muhammad Asif
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Huemer P, Wieser C, Stark W, Hebert PDN, Wiesmair B. DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) - a nearly perfect match of Linnean taxonomy. Biodivers Data J 2019; 7:e37734. [PMID: 31423084 PMCID: PMC6694074 DOI: 10.3897/bdj.7.e37734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023] Open
Abstract
The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Christian Wieser
- Landesmuseum Kärnten, Klagenfurt am Wörthersee, Austria Landesmuseum Kärnten Klagenfurt am Wörthersee Austria
| | | | - Paul D N Hebert
- Biodiversity Institute of Ontario, Guelph, Canada Biodiversity Institute of Ontario Guelph Canada
| | - Benjamin Wiesmair
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
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Ashfaq M, Blagoev G, Tahir HM, Khan AM, Mukhtar MK, Akhtar S, Butt A, Mansoor S, Hebert PDN. Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan. PLoS One 2019; 14:e0217086. [PMID: 31116764 PMCID: PMC6530854 DOI: 10.1371/journal.pone.0217086] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/04/2019] [Indexed: 01/16/2023] Open
Abstract
Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Abida Butt
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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Huemer P, Hebert PDN, Mutanen M, Wieser C, Wiesmair B, Hausmann A, Yakovlev R, Möst M, Gottsberger B, Strutzenberger P, Fiedler K. Large geographic distance versus small DNA barcode divergence: Insights from a comparison of European to South Siberian Lepidoptera. PLoS One 2018; 13:e0206668. [PMID: 30388147 PMCID: PMC6214556 DOI: 10.1371/journal.pone.0206668] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/17/2018] [Indexed: 12/16/2022] Open
Abstract
Spanning nearly 13,000 km, the Palearctic region provides an opportunity to examine the level of geographic coverage required for a DNA barcode reference library to be effective in identifying species with broad ranges. This study examines barcode divergences between populations of 102 species of Lepidoptera from Europe and South Siberia, sites roughly 6,000 km apart. While three-quarters of these species showed divergence between their Asian and European populations, these divergence values ranged between 0-1%, distinctly less than the distance to the Nearest-Neighbor species in all but a few cases. Our results suggest that further taxonomic studies may be required for 16 species that showed either extremely low interspecific or high intraspecific variation. For example, seven species pairs showed low or no barcode divergence, but four of these cases are likely to reflect taxonomic over-splitting while the others involve species pairs that are either young or show evidence for introgression. Conversely, some of the nine species with deep intraspecific divergence at varied spatial levels may include overlooked species. Although these 16 cases require further investigation, our overall results indicate that barcode reference libraries based on records from one locality can be very effective in identifying specimens across an extensive geographic area.
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Affiliation(s)
- Peter Huemer
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Benjamin Wiesmair
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | - Axel Hausmann
- Section Lepidoptera, Bavarian State Collection of Zoology, Munich, Germany
| | - Roman Yakovlev
- Ecology Department, Altai State University, Barnaul, Russia
- Tomsk State University, Tomsk, Russia
| | - Markus Möst
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Brigitte Gottsberger
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Konrad Fiedler
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
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Ekrem T, Stur E, Orton MG, Adamowicz SJ. DNA barcode data reveal biogeographic trends in Arctic non-biting midges. Genome 2018; 61:787-796. [DOI: 10.1139/gen-2018-0100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic – West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland – North American affinity, comparisons using Chao’s dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ∼4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.
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Affiliation(s)
- Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Matthew G. Orton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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